From bcec2cc719eef7e43827521bd281582a8b5ebe72 Mon Sep 17 00:00:00 2001 From: kMutagene Date: Thu, 27 Feb 2020 10:57:11 +0100 Subject: [PATCH 01/11] Fix GFF3 pretty printer --- src/BioFSharp.IO/FSIPrinters.fs | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/src/BioFSharp.IO/FSIPrinters.fs b/src/BioFSharp.IO/FSIPrinters.fs index ebb32a17..47d7cc6c 100644 --- a/src/BioFSharp.IO/FSIPrinters.fs +++ b/src/BioFSharp.IO/FSIPrinters.fs @@ -106,7 +106,7 @@ module FSIPrinters = ///print GFF3 formatted file as seen in the specifications. let prettyPrintGFF3 (input : seq>>) = toString id input - |> Seq.iter (fun x -> printfn "%s" x) + |> String.concat "\r\n" let prettyPrintGSE (gse:SOFT.Series.GSE) = @@ -264,4 +264,3 @@ Samples %s (gpl.PlatformMetadata.Contributor |> formatMultiEntries 4) (gpl.SeriesMetadata |> formatSeries 4) (gpl.SampleMetadata |> formatSamples 4) - From 48c5292a25258eeb4b775c360ea494baa80f72c5 Mon Sep 17 00:00:00 2001 From: kMutagene Date: Thu, 27 Feb 2020 14:25:07 +0100 Subject: [PATCH 02/11] Fix typo in SOFT convenience functions --- src/BioFSharp.IO/SOFT.fs | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/src/BioFSharp.IO/SOFT.fs b/src/BioFSharp.IO/SOFT.fs index 38346d62..4a149304 100644 --- a/src/BioFSharp.IO/SOFT.fs +++ b/src/BioFSharp.IO/SOFT.fs @@ -1483,14 +1483,13 @@ module SOFT = let getAssociatedPlatformAccessions (gse:GSE) = gse.PlatformMetadata |> Map.toList - |> List.map snd - |> List.map (fun record -> record.Accession) + |> List.map fst ///returns sample metadata associated with the input series GSE representation let getAssociatedSamples (gse:GSE) = gse.SampleMetadata |> Map.toList - |> List.map fst + |> List.map snd ///returns sample accessions associated with the input series GSE representation let getAssociatedSampleAccessions (gse:GSE) = @@ -1556,7 +1555,7 @@ module SOFT = let getAssociatedSamples (gpl:GPL) = gpl.SampleMetadata |> Map.toList - |> List.map fst + |> List.map snd ///returns sample accessions associated with the input platform GPL representation let getAssociatedSampleAccessions (gpl:GPL) = From 97cca9bd06f63455ebafbf3cbb8029a0651137cb Mon Sep 17 00:00:00 2001 From: kMutagene Date: Thu, 27 Feb 2020 14:25:28 +0100 Subject: [PATCH 03/11] Add additional SOFT prettyPrinters --- src/BioFSharp.IO/FSIPrinters.fs | 298 ++++++++++++++++++++------------ 1 file changed, 190 insertions(+), 108 deletions(-) diff --git a/src/BioFSharp.IO/FSIPrinters.fs b/src/BioFSharp.IO/FSIPrinters.fs index 47d7cc6c..70638593 100644 --- a/src/BioFSharp.IO/FSIPrinters.fs +++ b/src/BioFSharp.IO/FSIPrinters.fs @@ -12,7 +12,103 @@ module FSIPrinters = open BioFSharp.IO.GFF3 open FSharpAux open System.Text + + module internal FormatHelpers = + + module SOFT = + + let formatSingleEntry rootIdent (s: string) = + let ident = [for i in [1 .. (4*rootIdent)] do yield " "] |> String.concat "" + s + |> String.split ' ' + |> Array.chunkBySize 15 + |> Array.map (String.concat " ") + |> Array.mapi (fun i s -> if i = 0 then s else sprintf "%s%s" ident s) + |> String.concat "\r\n" + + let formatMultiEntries rootIdent (l: string list) = + let ident = [for i in [1 .. (4*rootIdent)] do yield " "] |> String.concat "" + l + |> List.map + (fun summary -> + summary + |> String.split ' ' + |> Array.chunkBySize 15 + |> Array.map (String.concat " ") + ) + |> Array.concat + |> Array.mapi (fun i s -> if i = 0 then s else sprintf "%s%s" ident s) + |> String.concat "\r\n" + + let formatSamples rootIdent (sm : Map) = + let ident = [for i in [1 .. (4*rootIdent)] do yield " "] |> String.concat "" + sm + |> Map.toList + |> List.map + (fun (k,v) -> + sprintf "%s => %s" k v.Title + ) + |> List.mapi (fun i s -> if i = 0 then s else sprintf "%s%s" ident s) + |> fun lines -> + if lines.Length > 15 then + let morelineCount = lines.Length - 15 + [ + yield! lines.[0..14] + sprintf "%s(...and %i more)" ident morelineCount + ] + |> String.concat "\r\n" + else + lines |> String.concat "\r\n" + let formatPlatforms rootIdent (sm : Map) = + let ident = [for i in [1 .. (4*rootIdent)] do yield " "] |> String.concat "" + sm + |> Map.toList + |> List.map + (fun (k,v) -> + sprintf "%s => %s" k v.Title + ) + |> List.mapi (fun i s -> if i = 0 then s else sprintf "%s%s" ident s) + |> fun lines -> + if lines.Length > 15 then + let morelineCount = lines.Length - 15 + [ + yield! lines.[0..14] + sprintf "%s(...and %i more)" ident morelineCount + ] + |> String.concat "\r\n" + else + lines |> String.concat "\r\n" + + let formatSeries rootIdent (sm : Map) = + let ident = [for i in [1 .. (4*rootIdent)] do yield " "] |> String.concat "" + sm + |> Map.toList + |> List.map + (fun (k,v) -> + sprintf "%s => %s" k v.Title + ) + |> List.mapi (fun i s -> if i = 0 then s else sprintf "%s%s" ident s) + |> fun lines -> + if lines.Length > 15 then + let morelineCount = lines.Length - 15 + [ + yield! lines.[0..14] + sprintf "%s(...and %i more)" ident morelineCount + ] + |> String.concat "\r\n" + else + lines |> String.concat "\r\n" + + let formatMultiChannelEntry rootIdent l = + l + |> List.groupBy fst + |> List.map (fun (i,c) -> (sprintf "[CHANNEL %i]\r\n" i ) :: (c |> List.map snd)) + |> List.concat + |> formatMultiEntries rootIdent + + open FormatHelpers + ///print BioItems by using symbols for AminoAcids and Nucleotides, and the name of Modifications in [brackets] let prettyPrintBioItem (a: 'a when 'a :> IBioItem) = match (a :> IBioItem) with @@ -108,56 +204,85 @@ module FSIPrinters = toString id input |> String.concat "\r\n" + let prettyPrintSampleRecord (sample:SOFT.SampleRecord) = + sprintf + """ +METADATA FOR SAMPLE RECORD %s +===========================%s - let prettyPrintGSE (gse:SOFT.Series.GSE) = +Title: %s - let formatSingleEntry rootIdent (s: string) = - let ident = [for i in [1 .. (4*rootIdent)] do yield " "] |> String.concat "" - s - |> String.split ' ' - |> Array.chunkBySize 15 - |> Array.map (String.concat " ") - |> Array.mapi (fun i s -> if i = 0 then s else sprintf "%s%s" ident s) - |> String.concat "\r\n" - - - let formatMultiEntries rootIdent (l: string list) = - let ident = [for i in [1 .. (4*rootIdent)] do yield " "] |> String.concat "" - l - |> List.map - (fun summary -> - summary - |> String.split ' ' - |> Array.chunkBySize 15 - |> Array.map (String.concat " ") - ) - |> Array.concat - |> Array.mapi (fun i s -> if i = 0 then s else sprintf "%s%s" ident s) - |> String.concat "\r\n" - - let formatSamples rootIdent (sm : Map) = - let ident = [for i in [1 .. (4*rootIdent)] do yield " "] |> String.concat "" - sm - |> Map.toList - |> List.map - (fun (k,v) -> - sprintf "%s => %s" k v.Title - ) - |> List.mapi (fun i s -> if i = 0 then s else sprintf "%s%s" ident s) - |> String.concat "\r\n" +Type(s): %s - - let formatPlatforms rootIdent (sm : Map) = - let ident = [for i in [1 .. (4*rootIdent)] do yield " "] |> String.concat "" - sm - |> Map.toList - |> List.map - (fun (k,v) -> - sprintf "%s => %s" k v.Title - ) - |> List.mapi (fun i s -> if i = 0 then s else sprintf "%s%s" ident s) - |> String.concat "\r\n" +Organism(s) %s + +Characteristics: %s + +Description: %s + +(For more Metadata, access the type directly) + """ + sample.Accession + (sample.Accession |> String.map (fun c -> '=')) + (sample.Title |> SOFT.formatSingleEntry 5) + (sample.Type |> SOFT.formatSingleEntry 5) + (sample.Organism |> SOFT.formatMultiChannelEntry 5) + (sample.Characteristics |> SOFT.formatMultiChannelEntry 5) + (sample.Description |> SOFT.formatMultiEntries 5) + + let prettyPrintSeriesRecord (series:SOFT.SeriesRecord) = + sprintf + """ +GEO SERIES RECORD %s +==================%s + +Type(s): %s + +Title: %s + +Contributor(s): %s + +Design: %s + +Summary: %s + +(For more Metadata, access the type directly) + """ + series.Accession + (series.Accession |> String.map (fun c -> '=')) + (series.Type |> SOFT.formatMultiEntries 4) + (series.Title |> SOFT.formatSingleEntry 4) + (series.Contributor |> SOFT.formatMultiEntries 4) + (series.OverallDesign |> SOFT.formatMultiEntries 4) + (series.Summary |> SOFT.formatMultiEntries 4) + + let prettyPrintPlatformRecord (platform:SOFT.PlatformRecord) = + sprintf + """ +GEO PLATFORM RECORD %s +====================%s + +Title: %s + +Organism(s): %s + +Description: %s + +Technology: %s +Contributor(s): %s + +(For more Metadata, access the type directly) + """ + platform.Accession + (platform.Accession |> String.map (fun c -> '=')) + (platform.Title |> SOFT.formatSingleEntry 4) + (platform.Organism |> SOFT.formatMultiEntries 4) + (platform.Description |> SOFT.formatMultiEntries 4) + (platform.Technology |> SOFT.formatSingleEntry 4) + (platform.Contributor |> SOFT.formatMultiEntries 4) + + let prettyPrintGSE (gse:SOFT.Series.GSE) = sprintf """ GEO SERIES RECORD %s @@ -176,66 +301,20 @@ Design: %s Summary: %s Samples %s + +(For more Metadata, access the type directly) """ gse.SeriesMetadata.Accession (gse.SeriesMetadata.Accession |> String.map (fun c -> '=')) - (gse.SeriesMetadata.Type |> formatMultiEntries 4) - (gse.PlatformMetadata |> formatPlatforms 4) - (gse.SeriesMetadata.Title |> formatSingleEntry 4) - (gse.SeriesMetadata.Contributor |> formatMultiEntries 4) - (gse.SeriesMetadata.OverallDesign |> formatMultiEntries 4) - (gse.SeriesMetadata.Summary |> formatMultiEntries 4) - (gse.SampleMetadata |> formatSamples 4) + (gse.SeriesMetadata.Type |> SOFT.formatMultiEntries 4) + (gse.PlatformMetadata |> SOFT.formatPlatforms 4) + (gse.SeriesMetadata.Title |> SOFT.formatSingleEntry 4) + (gse.SeriesMetadata.Contributor |> SOFT.formatMultiEntries 4) + (gse.SeriesMetadata.OverallDesign |> SOFT.formatMultiEntries 4) + (gse.SeriesMetadata.Summary |> SOFT.formatMultiEntries 4) + (gse.SampleMetadata |> SOFT.formatSamples 4) let prettyPrintGPL (gpl:SOFT.Platform.GPL) = - - let formatSingleEntry rootIdent (s: string) = - let ident = [for i in [1 .. (4*rootIdent)] do yield " "] |> String.concat "" - s - |> String.split ' ' - |> Array.chunkBySize 15 - |> Array.map (String.concat " ") - |> Array.mapi (fun i s -> if i = 0 then s else sprintf "%s%s" ident s) - |> String.concat "\r\n" - - - let formatMultiEntries rootIdent (l: string list) = - let ident = [for i in [1 .. (4*rootIdent)] do yield " "] |> String.concat "" - l - |> List.map - (fun summary -> - summary - |> String.split ' ' - |> Array.chunkBySize 15 - |> Array.map (String.concat " ") - ) - |> Array.concat - |> Array.mapi (fun i s -> if i = 0 then s else sprintf "%s%s" ident s) - |> String.concat "\r\n" - - let formatSamples rootIdent (sm : Map) = - let ident = [for i in [1 .. (4*rootIdent)] do yield " "] |> String.concat "" - sm - |> Map.toList - |> List.map - (fun (k,v) -> - sprintf "%s => %s" k v.Title - ) - |> List.mapi (fun i s -> if i = 0 then s else sprintf "%s%s" ident s) - |> String.concat "\r\n" - - - let formatSeries rootIdent (sm : Map) = - let ident = [for i in [1 .. (4*rootIdent)] do yield " "] |> String.concat "" - sm - |> Map.toList - |> List.map - (fun (k,v) -> - sprintf "%s => %s" k v.Title - ) - |> List.mapi (fun i s -> if i = 0 then s else sprintf "%s%s" ident s) - |> String.concat "\r\n" - sprintf """ GEO PLATFORM RECORD %s @@ -254,13 +333,16 @@ Contributor(s): %s Series(s): %s Samples %s + +(For more Metadata, access the type directly) """ gpl.PlatformMetadata.Accession (gpl.PlatformMetadata.Accession |> String.map (fun c -> '=')) - (gpl.PlatformMetadata.Title |> formatSingleEntry 4) - (gpl.PlatformMetadata.Organism |> formatMultiEntries 4) - (gpl.PlatformMetadata.Description |> formatMultiEntries 4) - (gpl.PlatformMetadata.Technology |> formatSingleEntry 4) - (gpl.PlatformMetadata.Contributor |> formatMultiEntries 4) - (gpl.SeriesMetadata |> formatSeries 4) - (gpl.SampleMetadata |> formatSamples 4) + (gpl.PlatformMetadata.Title |> SOFT.formatSingleEntry 4) + (gpl.PlatformMetadata.Organism |> SOFT.formatMultiEntries 4) + (gpl.PlatformMetadata.Description |> SOFT.formatMultiEntries 4) + (gpl.PlatformMetadata.Technology |> SOFT.formatSingleEntry 4) + (gpl.PlatformMetadata.Contributor |> SOFT.formatMultiEntries 4) + (gpl.SeriesMetadata |> SOFT.formatSeries 4) + (gpl.SampleMetadata |> SOFT.formatSamples 4) + From 130e1c63264989978e54f114dbd04b6dfb9458d3 Mon Sep 17 00:00:00 2001 From: kMutagene Date: Thu, 27 Feb 2020 14:26:09 +0100 Subject: [PATCH 04/11] Add load script for pretty printers to BioFSharp.IO --- src/BioFSharp.IO/BioFSharp.IO.fsproj | 3 +++ src/BioFSharp.IO/BioFSharp.IO.fsx | 28 +++++++++++++++++++++++----- 2 files changed, 26 insertions(+), 5 deletions(-) diff --git a/src/BioFSharp.IO/BioFSharp.IO.fsproj b/src/BioFSharp.IO/BioFSharp.IO.fsproj index 57655c44..56a7cd08 100644 --- a/src/BioFSharp.IO/BioFSharp.IO.fsproj +++ b/src/BioFSharp.IO/BioFSharp.IO.fsproj @@ -23,6 +23,9 @@ Debug;Release;Mono;DotnetCore + + PreserveNewest + diff --git a/src/BioFSharp.IO/BioFSharp.IO.fsx b/src/BioFSharp.IO/BioFSharp.IO.fsx index 17cc2ca5..5f1ceb4d 100644 --- a/src/BioFSharp.IO/BioFSharp.IO.fsx +++ b/src/BioFSharp.IO/BioFSharp.IO.fsx @@ -1,8 +1,26 @@ -// Learn more about F# at http://fsharp.net. See the 'F# Tutorial' project -// for more guidance on F# programming. +#nowarn "211" +//Adapted from https://github.com/fslaborg/Deedle/blob/master/src/Deedle/Deedle.fsx -//#load "Library1.fs" -//open BioFSharp.IO +// Standard NuGet or Paket location +#I "." +#I "lib/net45" -// Define your library scripting code here +// Try various folders that people might like +#I "bin/net45" +#I "../bin/net45" +#I "../../bin/net45" +#I "../../bin/BioFSharp.IO/net45" +#I "../../../bin/net45" +#I "lib" +// Reference BioFSharp.IO +#r "BioFSharp.IO.dll" + +open BioFSharp.IO + +do fsi.AddPrinter(FSIPrinters.prettyPrintBioCollection) +do fsi.AddPrinter(FSIPrinters.prettyPrintBioItem) +do fsi.AddPrinter(FSIPrinters.prettyPrintClustal) +do fsi.AddPrinter(FSIPrinters.prettyPrintGFF3) +do fsi.AddPrinter(FSIPrinters.prettyPrintGPL) +do fsi.AddPrinter(FSIPrinters.prettyPrintGSE) From 02e33f9be1b652b96604ac98aa852c3d5549cfbc Mon Sep 17 00:00:00 2001 From: kMutagene Date: Thu, 27 Feb 2020 17:00:15 +0100 Subject: [PATCH 05/11] Improve FSIPrinter docs and add SOFT Parsing docs --- BioFSharp.sln | 1 + docsrc/content/FSIPrinters.fsx | 98 +- docsrc/content/SOFT.fsx | 94 + docsrc/content/data/GPL15922_family.soft | 11252 +++++++++++++++++++++ docsrc/content/data/GSE71469_family.soft | 2793 +++++ docsrc/tools/templates/template.cshtml | 2 + 6 files changed, 14238 insertions(+), 2 deletions(-) create mode 100644 docsrc/content/SOFT.fsx create mode 100644 docsrc/content/data/GPL15922_family.soft create mode 100644 docsrc/content/data/GSE71469_family.soft diff --git a/BioFSharp.sln b/BioFSharp.sln index 75f0ce20..9f8d8aa5 100644 --- a/BioFSharp.sln +++ b/BioFSharp.sln @@ -55,6 +55,7 @@ Project("{2150E333-8FDC-42A3-9474-1A3956D46DE8}") = "content", "content", "{8E6D docsrc\content\Obo.fsx = docsrc\content\Obo.fsx docsrc\content\PetideClassification.fsx = docsrc\content\PetideClassification.fsx docsrc\content\Readers.fsx = docsrc\content\Readers.fsx + docsrc\content\SOFT.fsx = docsrc\content\SOFT.fsx docsrc\content\StringMatching.fsx = docsrc\content\StringMatching.fsx docsrc\content\tutorial.fsx = docsrc\content\tutorial.fsx docsrc\content\UniProt.fsx = docsrc\content\UniProt.fsx diff --git a/docsrc/content/FSIPrinters.fsx b/docsrc/content/FSIPrinters.fsx index 787eb0d6..a9555419 100644 --- a/docsrc/content/FSIPrinters.fsx +++ b/docsrc/content/FSIPrinters.fsx @@ -23,7 +23,11 @@ a bunch of functions to view our data types in a structured string format. This visual investigation. To use these printers, use the `fsi.AddPrinter` function to register the desired printer. This will override the default printing behaviour of the respective type in the FSI. -Currently, the following printers are implemented: +We also provide a `BioFSharp.IO.fsx` convenience script in our nuget packages, that registers all (except modification printers) printers to the FSI. +just `#load` the script and you get all the printing goodness. + + +However, if you want to selectively register FSI printers,here are the currently implemented ones: BioItems -------- @@ -173,4 +177,94 @@ Console output using `prettyPrintClustal`: //register the desired printer fsi.AddPrinter(FSIPrinters.prettyPrintClustal) -(*** include-value:clustalPrnt ***) \ No newline at end of file +(*** include-value:clustalPrnt ***) + + +(** +SOFT +---- +There are 5 printers available: + +`prettyPrintGSE` and `prettyPrintGPL` format the top level types `SOFT.Series.GSE` and `SOFT.Platform.GPL` including associated record metadata. + +`prettyPrintSampleRecord`,`prettyPrintSeriesRecord`, and `prettyPrintPlatformRecord` format single record metadata. + +All SOFT types are very large and hard to read from standard output, especially the nested top level types, so we will omitt the standard output for readability. +*) + +//register the desired printers +fsi.AddPrinter(FSIPrinters.prettyPrintGPL) +fsi.AddPrinter(FSIPrinters.prettyPrintGSE) + +fsi.AddPrinter(FSIPrinters.prettyPrintSampleRecord) +fsi.AddPrinter(FSIPrinters.prettyPrintSeriesRecord) +fsi.AddPrinter(FSIPrinters.prettyPrintPlatformRecord) + +let gplPath = __SOURCE_DIRECTORY__ + "/data/GPL15922_family.soft" + +let gpl15922 = SOFT.Platform.fromFile gplPath + +(***hide***) +let gplPrnt = FSIPrinters.prettyPrintGPL gpl15922 + +(** +Console output using `prettyPrintGPL`: +*) + +(*** include-value:gplPrnt ***) + +let gsePath = __SOURCE_DIRECTORY__ + "/data/GSE71469_family.soft" + +let gse71469 = SOFT.Series.fromFile gsePath + +(***hide***) +let gsePrnt = FSIPrinters.prettyPrintGSE gse71469 + +(** +Console output using `prettyPrintGSE`: +*) + +(*** include-value:gsePrnt ***) + +let smplRecord = + gse71469 + |> SOFT.Series.getAssociatedSamples + |> List.item 0 + +(***hide***) +let smplPrint = FSIPrinters.prettyPrintSampleRecord smplRecord + +(** +Console output using `prettyPrintSampleRecord`: +*) + +(*** include-value:smplPrint ***) + +let seriesRecord = + gpl15922 + |> SOFT.Platform.getAssociatedSeries + |> List.item 0 + +(***hide***) +let seriesPrint = FSIPrinters.prettyPrintSeriesRecord seriesRecord + +(** +Console output using `prettyPrintSeriesRecord`: +*) + +(*** include-value:seriesPrint ***) + + +let pltfrmRecord = + gse71469 + |> SOFT.Series.getAssociatedPlatforms + |> List.item 0 + +(***hide***) +let pltfrmPrint = FSIPrinters.prettyPrintPlatformRecord pltfrmRecord + +(** +Console output using `prettyPrintSampleRecord`: +*) + +(*** include-value:pltfrmPrint ***) diff --git a/docsrc/content/SOFT.fsx b/docsrc/content/SOFT.fsx new file mode 100644 index 00000000..75e8e749 --- /dev/null +++ b/docsrc/content/SOFT.fsx @@ -0,0 +1,94 @@ +(*** hide ***) +// This block of code is omitted in the generated HTML documentation. Use +// it to define helpers that you do not want to show in the documentation. +#I @"../../bin/BioFSharp/net47/" +#I @"../../bin/BioFSharp.BioDB/net45/" +#I @"../../bin/BioFSharp.ImgP/net47" +#I @"../../bin/BioFSharp.IO/net47/" +#I @"../../bin/BioFSharp.Parallel/net47/" +#I @"../../bin/BioFSharp.Stats/net47/" +#I @"../../bin/BioFSharp.Vis/net47/" +#r @"../../lib/Formatting/FSharp.Plotly.dll" +#r "FSharpAux.dll" +#r "FSharpAux.IO.dll" +#r "BioFSharp.dll" +#r "BioFSharp.IO.dll" + +open BioFSharp + +open FSharpAux + +(** +Parsing SOFT formatted family files +=================================== + +GEO (Gene Expression Omnibus) is a data repository of high-throughput gene expression and hybridization array data. All record metadata are provided in the [soft format](https://www.ncbi.nlm.nih.gov/geo/info/soft.html) , +which can be parsed and analyzed using the `BioFSharp.IO.SOFT` module. + +SOFT types are very large and hard to read from standard FSI output, especially the nested top level types, so we will omitt the standard output for readability and use +the FSI printers provided in `BioFSharp.IO.FSIPrinters`. +*) + +open BioFSharp.IO + +//register the desired printers +fsi.AddPrinter(FSIPrinters.prettyPrintGPL) +fsi.AddPrinter(FSIPrinters.prettyPrintGSE) + +fsi.AddPrinter(FSIPrinters.prettyPrintSampleRecord) +fsi.AddPrinter(FSIPrinters.prettyPrintSeriesRecord) +fsi.AddPrinter(FSIPrinters.prettyPrintPlatformRecord) + + +(** +Parsing platform (GPL) files +---------------------------- + +Soft formatted platform family files can be parsed using the `SOFT.Platform.fromFile` function. + +As the format (.soft) does not specify the type of record (GSE or GPL), please make sure that you only +parse GPL*.soft files with this functions, as other files may return errors +*) + +let testPlatform = SOFT.Platform.fromFile (__SOURCE_DIRECTORY__ + "/data/GPL15922_family.soft") + +(** +Parsing series (GSE) files +-------------------------- + +Soft formatted series family files can be parsed using the `SOFT.Platform.fromFile` function. + +As the format (.soft) does not specify the type of record (GSE or GPL), please make sure that you only +parse GSE*.soft files with this functions, as other files may return errors +*) + +let testSeries = SOFT.Series.fromFile (__SOURCE_DIRECTORY__ + "/data/GSE71469_family.soft") + +(** +Convenience functions +--------------------- + +We implemented some convenience functions for `SOFT.Platform.GPL` and `SOFT.Series.GSE`. + +`Platform.getAssociatedSampleAccessions` for example retrieves all associated sample accessions. This could be usefull for batch downloads of these files. +*) + +let sampleAccessions = + testPlatform |> SOFT.Platform.getAssociatedSampleAccessions + +(*** include-value:sampleAccessions ***) + +(** +This can be especially usefull to retrieve all samples that are associated with this platform (e.g. for example for meta analysis of the files). + +The full sample records can also be retrieved, which makes it possible to access even more metadata: +*) + +let relations = + testPlatform + |> SOFT.Platform.getAssociatedSamples + |> List.map (fun x -> x.Relation) + //showing only the first 5 relations for ease of view + |> fun x -> x.[0..4] + +(*** include-value:relations ***) diff --git a/docsrc/content/data/GPL15922_family.soft b/docsrc/content/data/GPL15922_family.soft new file mode 100644 index 00000000..70f18be7 --- /dev/null +++ b/docsrc/content/data/GPL15922_family.soft @@ -0,0 +1,11252 @@ +^DATABASE = GeoMiame +!Database_name = Gene Expression Omnibus (GEO) +!Database_institute = NCBI NLM NIH +!Database_web_link = http://www.ncbi.nlm.nih.gov/geo +!Database_email = geo@ncbi.nlm.nih.gov +^PLATFORM = GPL15922 +!Platform_title = Illumina HiSeq 2000 (Chlamydomonas reinhardtii) +!Platform_geo_accession = GPL15922 +!Platform_status = Public on Aug 10 2012 +!Platform_submission_date = Aug 10 2012 +!Platform_last_update_date = Apr 24 2015 +!Platform_technology = high-throughput sequencing +!Platform_distribution = virtual +!Platform_organism = Chlamydomonas reinhardtii +!Platform_taxid = 3055 +!Platform_contact_name = ,,GEO +!Platform_contact_country = USA +!Platform_sample_id = GSM983943 +!Platform_sample_id = GSM983944 +!Platform_sample_id = GSM983945 +!Platform_sample_id = GSM983946 +!Platform_sample_id = GSM983947 +!Platform_sample_id = GSM983948 +!Platform_sample_id = GSM983949 +!Platform_sample_id = GSM983950 +!Platform_sample_id = GSM983951 +!Platform_sample_id = GSM983952 +!Platform_sample_id = GSM983953 +!Platform_sample_id = GSM983954 +!Platform_sample_id = GSM983955 +!Platform_sample_id = GSM983956 +!Platform_sample_id = GSM983957 +!Platform_sample_id = GSM983958 +!Platform_sample_id = GSM1087792 +!Platform_sample_id = GSM1087793 +!Platform_sample_id = GSM1087794 +!Platform_sample_id = GSM1087795 +!Platform_sample_id = GSM1087796 +!Platform_sample_id = GSM1087797 +!Platform_sample_id = GSM1087798 +!Platform_sample_id = GSM1087799 +!Platform_sample_id = GSM1087800 +!Platform_sample_id = GSM1332630 +!Platform_sample_id = GSM1332631 +!Platform_sample_id = GSM1332632 +!Platform_sample_id = GSM1332633 +!Platform_sample_id = GSM1332634 +!Platform_sample_id = GSM1332635 +!Platform_sample_id = GSM1332636 +!Platform_sample_id = GSM1332637 +!Platform_sample_id = GSM1332638 +!Platform_sample_id = GSM1332639 +!Platform_sample_id = GSM1332640 +!Platform_sample_id = GSM1332641 +!Platform_sample_id = GSM1332642 +!Platform_sample_id = GSM1332643 +!Platform_sample_id = GSM1332644 +!Platform_sample_id = GSM1332645 +!Platform_sample_id = GSM1332646 +!Platform_sample_id = GSM1332647 +!Platform_sample_id = GSM1332648 +!Platform_sample_id = GSM1332649 +!Platform_sample_id = GSM1332650 +!Platform_sample_id = GSM1332651 +!Platform_sample_id = GSM1332652 +!Platform_sample_id = GSM1332653 +!Platform_sample_id = GSM1332654 +!Platform_sample_id = GSM1332655 +!Platform_sample_id = GSM1332656 +!Platform_sample_id = GSM1332657 +!Platform_sample_id = GSM1332658 +!Platform_sample_id = GSM1332659 +!Platform_sample_id = GSM1332660 +!Platform_sample_id = GSM1332661 +!Platform_sample_id = GSM1332662 +!Platform_sample_id = GSM1332663 +!Platform_sample_id = GSM1419589 +!Platform_sample_id = GSM1419590 +!Platform_sample_id = GSM1419591 +!Platform_sample_id = GSM1419592 +!Platform_sample_id = GSM1419593 +!Platform_sample_id = GSM1419594 +!Platform_sample_id = GSM1419595 +!Platform_sample_id = GSM1419596 +!Platform_sample_id = GSM1440761 +!Platform_sample_id = GSM1440762 +!Platform_sample_id = GSM1440763 +!Platform_sample_id = GSM1440764 +!Platform_sample_id = GSM1440765 +!Platform_sample_id = GSM1440766 +!Platform_sample_id = GSM1440767 +!Platform_sample_id = GSM1440768 +!Platform_sample_id = GSM1440769 +!Platform_sample_id = GSM1440770 +!Platform_sample_id = GSM1440771 +!Platform_sample_id = GSM1440772 +!Platform_sample_id = GSM1440773 +!Platform_sample_id = GSM1440774 +!Platform_sample_id = GSM1440775 +!Platform_sample_id = GSM1440776 +!Platform_sample_id = GSM1440777 +!Platform_sample_id = GSM1440778 +!Platform_sample_id = GSM1440779 +!Platform_sample_id = GSM1440780 +!Platform_sample_id = GSM1440781 +!Platform_sample_id = GSM1440782 +!Platform_sample_id = GSM1440783 +!Platform_sample_id = GSM1440784 +!Platform_sample_id = GSM1440785 +!Platform_sample_id = GSM1440786 +!Platform_sample_id = GSM1440787 +!Platform_sample_id = GSM1440788 +!Platform_sample_id = GSM1440789 +!Platform_sample_id = GSM1440790 +!Platform_sample_id = GSM1440791 +!Platform_sample_id = GSM1440792 +!Platform_sample_id = GSM1440793 +!Platform_sample_id = GSM1440794 +!Platform_sample_id = GSM1440795 +!Platform_sample_id = GSM1440796 +!Platform_sample_id = GSM1666091 +!Platform_sample_id = GSM1666092 +!Platform_sample_id = GSM1666093 +!Platform_sample_id = GSM1666094 +!Platform_sample_id = GSM1666095 +!Platform_sample_id = GSM1666096 +!Platform_sample_id = GSM1666097 +!Platform_sample_id = GSM1666098 +!Platform_sample_id = GSM1666099 +!Platform_sample_id = GSM1666100 +!Platform_sample_id = GSM1666101 +!Platform_sample_id = GSM1666102 +!Platform_sample_id = GSM1666103 +!Platform_sample_id = GSM1666104 +!Platform_sample_id = GSM1835200 +!Platform_sample_id = GSM1835201 +!Platform_sample_id = GSM1835202 +!Platform_sample_id = GSM1835203 +!Platform_sample_id = GSM1835204 +!Platform_sample_id = GSM1835205 +!Platform_sample_id = GSM1835206 +!Platform_sample_id = GSM1835207 +!Platform_sample_id = GSM1835208 +!Platform_sample_id = GSM1835209 +!Platform_sample_id = GSM1835210 +!Platform_sample_id = GSM1835211 +!Platform_sample_id = GSM1835212 +!Platform_sample_id = GSM1835213 +!Platform_sample_id = GSM1835214 +!Platform_sample_id = GSM1835215 +!Platform_sample_id = GSM1835216 +!Platform_sample_id = GSM1835217 +!Platform_sample_id = GSM1835218 +!Platform_sample_id = GSM1835219 +!Platform_sample_id = GSM1835220 +!Platform_sample_id = GSM1835221 +!Platform_sample_id = GSM1835222 +!Platform_sample_id = GSM1835223 +!Platform_sample_id = GSM1835224 +!Platform_sample_id = GSM1835225 +!Platform_sample_id = GSM1835226 +!Platform_sample_id = GSM1835227 +!Platform_sample_id = GSM1835228 +!Platform_sample_id = GSM1835229 +!Platform_sample_id = GSM1835230 +!Platform_sample_id = GSM1835231 +!Platform_sample_id = GSM1835232 +!Platform_sample_id = GSM1835233 +!Platform_sample_id = GSM1835234 +!Platform_sample_id = GSM1835235 +!Platform_sample_id = GSM1835236 +!Platform_sample_id = GSM1835237 +!Platform_sample_id = GSM1835238 +!Platform_sample_id = GSM1835239 +!Platform_sample_id = GSM1835240 +!Platform_sample_id = GSM1835241 +!Platform_sample_id = GSM1835242 +!Platform_sample_id = GSM1835243 +!Platform_sample_id = GSM1835244 +!Platform_sample_id = GSM1835245 +!Platform_sample_id = GSM1835246 +!Platform_sample_id = GSM1835247 +!Platform_sample_id = GSM1835248 +!Platform_sample_id = GSM1835249 +!Platform_sample_id = GSM1835250 +!Platform_sample_id = GSM1835251 +!Platform_sample_id = GSM1835252 +!Platform_sample_id = GSM1835253 +!Platform_sample_id = GSM1835254 +!Platform_sample_id = GSM1835255 +!Platform_sample_id = GSM2051194 +!Platform_sample_id = GSM2051195 +!Platform_sample_id = GSM2051196 +!Platform_sample_id = GSM2051197 +!Platform_sample_id = GSM2051198 +!Platform_sample_id = GSM2051199 +!Platform_sample_id = GSM2051200 +!Platform_sample_id = GSM2051201 +!Platform_sample_id = GSM2051202 +!Platform_sample_id = GSM2051203 +!Platform_sample_id = GSM2051204 +!Platform_sample_id = GSM2051205 +!Platform_sample_id = GSM2051206 +!Platform_sample_id = GSM2051207 +!Platform_sample_id = GSM2051208 +!Platform_sample_id = GSM2051209 +!Platform_sample_id = GSM2051210 +!Platform_sample_id = GSM2051211 +!Platform_sample_id = GSM2051212 +!Platform_sample_id = GSM2051213 +!Platform_sample_id = GSM2719230 +!Platform_sample_id = GSM2719231 +!Platform_sample_id = GSM2719232 +!Platform_sample_id = GSM2719233 +!Platform_sample_id = GSM2719234 +!Platform_sample_id = GSM2719235 +!Platform_sample_id = GSM2719236 +!Platform_sample_id = GSM2719237 +!Platform_sample_id = GSM2719238 +!Platform_sample_id = GSM2719239 +!Platform_sample_id = GSM2719240 +!Platform_sample_id = GSM2719241 +!Platform_sample_id = GSM2719242 +!Platform_sample_id = GSM2719243 +!Platform_sample_id = GSM3069464 +!Platform_sample_id = GSM3069465 +!Platform_sample_id = GSM3069466 +!Platform_sample_id = GSM3069467 +!Platform_sample_id = GSM3069468 +!Platform_sample_id = GSM3069469 +!Platform_sample_id = GSM3069470 +!Platform_sample_id = GSM3069471 +!Platform_sample_id = GSM3069472 +!Platform_sample_id = GSM3069473 +!Platform_sample_id = GSM3069474 +!Platform_sample_id = GSM3069475 +!Platform_sample_id = GSM3069476 +!Platform_sample_id = GSM3069477 +!Platform_sample_id = GSM3069478 +!Platform_sample_id = GSM3069479 +!Platform_series_id = GSE40031 +!Platform_series_id = GSE44611 +!Platform_series_id = GSE55253 +!Platform_series_id = GSE58786 +!Platform_series_id = GSE59629 +!Platform_series_id = GSE62690 +!Platform_series_id = GSE71469 +!Platform_series_id = GSE77388 +!Platform_series_id = GSE101944 +!Platform_series_id = GSE112394 +!Platform_data_row_count = 0 +^SAMPLE = GSM983943 +!Sample_title = JLDD4ANT0TS1 +!Sample_geo_accession = GSM983943 +!Sample_status = Public on Jan 10 2013 +!Sample_submission_date = Aug 10 2012 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas cultured cells +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 4A+ wild-type +!Sample_characteristics_ch1 = treatment: 0 mM +!Sample_characteristics_ch1 = light: dark +!Sample_treatment_protocol_ch1 = Cells (4A+ or hmox1) were innoculated in TAP medium (containing 0.5% v/v methanol with or without 0.1 mM BV IXα) at 5×104 cells/ml and grown in the dark at 22 C until the cell density reached ~2×106 cells/ml and then illuminated with white light (150 µmol photons m-2 s-1) for 30 minutes. Cells were harvested before and after light treatment and total RNA was extracted with Trizol and Qiagen RNeasy mini kit. +!Sample_growth_protocol_ch1 = All strains were maintained on TAP (Tris-Acetate-Phosphate) plates with modified recipe of trace metal elements {Kropat, 2011} at room temperature (22 C) under continuous illumination (30 μmol photons m−2 s−1). Liquid cultures were grown on a gyratory shaker (~100 rpm) heterotrophically on TAP medium in darkness. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was prepared as described previously {Castruita, 2011} and RNA quality was assessed by an Agilent 2100 Bioanalyzer at the UC Davis Genome Center. RNA-Seq libraries were sequenced as single-end 100mers using the HiSeq platform from Illumina. +!Sample_description = Chlamydomonas reinhardtii 4A+ wild-type +!Sample_data_processing = Illumina Casava1.8 software used for basecalling. +!Sample_data_processing = The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. +!Sample_data_processing = Expression estimates where obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. Final expression estimates and fold changes where obtained from the average of both technical and biological replicates. +!Sample_data_processing = Genome_build: version 4.0 assembly of the Chlamydomonas genome +!Sample_data_processing = Supplementary_files_format_and_content: Tab-delimited table with all genes (rows) and expression estimates (columns, in RPKMs) for every single library (or raw file, for a total or 16). +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX176002 +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01112491 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE40031 +!Sample_data_row_count = 0 +^SAMPLE = GSM983944 +!Sample_title = JLDD4ANT0TS2 +!Sample_geo_accession = GSM983944 +!Sample_status = Public on Jan 10 2013 +!Sample_submission_date = Aug 10 2012 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas cultured cells +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 4A+ wild-type +!Sample_characteristics_ch1 = treatment: 0 mM +!Sample_characteristics_ch1 = light: dark +!Sample_treatment_protocol_ch1 = Cells (4A+ or hmox1) were innoculated in TAP medium (containing 0.5% v/v methanol with or without 0.1 mM BV IXα) at 5×104 cells/ml and grown in the dark at 22 C until the cell density reached ~2×106 cells/ml and then illuminated with white light (150 µmol photons m-2 s-1) for 30 minutes. Cells were harvested before and after light treatment and total RNA was extracted with Trizol and Qiagen RNeasy mini kit. +!Sample_growth_protocol_ch1 = All strains were maintained on TAP (Tris-Acetate-Phosphate) plates with modified recipe of trace metal elements {Kropat, 2011} at room temperature (22 C) under continuous illumination (30 μmol photons m−2 s−1). Liquid cultures were grown on a gyratory shaker (~100 rpm) heterotrophically on TAP medium in darkness. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was prepared as described previously {Castruita, 2011} and RNA quality was assessed by an Agilent 2100 Bioanalyzer at the UC Davis Genome Center. RNA-Seq libraries were sequenced as single-end 100mers using the HiSeq platform from Illumina. +!Sample_description = Chlamydomonas reinhardtii 4A+ wild-type +!Sample_data_processing = Illumina Casava1.8 software used for basecalling. +!Sample_data_processing = The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. +!Sample_data_processing = Expression estimates where obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. Final expression estimates and fold changes where obtained from the average of both technical and biological replicates. +!Sample_data_processing = Genome_build: version 4.0 assembly of the Chlamydomonas genome +!Sample_data_processing = Supplementary_files_format_and_content: Tab-delimited table with all genes (rows) and expression estimates (columns, in RPKMs) for every single library (or raw file, for a total or 16). +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX176003 +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01112492 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE40031 +!Sample_data_row_count = 0 +^SAMPLE = GSM983945 +!Sample_title = JLDD4ANT05TS1 +!Sample_geo_accession = GSM983945 +!Sample_status = Public on Jan 10 2013 +!Sample_submission_date = Aug 10 2012 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas cultured cells +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 4A+ wild-type +!Sample_characteristics_ch1 = treatment: 0 mM +!Sample_characteristics_ch1 = light: 0.5h white light +!Sample_treatment_protocol_ch1 = Cells (4A+ or hmox1) were innoculated in TAP medium (containing 0.5% v/v methanol with or without 0.1 mM BV IXα) at 5×104 cells/ml and grown in the dark at 22 C until the cell density reached ~2×106 cells/ml and then illuminated with white light (150 µmol photons m-2 s-1) for 30 minutes. Cells were harvested before and after light treatment and total RNA was extracted with Trizol and Qiagen RNeasy mini kit. +!Sample_growth_protocol_ch1 = All strains were maintained on TAP (Tris-Acetate-Phosphate) plates with modified recipe of trace metal elements {Kropat, 2011} at room temperature (22 C) under continuous illumination (30 μmol photons m−2 s−1). Liquid cultures were grown on a gyratory shaker (~100 rpm) heterotrophically on TAP medium in darkness. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was prepared as described previously {Castruita, 2011} and RNA quality was assessed by an Agilent 2100 Bioanalyzer at the UC Davis Genome Center. RNA-Seq libraries were sequenced as single-end 100mers using the HiSeq platform from Illumina. +!Sample_description = Chlamydomonas reinhardtii 4A+ wild-type +!Sample_data_processing = Illumina Casava1.8 software used for basecalling. +!Sample_data_processing = The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. +!Sample_data_processing = Expression estimates where obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. Final expression estimates and fold changes where obtained from the average of both technical and biological replicates. +!Sample_data_processing = Genome_build: version 4.0 assembly of the Chlamydomonas genome +!Sample_data_processing = Supplementary_files_format_and_content: Tab-delimited table with all genes (rows) and expression estimates (columns, in RPKMs) for every single library (or raw file, for a total or 16). +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX176004 +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01112493 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE40031 +!Sample_data_row_count = 0 +^SAMPLE = GSM983946 +!Sample_title = JLDD4ANT05TS2 +!Sample_geo_accession = GSM983946 +!Sample_status = Public on Jan 10 2013 +!Sample_submission_date = Aug 10 2012 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas cultured cells +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 4A+ wild-type +!Sample_characteristics_ch1 = treatment: 0 mM +!Sample_characteristics_ch1 = light: 0.5h white light +!Sample_treatment_protocol_ch1 = Cells (4A+ or hmox1) were innoculated in TAP medium (containing 0.5% v/v methanol with or without 0.1 mM BV IXα) at 5×104 cells/ml and grown in the dark at 22 C until the cell density reached ~2×106 cells/ml and then illuminated with white light (150 µmol photons m-2 s-1) for 30 minutes. Cells were harvested before and after light treatment and total RNA was extracted with Trizol and Qiagen RNeasy mini kit. +!Sample_growth_protocol_ch1 = All strains were maintained on TAP (Tris-Acetate-Phosphate) plates with modified recipe of trace metal elements {Kropat, 2011} at room temperature (22 C) under continuous illumination (30 μmol photons m−2 s−1). Liquid cultures were grown on a gyratory shaker (~100 rpm) heterotrophically on TAP medium in darkness. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was prepared as described previously {Castruita, 2011} and RNA quality was assessed by an Agilent 2100 Bioanalyzer at the UC Davis Genome Center. RNA-Seq libraries were sequenced as single-end 100mers using the HiSeq platform from Illumina. +!Sample_description = Chlamydomonas reinhardtii 4A+ wild-type +!Sample_data_processing = Illumina Casava1.8 software used for basecalling. +!Sample_data_processing = The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. +!Sample_data_processing = Expression estimates where obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. Final expression estimates and fold changes where obtained from the average of both technical and biological replicates. +!Sample_data_processing = Genome_build: version 4.0 assembly of the Chlamydomonas genome +!Sample_data_processing = Supplementary_files_format_and_content: Tab-delimited table with all genes (rows) and expression estimates (columns, in RPKMs) for every single library (or raw file, for a total or 16). +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX176005 +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01112494 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE40031 +!Sample_data_row_count = 0 +^SAMPLE = GSM983947 +!Sample_title = JLDD4ABV0TS1 +!Sample_geo_accession = GSM983947 +!Sample_status = Public on Jan 10 2013 +!Sample_submission_date = Aug 10 2012 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas cultured cells +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 4A+ wild-type +!Sample_characteristics_ch1 = treatment: 0.1 mM +!Sample_characteristics_ch1 = light: dark +!Sample_treatment_protocol_ch1 = Cells (4A+ or hmox1) were innoculated in TAP medium (containing 0.5% v/v methanol with or without 0.1 mM BV IXα) at 5×104 cells/ml and grown in the dark at 22 C until the cell density reached ~2×106 cells/ml and then illuminated with white light (150 µmol photons m-2 s-1) for 30 minutes. Cells were harvested before and after light treatment and total RNA was extracted with Trizol and Qiagen RNeasy mini kit. +!Sample_growth_protocol_ch1 = All strains were maintained on TAP (Tris-Acetate-Phosphate) plates with modified recipe of trace metal elements {Kropat, 2011} at room temperature (22 C) under continuous illumination (30 μmol photons m−2 s−1). Liquid cultures were grown on a gyratory shaker (~100 rpm) heterotrophically on TAP medium in darkness. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was prepared as described previously {Castruita, 2011} and RNA quality was assessed by an Agilent 2100 Bioanalyzer at the UC Davis Genome Center. RNA-Seq libraries were sequenced as single-end 100mers using the HiSeq platform from Illumina. +!Sample_description = Chlamydomonas reinhardtii 4A+ wild-type +!Sample_data_processing = Illumina Casava1.8 software used for basecalling. +!Sample_data_processing = The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. +!Sample_data_processing = Expression estimates where obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. Final expression estimates and fold changes where obtained from the average of both technical and biological replicates. +!Sample_data_processing = Genome_build: version 4.0 assembly of the Chlamydomonas genome +!Sample_data_processing = Supplementary_files_format_and_content: Tab-delimited table with all genes (rows) and expression estimates (columns, in RPKMs) for every single library (or raw file, for a total or 16). +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX176006 +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01112495 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE40031 +!Sample_data_row_count = 0 +^SAMPLE = GSM983948 +!Sample_title = JLDD4ABV0TS2 +!Sample_geo_accession = GSM983948 +!Sample_status = Public on Jan 10 2013 +!Sample_submission_date = Aug 10 2012 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas cultured cells +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 4A+ wild-type +!Sample_characteristics_ch1 = treatment: 0.1 mM +!Sample_characteristics_ch1 = light: dark +!Sample_treatment_protocol_ch1 = Cells (4A+ or hmox1) were innoculated in TAP medium (containing 0.5% v/v methanol with or without 0.1 mM BV IXα) at 5×104 cells/ml and grown in the dark at 22 C until the cell density reached ~2×106 cells/ml and then illuminated with white light (150 µmol photons m-2 s-1) for 30 minutes. Cells were harvested before and after light treatment and total RNA was extracted with Trizol and Qiagen RNeasy mini kit. +!Sample_growth_protocol_ch1 = All strains were maintained on TAP (Tris-Acetate-Phosphate) plates with modified recipe of trace metal elements {Kropat, 2011} at room temperature (22 C) under continuous illumination (30 μmol photons m−2 s−1). Liquid cultures were grown on a gyratory shaker (~100 rpm) heterotrophically on TAP medium in darkness. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was prepared as described previously {Castruita, 2011} and RNA quality was assessed by an Agilent 2100 Bioanalyzer at the UC Davis Genome Center. RNA-Seq libraries were sequenced as single-end 100mers using the HiSeq platform from Illumina. +!Sample_description = Chlamydomonas reinhardtii 4A+ wild-type +!Sample_data_processing = Illumina Casava1.8 software used for basecalling. +!Sample_data_processing = The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. +!Sample_data_processing = Expression estimates where obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. Final expression estimates and fold changes where obtained from the average of both technical and biological replicates. +!Sample_data_processing = Genome_build: version 4.0 assembly of the Chlamydomonas genome +!Sample_data_processing = Supplementary_files_format_and_content: Tab-delimited table with all genes (rows) and expression estimates (columns, in RPKMs) for every single library (or raw file, for a total or 16). +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX176007 +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01112496 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE40031 +!Sample_data_row_count = 0 +^SAMPLE = GSM983949 +!Sample_title = JLDD4ABV05TS1 +!Sample_geo_accession = GSM983949 +!Sample_status = Public on Jan 10 2013 +!Sample_submission_date = Aug 10 2012 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas cultured cells +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 4A+ wild-type +!Sample_characteristics_ch1 = treatment: 0.1 mM +!Sample_characteristics_ch1 = light: 0.5h white light +!Sample_treatment_protocol_ch1 = Cells (4A+ or hmox1) were innoculated in TAP medium (containing 0.5% v/v methanol with or without 0.1 mM BV IXα) at 5×104 cells/ml and grown in the dark at 22 C until the cell density reached ~2×106 cells/ml and then illuminated with white light (150 µmol photons m-2 s-1) for 30 minutes. Cells were harvested before and after light treatment and total RNA was extracted with Trizol and Qiagen RNeasy mini kit. +!Sample_growth_protocol_ch1 = All strains were maintained on TAP (Tris-Acetate-Phosphate) plates with modified recipe of trace metal elements {Kropat, 2011} at room temperature (22 C) under continuous illumination (30 μmol photons m−2 s−1). Liquid cultures were grown on a gyratory shaker (~100 rpm) heterotrophically on TAP medium in darkness. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was prepared as described previously {Castruita, 2011} and RNA quality was assessed by an Agilent 2100 Bioanalyzer at the UC Davis Genome Center. RNA-Seq libraries were sequenced as single-end 100mers using the HiSeq platform from Illumina. +!Sample_description = Chlamydomonas reinhardtii 4A+ wild-type +!Sample_data_processing = Illumina Casava1.8 software used for basecalling. +!Sample_data_processing = The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. +!Sample_data_processing = Expression estimates where obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. Final expression estimates and fold changes where obtained from the average of both technical and biological replicates. +!Sample_data_processing = Genome_build: version 4.0 assembly of the Chlamydomonas genome +!Sample_data_processing = Supplementary_files_format_and_content: Tab-delimited table with all genes (rows) and expression estimates (columns, in RPKMs) for every single library (or raw file, for a total or 16). +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX176008 +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01112497 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE40031 +!Sample_data_row_count = 0 +^SAMPLE = GSM983950 +!Sample_title = JLDD4ABV05TS2 +!Sample_geo_accession = GSM983950 +!Sample_status = Public on Jan 10 2013 +!Sample_submission_date = Aug 10 2012 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas cultured cells +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 4A+ wild-type +!Sample_characteristics_ch1 = treatment: 0.1 mM +!Sample_characteristics_ch1 = light: 0.5h white light +!Sample_treatment_protocol_ch1 = Cells (4A+ or hmox1) were innoculated in TAP medium (containing 0.5% v/v methanol with or without 0.1 mM BV IXα) at 5×104 cells/ml and grown in the dark at 22 C until the cell density reached ~2×106 cells/ml and then illuminated with white light (150 µmol photons m-2 s-1) for 30 minutes. Cells were harvested before and after light treatment and total RNA was extracted with Trizol and Qiagen RNeasy mini kit. +!Sample_growth_protocol_ch1 = All strains were maintained on TAP (Tris-Acetate-Phosphate) plates with modified recipe of trace metal elements {Kropat, 2011} at room temperature (22 C) under continuous illumination (30 μmol photons m−2 s−1). Liquid cultures were grown on a gyratory shaker (~100 rpm) heterotrophically on TAP medium in darkness. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was prepared as described previously {Castruita, 2011} and RNA quality was assessed by an Agilent 2100 Bioanalyzer at the UC Davis Genome Center. RNA-Seq libraries were sequenced as single-end 100mers using the HiSeq platform from Illumina. +!Sample_description = Chlamydomonas reinhardtii 4A+ wild-type +!Sample_data_processing = Illumina Casava1.8 software used for basecalling. +!Sample_data_processing = The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. +!Sample_data_processing = Expression estimates where obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. Final expression estimates and fold changes where obtained from the average of both technical and biological replicates. +!Sample_data_processing = Genome_build: version 4.0 assembly of the Chlamydomonas genome +!Sample_data_processing = Supplementary_files_format_and_content: Tab-delimited table with all genes (rows) and expression estimates (columns, in RPKMs) for every single library (or raw file, for a total or 16). +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX176009 +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01112498 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE40031 +!Sample_data_row_count = 0 +^SAMPLE = GSM983951 +!Sample_title = JLDDhoNT0TS1 +!Sample_geo_accession = GSM983951 +!Sample_status = Public on Jan 10 2013 +!Sample_submission_date = Aug 10 2012 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas cultured cells +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: hmox1 mutant +!Sample_characteristics_ch1 = treatment: 0 mM +!Sample_characteristics_ch1 = light: dark +!Sample_treatment_protocol_ch1 = Cells (4A+ or hmox1) were innoculated in TAP medium (containing 0.5% v/v methanol with or without 0.1 mM BV IXα) at 5×104 cells/ml and grown in the dark at 22 C until the cell density reached ~2×106 cells/ml and then illuminated with white light (150 µmol photons m-2 s-1) for 30 minutes. Cells were harvested before and after light treatment and total RNA was extracted with Trizol and Qiagen RNeasy mini kit. +!Sample_growth_protocol_ch1 = All strains were maintained on TAP (Tris-Acetate-Phosphate) plates with modified recipe of trace metal elements {Kropat, 2011} at room temperature (22 C) under continuous illumination (30 μmol photons m−2 s−1). Liquid cultures were grown on a gyratory shaker (~100 rpm) heterotrophically on TAP medium in darkness. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was prepared as described previously {Castruita, 2011} and RNA quality was assessed by an Agilent 2100 Bioanalyzer at the UC Davis Genome Center. RNA-Seq libraries were sequenced as single-end 100mers using the HiSeq platform from Illumina. +!Sample_description = Chlamydomonas reinhardtii hmox1 mutant +!Sample_data_processing = Illumina Casava1.8 software used for basecalling. +!Sample_data_processing = The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. +!Sample_data_processing = Expression estimates where obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. Final expression estimates and fold changes where obtained from the average of both technical and biological replicates. +!Sample_data_processing = Genome_build: version 4.0 assembly of the Chlamydomonas genome +!Sample_data_processing = Supplementary_files_format_and_content: Tab-delimited table with all genes (rows) and expression estimates (columns, in RPKMs) for every single library (or raw file, for a total or 16). +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX176010 +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01112499 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE40031 +!Sample_data_row_count = 0 +^SAMPLE = GSM983952 +!Sample_title = JLDDhoNT0TS2 +!Sample_geo_accession = GSM983952 +!Sample_status = Public on Jan 10 2013 +!Sample_submission_date = Aug 10 2012 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas cultured cells +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: hmox1 mutant +!Sample_characteristics_ch1 = treatment: 0 mM +!Sample_characteristics_ch1 = light: dark +!Sample_treatment_protocol_ch1 = Cells (4A+ or hmox1) were innoculated in TAP medium (containing 0.5% v/v methanol with or without 0.1 mM BV IXα) at 5×104 cells/ml and grown in the dark at 22 C until the cell density reached ~2×106 cells/ml and then illuminated with white light (150 µmol photons m-2 s-1) for 30 minutes. Cells were harvested before and after light treatment and total RNA was extracted with Trizol and Qiagen RNeasy mini kit. +!Sample_growth_protocol_ch1 = All strains were maintained on TAP (Tris-Acetate-Phosphate) plates with modified recipe of trace metal elements {Kropat, 2011} at room temperature (22 C) under continuous illumination (30 μmol photons m−2 s−1). Liquid cultures were grown on a gyratory shaker (~100 rpm) heterotrophically on TAP medium in darkness. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was prepared as described previously {Castruita, 2011} and RNA quality was assessed by an Agilent 2100 Bioanalyzer at the UC Davis Genome Center. RNA-Seq libraries were sequenced as single-end 100mers using the HiSeq platform from Illumina. +!Sample_description = Chlamydomonas reinhardtii hmox1 mutant +!Sample_data_processing = Illumina Casava1.8 software used for basecalling. +!Sample_data_processing = The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. +!Sample_data_processing = Expression estimates where obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. Final expression estimates and fold changes where obtained from the average of both technical and biological replicates. +!Sample_data_processing = Genome_build: version 4.0 assembly of the Chlamydomonas genome +!Sample_data_processing = Supplementary_files_format_and_content: Tab-delimited table with all genes (rows) and expression estimates (columns, in RPKMs) for every single library (or raw file, for a total or 16). +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX176011 +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01112500 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE40031 +!Sample_data_row_count = 0 +^SAMPLE = GSM983953 +!Sample_title = JLDDhoNT05TS1 +!Sample_geo_accession = GSM983953 +!Sample_status = Public on Jan 10 2013 +!Sample_submission_date = Aug 10 2012 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas cultured cells +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: hmox1 mutant +!Sample_characteristics_ch1 = treatment: 0 mM +!Sample_characteristics_ch1 = light: 0.5h white light +!Sample_treatment_protocol_ch1 = Cells (4A+ or hmox1) were innoculated in TAP medium (containing 0.5% v/v methanol with or without 0.1 mM BV IXα) at 5×104 cells/ml and grown in the dark at 22 C until the cell density reached ~2×106 cells/ml and then illuminated with white light (150 µmol photons m-2 s-1) for 30 minutes. Cells were harvested before and after light treatment and total RNA was extracted with Trizol and Qiagen RNeasy mini kit. +!Sample_growth_protocol_ch1 = All strains were maintained on TAP (Tris-Acetate-Phosphate) plates with modified recipe of trace metal elements {Kropat, 2011} at room temperature (22 C) under continuous illumination (30 μmol photons m−2 s−1). Liquid cultures were grown on a gyratory shaker (~100 rpm) heterotrophically on TAP medium in darkness. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was prepared as described previously {Castruita, 2011} and RNA quality was assessed by an Agilent 2100 Bioanalyzer at the UC Davis Genome Center. RNA-Seq libraries were sequenced as single-end 100mers using the HiSeq platform from Illumina. +!Sample_description = Chlamydomonas reinhardtii hmox1 mutant +!Sample_data_processing = Illumina Casava1.8 software used for basecalling. +!Sample_data_processing = The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. +!Sample_data_processing = Expression estimates where obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. Final expression estimates and fold changes where obtained from the average of both technical and biological replicates. +!Sample_data_processing = Genome_build: version 4.0 assembly of the Chlamydomonas genome +!Sample_data_processing = Supplementary_files_format_and_content: Tab-delimited table with all genes (rows) and expression estimates (columns, in RPKMs) for every single library (or raw file, for a total or 16). +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX176012 +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01112501 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE40031 +!Sample_data_row_count = 0 +^SAMPLE = GSM983954 +!Sample_title = JLDDhoNT05TS2 +!Sample_geo_accession = GSM983954 +!Sample_status = Public on Jan 10 2013 +!Sample_submission_date = Aug 10 2012 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas cultured cells +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: hmox1 mutant +!Sample_characteristics_ch1 = treatment: 0 mM +!Sample_characteristics_ch1 = light: 0.5h white light +!Sample_treatment_protocol_ch1 = Cells (4A+ or hmox1) were innoculated in TAP medium (containing 0.5% v/v methanol with or without 0.1 mM BV IXα) at 5×104 cells/ml and grown in the dark at 22 C until the cell density reached ~2×106 cells/ml and then illuminated with white light (150 µmol photons m-2 s-1) for 30 minutes. Cells were harvested before and after light treatment and total RNA was extracted with Trizol and Qiagen RNeasy mini kit. +!Sample_growth_protocol_ch1 = All strains were maintained on TAP (Tris-Acetate-Phosphate) plates with modified recipe of trace metal elements {Kropat, 2011} at room temperature (22 C) under continuous illumination (30 μmol photons m−2 s−1). Liquid cultures were grown on a gyratory shaker (~100 rpm) heterotrophically on TAP medium in darkness. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was prepared as described previously {Castruita, 2011} and RNA quality was assessed by an Agilent 2100 Bioanalyzer at the UC Davis Genome Center. RNA-Seq libraries were sequenced as single-end 100mers using the HiSeq platform from Illumina. +!Sample_description = Chlamydomonas reinhardtii hmox1 mutant +!Sample_data_processing = Illumina Casava1.8 software used for basecalling. +!Sample_data_processing = The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. +!Sample_data_processing = Expression estimates where obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. Final expression estimates and fold changes where obtained from the average of both technical and biological replicates. +!Sample_data_processing = Genome_build: version 4.0 assembly of the Chlamydomonas genome +!Sample_data_processing = Supplementary_files_format_and_content: Tab-delimited table with all genes (rows) and expression estimates (columns, in RPKMs) for every single library (or raw file, for a total or 16). +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX176013 +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01112502 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE40031 +!Sample_data_row_count = 0 +^SAMPLE = GSM983955 +!Sample_title = JLDDhoBV0TS1 +!Sample_geo_accession = GSM983955 +!Sample_status = Public on Jan 10 2013 +!Sample_submission_date = Aug 10 2012 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas cultured cells +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: hmox1 mutant +!Sample_characteristics_ch1 = treatment: 0.1 mM +!Sample_characteristics_ch1 = light: dark +!Sample_treatment_protocol_ch1 = Cells (4A+ or hmox1) were innoculated in TAP medium (containing 0.5% v/v methanol with or without 0.1 mM BV IXα) at 5×104 cells/ml and grown in the dark at 22 C until the cell density reached ~2×106 cells/ml and then illuminated with white light (150 µmol photons m-2 s-1) for 30 minutes. Cells were harvested before and after light treatment and total RNA was extracted with Trizol and Qiagen RNeasy mini kit. +!Sample_growth_protocol_ch1 = All strains were maintained on TAP (Tris-Acetate-Phosphate) plates with modified recipe of trace metal elements {Kropat, 2011} at room temperature (22 C) under continuous illumination (30 μmol photons m−2 s−1). Liquid cultures were grown on a gyratory shaker (~100 rpm) heterotrophically on TAP medium in darkness. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was prepared as described previously {Castruita, 2011} and RNA quality was assessed by an Agilent 2100 Bioanalyzer at the UC Davis Genome Center. RNA-Seq libraries were sequenced as single-end 100mers using the HiSeq platform from Illumina. +!Sample_description = Chlamydomonas reinhardtii hmox1 mutant +!Sample_data_processing = Illumina Casava1.8 software used for basecalling. +!Sample_data_processing = The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. +!Sample_data_processing = Expression estimates where obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. Final expression estimates and fold changes where obtained from the average of both technical and biological replicates. +!Sample_data_processing = Genome_build: version 4.0 assembly of the Chlamydomonas genome +!Sample_data_processing = Supplementary_files_format_and_content: Tab-delimited table with all genes (rows) and expression estimates (columns, in RPKMs) for every single library (or raw file, for a total or 16). +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX176014 +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01112503 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE40031 +!Sample_data_row_count = 0 +^SAMPLE = GSM983956 +!Sample_title = JLDDhoBV0TS2 +!Sample_geo_accession = GSM983956 +!Sample_status = Public on Jan 10 2013 +!Sample_submission_date = Aug 10 2012 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas cultured cells +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: hmox1 mutant +!Sample_characteristics_ch1 = treatment: 0.1 mM +!Sample_characteristics_ch1 = light: dark +!Sample_treatment_protocol_ch1 = Cells (4A+ or hmox1) were innoculated in TAP medium (containing 0.5% v/v methanol with or without 0.1 mM BV IXα) at 5×104 cells/ml and grown in the dark at 22 C until the cell density reached ~2×106 cells/ml and then illuminated with white light (150 µmol photons m-2 s-1) for 30 minutes. Cells were harvested before and after light treatment and total RNA was extracted with Trizol and Qiagen RNeasy mini kit. +!Sample_growth_protocol_ch1 = All strains were maintained on TAP (Tris-Acetate-Phosphate) plates with modified recipe of trace metal elements {Kropat, 2011} at room temperature (22 C) under continuous illumination (30 μmol photons m−2 s−1). Liquid cultures were grown on a gyratory shaker (~100 rpm) heterotrophically on TAP medium in darkness. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was prepared as described previously {Castruita, 2011} and RNA quality was assessed by an Agilent 2100 Bioanalyzer at the UC Davis Genome Center. RNA-Seq libraries were sequenced as single-end 100mers using the HiSeq platform from Illumina. +!Sample_description = Chlamydomonas reinhardtii hmox1 mutant +!Sample_data_processing = Illumina Casava1.8 software used for basecalling. +!Sample_data_processing = The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. +!Sample_data_processing = Expression estimates where obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. Final expression estimates and fold changes where obtained from the average of both technical and biological replicates. +!Sample_data_processing = Genome_build: version 4.0 assembly of the Chlamydomonas genome +!Sample_data_processing = Supplementary_files_format_and_content: Tab-delimited table with all genes (rows) and expression estimates (columns, in RPKMs) for every single library (or raw file, for a total or 16). +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX176015 +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01112504 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE40031 +!Sample_data_row_count = 0 +^SAMPLE = GSM983957 +!Sample_title = JLDDhoBV05TS1 +!Sample_geo_accession = GSM983957 +!Sample_status = Public on Jan 10 2013 +!Sample_submission_date = Aug 10 2012 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas cultured cells +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: hmox1 mutant +!Sample_characteristics_ch1 = treatment: 0.1 mM +!Sample_characteristics_ch1 = light: 0.5h white light +!Sample_treatment_protocol_ch1 = Cells (4A+ or hmox1) were innoculated in TAP medium (containing 0.5% v/v methanol with or without 0.1 mM BV IXα) at 5×104 cells/ml and grown in the dark at 22 C until the cell density reached ~2×106 cells/ml and then illuminated with white light (150 µmol photons m-2 s-1) for 30 minutes. Cells were harvested before and after light treatment and total RNA was extracted with Trizol and Qiagen RNeasy mini kit. +!Sample_growth_protocol_ch1 = All strains were maintained on TAP (Tris-Acetate-Phosphate) plates with modified recipe of trace metal elements {Kropat, 2011} at room temperature (22 C) under continuous illumination (30 μmol photons m−2 s−1). Liquid cultures were grown on a gyratory shaker (~100 rpm) heterotrophically on TAP medium in darkness. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was prepared as described previously {Castruita, 2011} and RNA quality was assessed by an Agilent 2100 Bioanalyzer at the UC Davis Genome Center. RNA-Seq libraries were sequenced as single-end 100mers using the HiSeq platform from Illumina. +!Sample_description = Chlamydomonas reinhardtii hmox1 mutant +!Sample_data_processing = Illumina Casava1.8 software used for basecalling. +!Sample_data_processing = The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. +!Sample_data_processing = Expression estimates where obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. Final expression estimates and fold changes where obtained from the average of both technical and biological replicates. +!Sample_data_processing = Genome_build: version 4.0 assembly of the Chlamydomonas genome +!Sample_data_processing = Supplementary_files_format_and_content: Tab-delimited table with all genes (rows) and expression estimates (columns, in RPKMs) for every single library (or raw file, for a total or 16). +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX176016 +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01112505 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE40031 +!Sample_data_row_count = 0 +^SAMPLE = GSM983958 +!Sample_title = JLDDhoBV05TS2 +!Sample_geo_accession = GSM983958 +!Sample_status = Public on Jan 10 2013 +!Sample_submission_date = Aug 10 2012 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas cultured cells +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: hmox1 mutant +!Sample_characteristics_ch1 = treatment: 0.1 mM +!Sample_characteristics_ch1 = light: 0.5h white light +!Sample_treatment_protocol_ch1 = Cells (4A+ or hmox1) were innoculated in TAP medium (containing 0.5% v/v methanol with or without 0.1 mM BV IXα) at 5×104 cells/ml and grown in the dark at 22 C until the cell density reached ~2×106 cells/ml and then illuminated with white light (150 µmol photons m-2 s-1) for 30 minutes. Cells were harvested before and after light treatment and total RNA was extracted with Trizol and Qiagen RNeasy mini kit. +!Sample_growth_protocol_ch1 = All strains were maintained on TAP (Tris-Acetate-Phosphate) plates with modified recipe of trace metal elements {Kropat, 2011} at room temperature (22 C) under continuous illumination (30 μmol photons m−2 s−1). Liquid cultures were grown on a gyratory shaker (~100 rpm) heterotrophically on TAP medium in darkness. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was prepared as described previously {Castruita, 2011} and RNA quality was assessed by an Agilent 2100 Bioanalyzer at the UC Davis Genome Center. RNA-Seq libraries were sequenced as single-end 100mers using the HiSeq platform from Illumina. +!Sample_description = Chlamydomonas reinhardtii hmox1 mutant +!Sample_data_processing = Illumina Casava1.8 software used for basecalling. +!Sample_data_processing = The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. +!Sample_data_processing = Expression estimates where obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. Final expression estimates and fold changes where obtained from the average of both technical and biological replicates. +!Sample_data_processing = Genome_build: version 4.0 assembly of the Chlamydomonas genome +!Sample_data_processing = Supplementary_files_format_and_content: Tab-delimited table with all genes (rows) and expression estimates (columns, in RPKMs) for every single library (or raw file, for a total or 16). +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX176017 +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01112506 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE40031 +!Sample_data_row_count = 0 +^SAMPLE = GSM1087792 +!Sample_title = C.reinhardtii _Fe_Long_0_hours +!Sample_geo_accession = GSM1087792 +!Sample_status = Public on Feb 20 2014 +!Sample_submission_date = Feb 25 2013 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas cultured cells +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: CC-4532 (2137) +!Sample_characteristics_ch1 = treatment: iron deprivation +!Sample_characteristics_ch1 = cultured in: TAP medium without Fe-EDTA for 0h +!Sample_treatment_protocol_ch1 = Cells were grown to mid-logarithmic phase (approximately 4 x 10e6 cells mL-1), collected by centrifugation (2,500 xg for 5 min at room temperature), washed twice in TAP medium lacking Fe-EDTA and inoculated into fresh TAP medium lacking Fe-EDTA and sampled at the indicated times. +!Sample_growth_protocol_ch1 = Cells were cultured under continuous light of ~90 μmol photon m-2s-1 at 24C in liquid and on solid Tris-Acetate-Phosphate (TAP) medium. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Nucleic acids were isolated and analyzed according to standard procedures by hybridization or on an Agilent 2100 Bioanalyzer. For quantitative transcriptomes, RNAs were sequenced at Illumina HiSeq 2000 platform (UCLA). +!Sample_description = SMEU37Fe0h.TS +!Sample_data_processing = Illumina's proprietary software was used for basecalling. +!Sample_data_processing = The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. +!Sample_data_processing = Expression estimates where obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. Final expression estimates and fold changes where obtained from the average of both technical and biological replicates. +!Sample_data_processing = Genome_build: version 4.0 assembly of the Chlamydomonas genome (http://genome.jgi-psf.org/Chlre4/Chlre4.home.html) +!Sample_data_processing = Supplementary_files_format_and_content: Processed files correpond to expression estimates per lane, in units of RPKMs. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245324 +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924672 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE44611 +!Sample_data_row_count = 0 +^SAMPLE = GSM1087793 +!Sample_title = C.reinhardtii _Fe_Long_0.5_hours +!Sample_geo_accession = GSM1087793 +!Sample_status = Public on Feb 20 2014 +!Sample_submission_date = Feb 25 2013 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas cultured cells +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: CC-4532 (2137) +!Sample_characteristics_ch1 = treatment: iron deprivation +!Sample_characteristics_ch1 = cultured in: TAP medium without Fe-EDTA for 0.5h +!Sample_treatment_protocol_ch1 = Cells were grown to mid-logarithmic phase (approximately 4 x 10e6 cells mL-1), collected by centrifugation (2,500 xg for 5 min at room temperature), washed twice in TAP medium lacking Fe-EDTA and inoculated into fresh TAP medium lacking Fe-EDTA and sampled at the indicated times. +!Sample_growth_protocol_ch1 = Cells were cultured under continuous light of ~90 μmol photon m-2s-1 at 24C in liquid and on solid Tris-Acetate-Phosphate (TAP) medium. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Nucleic acids were isolated and analyzed according to standard procedures by hybridization or on an Agilent 2100 Bioanalyzer. For quantitative transcriptomes, RNAs were sequenced at Illumina HiSeq 2000 platform (UCLA). +!Sample_description = SMEU37Fe05hTS +!Sample_data_processing = Illumina's proprietary software was used for basecalling. +!Sample_data_processing = The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. +!Sample_data_processing = Expression estimates where obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. Final expression estimates and fold changes where obtained from the average of both technical and biological replicates. +!Sample_data_processing = Genome_build: version 4.0 assembly of the Chlamydomonas genome (http://genome.jgi-psf.org/Chlre4/Chlre4.home.html) +!Sample_data_processing = Supplementary_files_format_and_content: Processed files correpond to expression estimates per lane, in units of RPKMs. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245325 +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924673 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE44611 +!Sample_data_row_count = 0 +^SAMPLE = GSM1087794 +!Sample_title = C.reinhardtii _Fe_Long_1_hours +!Sample_geo_accession = GSM1087794 +!Sample_status = Public on Feb 20 2014 +!Sample_submission_date = Feb 25 2013 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas cultured cells +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: CC-4532 (2137) +!Sample_characteristics_ch1 = treatment: iron deprivation +!Sample_characteristics_ch1 = cultured in: TAP medium without Fe-EDTA for 1h +!Sample_treatment_protocol_ch1 = Cells were grown to mid-logarithmic phase (approximately 4 x 10e6 cells mL-1), collected by centrifugation (2,500 xg for 5 min at room temperature), washed twice in TAP medium lacking Fe-EDTA and inoculated into fresh TAP medium lacking Fe-EDTA and sampled at the indicated times. +!Sample_growth_protocol_ch1 = Cells were cultured under continuous light of ~90 μmol photon m-2s-1 at 24C in liquid and on solid Tris-Acetate-Phosphate (TAP) medium. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Nucleic acids were isolated and analyzed according to standard procedures by hybridization or on an Agilent 2100 Bioanalyzer. For quantitative transcriptomes, RNAs were sequenced at Illumina HiSeq 2000 platform (UCLA). +!Sample_description = SMEU37Fe1hTS +!Sample_data_processing = Illumina's proprietary software was used for basecalling. +!Sample_data_processing = The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. +!Sample_data_processing = Expression estimates where obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. Final expression estimates and fold changes where obtained from the average of both technical and biological replicates. +!Sample_data_processing = Genome_build: version 4.0 assembly of the Chlamydomonas genome (http://genome.jgi-psf.org/Chlre4/Chlre4.home.html) +!Sample_data_processing = Supplementary_files_format_and_content: Processed files correpond to expression estimates per lane, in units of RPKMs. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245326 +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924674 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE44611 +!Sample_data_row_count = 0 +^SAMPLE = GSM1087795 +!Sample_title = C.reinhardtii _Fe_Long_2_hours +!Sample_geo_accession = GSM1087795 +!Sample_status = Public on Feb 20 2014 +!Sample_submission_date = Feb 25 2013 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas cultured cells +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: CC-4532 (2137) +!Sample_characteristics_ch1 = treatment: iron deprivation +!Sample_characteristics_ch1 = cultured in: TAP medium without Fe-EDTA for 2h +!Sample_treatment_protocol_ch1 = Cells were grown to mid-logarithmic phase (approximately 4 x 10e6 cells mL-1), collected by centrifugation (2,500 xg for 5 min at room temperature), washed twice in TAP medium lacking Fe-EDTA and inoculated into fresh TAP medium lacking Fe-EDTA and sampled at the indicated times. +!Sample_growth_protocol_ch1 = Cells were cultured under continuous light of ~90 μmol photon m-2s-1 at 24C in liquid and on solid Tris-Acetate-Phosphate (TAP) medium. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Nucleic acids were isolated and analyzed according to standard procedures by hybridization or on an Agilent 2100 Bioanalyzer. For quantitative transcriptomes, RNAs were sequenced at Illumina HiSeq 2000 platform (UCLA). +!Sample_description = SMEU37Fe2hTS +!Sample_data_processing = Illumina's proprietary software was used for basecalling. +!Sample_data_processing = The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. +!Sample_data_processing = Expression estimates where obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. Final expression estimates and fold changes where obtained from the average of both technical and biological replicates. +!Sample_data_processing = Genome_build: version 4.0 assembly of the Chlamydomonas genome (http://genome.jgi-psf.org/Chlre4/Chlre4.home.html) +!Sample_data_processing = Supplementary_files_format_and_content: Processed files correpond to expression estimates per lane, in units of RPKMs. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245327 +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924675 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE44611 +!Sample_data_row_count = 0 +^SAMPLE = GSM1087796 +!Sample_title = C.reinhardtii _Fe_Long_4_hours +!Sample_geo_accession = GSM1087796 +!Sample_status = Public on Feb 20 2014 +!Sample_submission_date = Feb 25 2013 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas cultured cells +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: CC-4532 (2137) +!Sample_characteristics_ch1 = treatment: iron deprivation +!Sample_characteristics_ch1 = cultured in: TAP medium without Fe-EDTA for 4h +!Sample_treatment_protocol_ch1 = Cells were grown to mid-logarithmic phase (approximately 4 x 10e6 cells mL-1), collected by centrifugation (2,500 xg for 5 min at room temperature), washed twice in TAP medium lacking Fe-EDTA and inoculated into fresh TAP medium lacking Fe-EDTA and sampled at the indicated times. +!Sample_growth_protocol_ch1 = Cells were cultured under continuous light of ~90 μmol photon m-2s-1 at 24C in liquid and on solid Tris-Acetate-Phosphate (TAP) medium. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Nucleic acids were isolated and analyzed according to standard procedures by hybridization or on an Agilent 2100 Bioanalyzer. For quantitative transcriptomes, RNAs were sequenced at Illumina HiSeq 2000 platform (UCLA). +!Sample_description = SMEU37Fe4hTS +!Sample_data_processing = Illumina's proprietary software was used for basecalling. +!Sample_data_processing = The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. +!Sample_data_processing = Expression estimates where obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. Final expression estimates and fold changes where obtained from the average of both technical and biological replicates. +!Sample_data_processing = Genome_build: version 4.0 assembly of the Chlamydomonas genome (http://genome.jgi-psf.org/Chlre4/Chlre4.home.html) +!Sample_data_processing = Supplementary_files_format_and_content: Processed files correpond to expression estimates per lane, in units of RPKMs. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245328 +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924676 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE44611 +!Sample_data_row_count = 0 +^SAMPLE = GSM1087797 +!Sample_title = C.reinhardtii _Fe_Long_8_hours +!Sample_geo_accession = GSM1087797 +!Sample_status = Public on Feb 20 2014 +!Sample_submission_date = Feb 25 2013 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas cultured cells +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: CC-4532 (2137) +!Sample_characteristics_ch1 = treatment: iron deprivation +!Sample_characteristics_ch1 = cultured in: TAP medium without Fe-EDTA for 8h +!Sample_treatment_protocol_ch1 = Cells were grown to mid-logarithmic phase (approximately 4 x 10e6 cells mL-1), collected by centrifugation (2,500 xg for 5 min at room temperature), washed twice in TAP medium lacking Fe-EDTA and inoculated into fresh TAP medium lacking Fe-EDTA and sampled at the indicated times. +!Sample_growth_protocol_ch1 = Cells were cultured under continuous light of ~90 μmol photon m-2s-1 at 24C in liquid and on solid Tris-Acetate-Phosphate (TAP) medium. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Nucleic acids were isolated and analyzed according to standard procedures by hybridization or on an Agilent 2100 Bioanalyzer. For quantitative transcriptomes, RNAs were sequenced at Illumina HiSeq 2000 platform (UCLA). +!Sample_description = SMEU37Fe8hTS +!Sample_data_processing = Illumina's proprietary software was used for basecalling. +!Sample_data_processing = The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. +!Sample_data_processing = Expression estimates where obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. Final expression estimates and fold changes where obtained from the average of both technical and biological replicates. +!Sample_data_processing = Genome_build: version 4.0 assembly of the Chlamydomonas genome (http://genome.jgi-psf.org/Chlre4/Chlre4.home.html) +!Sample_data_processing = Supplementary_files_format_and_content: Processed files correpond to expression estimates per lane, in units of RPKMs. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245329 +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924677 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE44611 +!Sample_data_row_count = 0 +^SAMPLE = GSM1087798 +!Sample_title = C.reinhardtii _Fe_Long_12_hours +!Sample_geo_accession = GSM1087798 +!Sample_status = Public on Feb 20 2014 +!Sample_submission_date = Feb 25 2013 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas cultured cells +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: CC-4532 (2137) +!Sample_characteristics_ch1 = treatment: iron deprivation +!Sample_characteristics_ch1 = cultured in: TAP medium without Fe-EDTA for 12h +!Sample_treatment_protocol_ch1 = Cells were grown to mid-logarithmic phase (approximately 4 x 10e6 cells mL-1), collected by centrifugation (2,500 xg for 5 min at room temperature), washed twice in TAP medium lacking Fe-EDTA and inoculated into fresh TAP medium lacking Fe-EDTA and sampled at the indicated times. +!Sample_growth_protocol_ch1 = Cells were cultured under continuous light of ~90 μmol photon m-2s-1 at 24C in liquid and on solid Tris-Acetate-Phosphate (TAP) medium. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Nucleic acids were isolated and analyzed according to standard procedures by hybridization or on an Agilent 2100 Bioanalyzer. For quantitative transcriptomes, RNAs were sequenced at Illumina HiSeq 2000 platform (UCLA). +!Sample_description = SMEU37Fe12hTS +!Sample_data_processing = Illumina's proprietary software was used for basecalling. +!Sample_data_processing = The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. +!Sample_data_processing = Expression estimates where obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. Final expression estimates and fold changes where obtained from the average of both technical and biological replicates. +!Sample_data_processing = Genome_build: version 4.0 assembly of the Chlamydomonas genome (http://genome.jgi-psf.org/Chlre4/Chlre4.home.html) +!Sample_data_processing = Supplementary_files_format_and_content: Processed files correpond to expression estimates per lane, in units of RPKMs. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245330 +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924678 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE44611 +!Sample_data_row_count = 0 +^SAMPLE = GSM1087799 +!Sample_title = C.reinhardtii _Fe_Long_24_hours +!Sample_geo_accession = GSM1087799 +!Sample_status = Public on Feb 20 2014 +!Sample_submission_date = Feb 25 2013 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas cultured cells +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: CC-4532 (2137) +!Sample_characteristics_ch1 = treatment: iron deprivation +!Sample_characteristics_ch1 = cultured in: TAP medium without Fe-EDTA for 24h +!Sample_treatment_protocol_ch1 = Cells were grown to mid-logarithmic phase (approximately 4 x 10e6 cells mL-1), collected by centrifugation (2,500 xg for 5 min at room temperature), washed twice in TAP medium lacking Fe-EDTA and inoculated into fresh TAP medium lacking Fe-EDTA and sampled at the indicated times. +!Sample_growth_protocol_ch1 = Cells were cultured under continuous light of ~90 μmol photon m-2s-1 at 24C in liquid and on solid Tris-Acetate-Phosphate (TAP) medium. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Nucleic acids were isolated and analyzed according to standard procedures by hybridization or on an Agilent 2100 Bioanalyzer. For quantitative transcriptomes, RNAs were sequenced at Illumina HiSeq 2000 platform (UCLA). +!Sample_description = SMEU37Fe24hTS +!Sample_data_processing = Illumina's proprietary software was used for basecalling. +!Sample_data_processing = The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. +!Sample_data_processing = Expression estimates where obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. Final expression estimates and fold changes where obtained from the average of both technical and biological replicates. +!Sample_data_processing = Genome_build: version 4.0 assembly of the Chlamydomonas genome (http://genome.jgi-psf.org/Chlre4/Chlre4.home.html) +!Sample_data_processing = Supplementary_files_format_and_content: Processed files correpond to expression estimates per lane, in units of RPKMs. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245331 +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924679 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE44611 +!Sample_data_row_count = 0 +^SAMPLE = GSM1087800 +!Sample_title = C.reinhardtii _Fe_Long_48_hours +!Sample_geo_accession = GSM1087800 +!Sample_status = Public on Feb 20 2014 +!Sample_submission_date = Feb 25 2013 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas cultured cells +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: CC-4532 (2137) +!Sample_characteristics_ch1 = treatment: iron deprivation +!Sample_characteristics_ch1 = cultured in: TAP medium without Fe-EDTA for 48h +!Sample_treatment_protocol_ch1 = Cells were grown to mid-logarithmic phase (approximately 4 x 10e6 cells mL-1), collected by centrifugation (2,500 xg for 5 min at room temperature), washed twice in TAP medium lacking Fe-EDTA and inoculated into fresh TAP medium lacking Fe-EDTA and sampled at the indicated times. +!Sample_growth_protocol_ch1 = Cells were cultured under continuous light of ~90 μmol photon m-2s-1 at 24C in liquid and on solid Tris-Acetate-Phosphate (TAP) medium. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Nucleic acids were isolated and analyzed according to standard procedures by hybridization or on an Agilent 2100 Bioanalyzer. For quantitative transcriptomes, RNAs were sequenced at Illumina HiSeq 2000 platform (UCLA). +!Sample_description = SMEU37Fe48hTS +!Sample_data_processing = Illumina's proprietary software was used for basecalling. +!Sample_data_processing = The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. +!Sample_data_processing = Expression estimates where obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. Final expression estimates and fold changes where obtained from the average of both technical and biological replicates. +!Sample_data_processing = Genome_build: version 4.0 assembly of the Chlamydomonas genome (http://genome.jgi-psf.org/Chlre4/Chlre4.home.html) +!Sample_data_processing = Supplementary_files_format_and_content: Processed files correpond to expression estimates per lane, in units of RPKMs. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX245332 +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN01924680 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE44611 +!Sample_data_row_count = 0 +^SAMPLE = GSM1332630 +!Sample_title = Chlamydomonas reinhardtii CC-4349 minus N 0h pre-wash +!Sample_geo_accession = GSM1332630 +!Sample_status = Public on Mar 09 2014 +!Sample_submission_date = Feb 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas cultured cells, CC-4349, minus nitrogen, pre-wash +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain/background: CC-4349 +!Sample_characteristics_ch1 = treatment: minus nitrogen +!Sample_characteristics_ch1 = time point: pre-wash +!Sample_treatment_protocol_ch1 = Once the cultures had reached 4x10^6 cells per mL they were washed in HSM - ammonium chloride and resuspended in 2.8 l flasks to a final cell density of 2x10^6 cells per ml, final volume of 1 l. Cells for RNA preparation were sampled at the indicated timepoints. +!Sample_growth_protocol_ch1 = Cultures used for the experiments to generate RNA for RNA-sequencing were grown in 1000 ml HSM-medium in 2.8 l flasks in the light (25 µmol photons per m2 per s) under the same conditions until they had reached a cell density of 4x10^6 cells per mL. They were then processed as indicated in the treatment protocol. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was isolated at time-points indicated in the text according to a method described in Boyle et al. 2012. +!Sample_extract_protocol_ch1 = For quantitative transcriptomes, RNAs were sequenced at LANL. +!Sample_description = UGTWcwNa0aHS1 +!Sample_description = Illumina's RNA-Seq whole transcriptome analysis. +!Sample_description = mRNA +!Sample_data_processing = Illumina's proprietary software was used for basecalling. +!Sample_data_processing = The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. +!Sample_data_processing = Expression estimates were obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. +!Sample_data_processing = Genome_build: Version 4.0 assembly of the Chlamydomonas genome (http://genome.jgi-psf.org/Chlre4/Chlre4.home.html) +!Sample_data_processing = Supplementary_files_format_and_content: Processed data file corresponds to expression estimates per sample, in units of RPKMs. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02649437 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX474534 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE55253 +!Sample_data_row_count = 0 +^SAMPLE = GSM1332631 +!Sample_title = Chlamydomonas reinhardtii CC-4349 minus N 0h +!Sample_geo_accession = GSM1332631 +!Sample_status = Public on Mar 09 2014 +!Sample_submission_date = Feb 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas cultured cells, CC-4349, minus nitrogen, 0h +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain/background: CC-4349 +!Sample_characteristics_ch1 = treatment: minus nitrogen +!Sample_characteristics_ch1 = time point: 0h +!Sample_treatment_protocol_ch1 = Once the cultures had reached 4x10^6 cells per mL they were washed in HSM - ammonium chloride and resuspended in 2.8 l flasks to a final cell density of 2x10^6 cells per ml, final volume of 1 l. Cells for RNA preparation were sampled at the indicated timepoints. +!Sample_growth_protocol_ch1 = Cultures used for the experiments to generate RNA for RNA-sequencing were grown in 1000 ml HSM-medium in 2.8 l flasks in the light (25 µmol photons per m2 per s) under the same conditions until they had reached a cell density of 4x10^6 cells per mL. They were then processed as indicated in the treatment protocol. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was isolated at time-points indicated in the text according to a method described in Boyle et al. 2012. +!Sample_extract_protocol_ch1 = For quantitative transcriptomes, RNAs were sequenced at LANL. +!Sample_description = UGTWcwna0bHS1 +!Sample_description = Illumina's RNA-Seq whole transcriptome analysis. +!Sample_description = mRNA +!Sample_data_processing = Illumina's proprietary software was used for basecalling. +!Sample_data_processing = The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. +!Sample_data_processing = Expression estimates were obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. +!Sample_data_processing = Genome_build: Version 4.0 assembly of the Chlamydomonas genome (http://genome.jgi-psf.org/Chlre4/Chlre4.home.html) +!Sample_data_processing = Supplementary_files_format_and_content: Processed data file corresponds to expression estimates per sample, in units of RPKMs. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02649444 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX474535 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE55253 +!Sample_data_row_count = 0 +^SAMPLE = GSM1332632 +!Sample_title = Chlamydomonas reinhardtii CC-4349 minus N 0.5h +!Sample_geo_accession = GSM1332632 +!Sample_status = Public on Mar 09 2014 +!Sample_submission_date = Feb 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas cultured cells, CC-4349, minus nitrogen, 0.5h +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain/background: CC-4349 +!Sample_characteristics_ch1 = treatment: minus nitrogen +!Sample_characteristics_ch1 = time point: 0.5h +!Sample_treatment_protocol_ch1 = Once the cultures had reached 4x10^6 cells per mL they were washed in HSM - ammonium chloride and resuspended in 2.8 l flasks to a final cell density of 2x10^6 cells per ml, final volume of 1 l. Cells for RNA preparation were sampled at the indicated timepoints. +!Sample_growth_protocol_ch1 = Cultures used for the experiments to generate RNA for RNA-sequencing were grown in 1000 ml HSM-medium in 2.8 l flasks in the light (25 µmol photons per m2 per s) under the same conditions until they had reached a cell density of 4x10^6 cells per mL. They were then processed as indicated in the treatment protocol. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was isolated at time-points indicated in the text according to a method described in Boyle et al. 2012. +!Sample_extract_protocol_ch1 = For quantitative transcriptomes, RNAs were sequenced at LANL. +!Sample_description = UGTWcwna05HS1 +!Sample_description = Illumina's RNA-Seq whole transcriptome analysis. +!Sample_description = mRNA +!Sample_data_processing = Illumina's proprietary software was used for basecalling. +!Sample_data_processing = The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. +!Sample_data_processing = Expression estimates were obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. +!Sample_data_processing = Genome_build: Version 4.0 assembly of the Chlamydomonas genome (http://genome.jgi-psf.org/Chlre4/Chlre4.home.html) +!Sample_data_processing = Supplementary_files_format_and_content: Processed data file corresponds to expression estimates per sample, in units of RPKMs. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02649442 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX474536 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE55253 +!Sample_data_row_count = 0 +^SAMPLE = GSM1332633 +!Sample_title = Chlamydomonas reinhardtii CC-4349 minus N 2h +!Sample_geo_accession = GSM1332633 +!Sample_status = Public on Mar 09 2014 +!Sample_submission_date = Feb 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas cultured cells, CC-4349, minus nitrogen, 2h +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain/background: CC-4349 +!Sample_characteristics_ch1 = treatment: minus nitrogen +!Sample_characteristics_ch1 = time point: 2h +!Sample_treatment_protocol_ch1 = Once the cultures had reached 4x10^6 cells per mL they were washed in HSM - ammonium chloride and resuspended in 2.8 l flasks to a final cell density of 2x10^6 cells per ml, final volume of 1 l. Cells for RNA preparation were sampled at the indicated timepoints. +!Sample_growth_protocol_ch1 = Cultures used for the experiments to generate RNA for RNA-sequencing were grown in 1000 ml HSM-medium in 2.8 l flasks in the light (25 µmol photons per m2 per s) under the same conditions until they had reached a cell density of 4x10^6 cells per mL. They were then processed as indicated in the treatment protocol. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was isolated at time-points indicated in the text according to a method described in Boyle et al. 2012. +!Sample_extract_protocol_ch1 = For quantitative transcriptomes, RNAs were sequenced at LANL. +!Sample_description = UGTWcwna2HS1 +!Sample_description = Illumina's RNA-Seq whole transcriptome analysis. +!Sample_description = mRNA +!Sample_data_processing = Illumina's proprietary software was used for basecalling. +!Sample_data_processing = The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. +!Sample_data_processing = Expression estimates were obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. +!Sample_data_processing = Genome_build: Version 4.0 assembly of the Chlamydomonas genome (http://genome.jgi-psf.org/Chlre4/Chlre4.home.html) +!Sample_data_processing = Supplementary_files_format_and_content: Processed data file corresponds to expression estimates per sample, in units of RPKMs. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02649448 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX474537 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE55253 +!Sample_data_row_count = 0 +^SAMPLE = GSM1332634 +!Sample_title = Chlamydomonas reinhardtii CC-4349 minus N 4h +!Sample_geo_accession = GSM1332634 +!Sample_status = Public on Mar 09 2014 +!Sample_submission_date = Feb 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas cultured cells, CC-4349, minus nitrogen, 4h +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain/background: CC-4349 +!Sample_characteristics_ch1 = treatment: minus nitrogen +!Sample_characteristics_ch1 = time point: 4h +!Sample_treatment_protocol_ch1 = Once the cultures had reached 4x10^6 cells per mL they were washed in HSM - ammonium chloride and resuspended in 2.8 l flasks to a final cell density of 2x10^6 cells per ml, final volume of 1 l. Cells for RNA preparation were sampled at the indicated timepoints. +!Sample_growth_protocol_ch1 = Cultures used for the experiments to generate RNA for RNA-sequencing were grown in 1000 ml HSM-medium in 2.8 l flasks in the light (25 µmol photons per m2 per s) under the same conditions until they had reached a cell density of 4x10^6 cells per mL. They were then processed as indicated in the treatment protocol. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was isolated at time-points indicated in the text according to a method described in Boyle et al. 2012. +!Sample_extract_protocol_ch1 = For quantitative transcriptomes, RNAs were sequenced at LANL. +!Sample_description = UGTWcwna4HS1 +!Sample_description = Illumina's RNA-Seq whole transcriptome analysis. +!Sample_description = mRNA +!Sample_data_processing = Illumina's proprietary software was used for basecalling. +!Sample_data_processing = The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. +!Sample_data_processing = Expression estimates were obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. +!Sample_data_processing = Genome_build: Version 4.0 assembly of the Chlamydomonas genome (http://genome.jgi-psf.org/Chlre4/Chlre4.home.html) +!Sample_data_processing = Supplementary_files_format_and_content: Processed data file corresponds to expression estimates per sample, in units of RPKMs. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02649447 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX474538 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE55253 +!Sample_data_row_count = 0 +^SAMPLE = GSM1332635 +!Sample_title = Chlamydomonas reinhardtii CC-4349 minus N 8h +!Sample_geo_accession = GSM1332635 +!Sample_status = Public on Mar 09 2014 +!Sample_submission_date = Feb 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas cultured cells, CC-4349, minus nitrogen, 8h +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain/background: CC-4349 +!Sample_characteristics_ch1 = treatment: minus nitrogen +!Sample_characteristics_ch1 = time point: 8h +!Sample_treatment_protocol_ch1 = Once the cultures had reached 4x10^6 cells per mL they were washed in HSM - ammonium chloride and resuspended in 2.8 l flasks to a final cell density of 2x10^6 cells per ml, final volume of 1 l. Cells for RNA preparation were sampled at the indicated timepoints. +!Sample_growth_protocol_ch1 = Cultures used for the experiments to generate RNA for RNA-sequencing were grown in 1000 ml HSM-medium in 2.8 l flasks in the light (25 µmol photons per m2 per s) under the same conditions until they had reached a cell density of 4x10^6 cells per mL. They were then processed as indicated in the treatment protocol. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was isolated at time-points indicated in the text according to a method described in Boyle et al. 2012. +!Sample_extract_protocol_ch1 = For quantitative transcriptomes, RNAs were sequenced at LANL. +!Sample_description = UGTWcwna8HS1 +!Sample_description = Illumina's RNA-Seq whole transcriptome analysis. +!Sample_description = mRNA +!Sample_data_processing = Illumina's proprietary software was used for basecalling. +!Sample_data_processing = The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. +!Sample_data_processing = Expression estimates were obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. +!Sample_data_processing = Genome_build: Version 4.0 assembly of the Chlamydomonas genome (http://genome.jgi-psf.org/Chlre4/Chlre4.home.html) +!Sample_data_processing = Supplementary_files_format_and_content: Processed data file corresponds to expression estimates per sample, in units of RPKMs. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02649445 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX474539 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE55253 +!Sample_data_row_count = 0 +^SAMPLE = GSM1332636 +!Sample_title = Chlamydomonas reinhardtii CC-4349 minus N 12h +!Sample_geo_accession = GSM1332636 +!Sample_status = Public on Mar 09 2014 +!Sample_submission_date = Feb 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas cultured cells, CC-4349, minus nitrogen, 12h +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain/background: CC-4349 +!Sample_characteristics_ch1 = treatment: minus nitrogen +!Sample_characteristics_ch1 = time point: 12h +!Sample_treatment_protocol_ch1 = Once the cultures had reached 4x10^6 cells per mL they were washed in HSM - ammonium chloride and resuspended in 2.8 l flasks to a final cell density of 2x10^6 cells per ml, final volume of 1 l. Cells for RNA preparation were sampled at the indicated timepoints. +!Sample_growth_protocol_ch1 = Cultures used for the experiments to generate RNA for RNA-sequencing were grown in 1000 ml HSM-medium in 2.8 l flasks in the light (25 µmol photons per m2 per s) under the same conditions until they had reached a cell density of 4x10^6 cells per mL. They were then processed as indicated in the treatment protocol. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was isolated at time-points indicated in the text according to a method described in Boyle et al. 2012. +!Sample_extract_protocol_ch1 = For quantitative transcriptomes, RNAs were sequenced at LANL. +!Sample_description = UGTWcwna12HS1 +!Sample_description = Illumina's RNA-Seq whole transcriptome analysis. +!Sample_description = mRNA +!Sample_data_processing = Illumina's proprietary software was used for basecalling. +!Sample_data_processing = The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. +!Sample_data_processing = Expression estimates were obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. +!Sample_data_processing = Genome_build: Version 4.0 assembly of the Chlamydomonas genome (http://genome.jgi-psf.org/Chlre4/Chlre4.home.html) +!Sample_data_processing = Supplementary_files_format_and_content: Processed data file corresponds to expression estimates per sample, in units of RPKMs. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02649443 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX474540 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE55253 +!Sample_data_row_count = 0 +^SAMPLE = GSM1332637 +!Sample_title = Chlamydomonas reinhardtii CC-4349 minus N 24h +!Sample_geo_accession = GSM1332637 +!Sample_status = Public on Mar 09 2014 +!Sample_submission_date = Feb 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas cultured cells, CC-4349, minus nitrogen, 24h +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain/background: CC-4349 +!Sample_characteristics_ch1 = treatment: minus nitrogen +!Sample_characteristics_ch1 = time point: 24h +!Sample_treatment_protocol_ch1 = Once the cultures had reached 4x10^6 cells per mL they were washed in HSM - ammonium chloride and resuspended in 2.8 l flasks to a final cell density of 2x10^6 cells per ml, final volume of 1 l. Cells for RNA preparation were sampled at the indicated timepoints. +!Sample_growth_protocol_ch1 = Cultures used for the experiments to generate RNA for RNA-sequencing were grown in 1000 ml HSM-medium in 2.8 l flasks in the light (25 µmol photons per m2 per s) under the same conditions until they had reached a cell density of 4x10^6 cells per mL. They were then processed as indicated in the treatment protocol. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was isolated at time-points indicated in the text according to a method described in Boyle et al. 2012. +!Sample_extract_protocol_ch1 = For quantitative transcriptomes, RNAs were sequenced at LANL. +!Sample_description = UGTWcwna24HS1 +!Sample_description = Illumina's RNA-Seq whole transcriptome analysis. +!Sample_description = mRNA +!Sample_data_processing = Illumina's proprietary software was used for basecalling. +!Sample_data_processing = The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. +!Sample_data_processing = Expression estimates were obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. +!Sample_data_processing = Genome_build: Version 4.0 assembly of the Chlamydomonas genome (http://genome.jgi-psf.org/Chlre4/Chlre4.home.html) +!Sample_data_processing = Supplementary_files_format_and_content: Processed data file corresponds to expression estimates per sample, in units of RPKMs. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02649449 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX474541 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE55253 +!Sample_data_row_count = 0 +^SAMPLE = GSM1332638 +!Sample_title = Chlamydomonas reinhardtii CC-4349 minus N 48h +!Sample_geo_accession = GSM1332638 +!Sample_status = Public on Mar 09 2014 +!Sample_submission_date = Feb 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas cultured cells, CC-4349, minus nitrogen, 48h +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain/background: CC-4349 +!Sample_characteristics_ch1 = treatment: minus nitrogen +!Sample_characteristics_ch1 = time point: 48h +!Sample_treatment_protocol_ch1 = Once the cultures had reached 4x10^6 cells per mL they were washed in HSM - ammonium chloride and resuspended in 2.8 l flasks to a final cell density of 2x10^6 cells per ml, final volume of 1 l. Cells for RNA preparation were sampled at the indicated timepoints. +!Sample_growth_protocol_ch1 = Cultures used for the experiments to generate RNA for RNA-sequencing were grown in 1000 ml HSM-medium in 2.8 l flasks in the light (25 µmol photons per m2 per s) under the same conditions until they had reached a cell density of 4x10^6 cells per mL. They were then processed as indicated in the treatment protocol. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was isolated at time-points indicated in the text according to a method described in Boyle et al. 2012. +!Sample_extract_protocol_ch1 = For quantitative transcriptomes, RNAs were sequenced at LANL. +!Sample_description = UGTWcwna48HS1 +!Sample_description = Illumina's RNA-Seq whole transcriptome analysis. +!Sample_description = mRNA +!Sample_data_processing = Illumina's proprietary software was used for basecalling. +!Sample_data_processing = The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. +!Sample_data_processing = Expression estimates were obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. +!Sample_data_processing = Genome_build: Version 4.0 assembly of the Chlamydomonas genome (http://genome.jgi-psf.org/Chlre4/Chlre4.home.html) +!Sample_data_processing = Supplementary_files_format_and_content: Processed data file corresponds to expression estimates per sample, in units of RPKMs. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02649450 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX474542 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE55253 +!Sample_data_row_count = 0 +^SAMPLE = GSM1332639 +!Sample_title = Chlamydomonas reinhardtii CC-4349 48h minus N, 0h + acetate +!Sample_geo_accession = GSM1332639 +!Sample_status = Public on Mar 09 2014 +!Sample_submission_date = Feb 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas cultured cells, CC-4349, 48 h minus nitrogen, 0h after acetate boost +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain/background: CC-4349 +!Sample_characteristics_ch1 = treatment: 48 h minus nitrogen, then acetate boost +!Sample_characteristics_ch1 = time point: 0h after acetate boost +!Sample_treatment_protocol_ch1 = Once the cultures had reached 4x10^6 cells per mL they were washed in HSM - ammonium chloride and resuspended in 2.8 l flasks to a final cell density of 2x10^6 cells per ml, final volume of 1 l. Cells for RNA preparation were sampled at the indicated timepoints. +!Sample_growth_protocol_ch1 = Cultures used for the experiments to generate RNA for RNA-sequencing were grown in 1000 ml HSM-medium in 2.8 l flasks in the light (25 µmol photons per m2 per s) under the same conditions until they had reached a cell density of 4x10^6 cells per mL. They were then processed as indicated in the treatment protocol. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was isolated at time-points indicated in the text according to a method described in Boyle et al. 2012. +!Sample_extract_protocol_ch1 = For quantitative transcriptomes, RNAs were sequenced at LANL. +!Sample_description = UGTWcwnA0bHS1 +!Sample_description = Illumina's RNA-Seq whole transcriptome analysis. +!Sample_description = mRNA +!Sample_data_processing = Illumina's proprietary software was used for basecalling. +!Sample_data_processing = The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. +!Sample_data_processing = Expression estimates were obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. +!Sample_data_processing = Genome_build: Version 4.0 assembly of the Chlamydomonas genome (http://genome.jgi-psf.org/Chlre4/Chlre4.home.html) +!Sample_data_processing = Supplementary_files_format_and_content: Processed data file corresponds to expression estimates per sample, in units of RPKMs. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02649446 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX474543 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE55253 +!Sample_data_row_count = 0 +^SAMPLE = GSM1332640 +!Sample_title = Chlamydomonas reinhardtii CC-4349 48h minus N, 0.5h + acetate +!Sample_geo_accession = GSM1332640 +!Sample_status = Public on Mar 09 2014 +!Sample_submission_date = Feb 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas cultured cells, CC-4349, 48 h minus nitrogen, 0.5h after acetate boost +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain/background: CC-4349 +!Sample_characteristics_ch1 = treatment: 48 h minus nitrogen, then acetate boost +!Sample_characteristics_ch1 = time point: 0.5h after acetate boost +!Sample_treatment_protocol_ch1 = Once the cultures had reached 4x10^6 cells per mL they were washed in HSM - ammonium chloride and resuspended in 2.8 l flasks to a final cell density of 2x10^6 cells per ml, final volume of 1 l. Cells for RNA preparation were sampled at the indicated timepoints. +!Sample_growth_protocol_ch1 = Cultures used for the experiments to generate RNA for RNA-sequencing were grown in 1000 ml HSM-medium in 2.8 l flasks in the light (25 µmol photons per m2 per s) under the same conditions until they had reached a cell density of 4x10^6 cells per mL. They were then processed as indicated in the treatment protocol. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was isolated at time-points indicated in the text according to a method described in Boyle et al. 2012. +!Sample_extract_protocol_ch1 = For quantitative transcriptomes, RNAs were sequenced at LANL. +!Sample_description = UGTWcwnA05HS1 +!Sample_description = Illumina's RNA-Seq whole transcriptome analysis. +!Sample_description = mRNA +!Sample_data_processing = Illumina's proprietary software was used for basecalling. +!Sample_data_processing = The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. +!Sample_data_processing = Expression estimates were obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. +!Sample_data_processing = Genome_build: Version 4.0 assembly of the Chlamydomonas genome (http://genome.jgi-psf.org/Chlre4/Chlre4.home.html) +!Sample_data_processing = Supplementary_files_format_and_content: Processed data file corresponds to expression estimates per sample, in units of RPKMs. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02649453 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX474544 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE55253 +!Sample_data_row_count = 0 +^SAMPLE = GSM1332641 +!Sample_title = Chlamydomonas reinhardtii CC-4349 48h minus N, 2h + acetate +!Sample_geo_accession = GSM1332641 +!Sample_status = Public on Mar 09 2014 +!Sample_submission_date = Feb 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas cultured cells, CC-4349, 48 h minus nitrogen, 2h after acetate boost +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain/background: CC-4349 +!Sample_characteristics_ch1 = treatment: 48 h minus nitrogen, then acetate boost +!Sample_characteristics_ch1 = time point: 2h after acetate boost +!Sample_treatment_protocol_ch1 = Once the cultures had reached 4x10^6 cells per mL they were washed in HSM - ammonium chloride and resuspended in 2.8 l flasks to a final cell density of 2x10^6 cells per ml, final volume of 1 l. Cells for RNA preparation were sampled at the indicated timepoints. +!Sample_growth_protocol_ch1 = Cultures used for the experiments to generate RNA for RNA-sequencing were grown in 1000 ml HSM-medium in 2.8 l flasks in the light (25 µmol photons per m2 per s) under the same conditions until they had reached a cell density of 4x10^6 cells per mL. They were then processed as indicated in the treatment protocol. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was isolated at time-points indicated in the text according to a method described in Boyle et al. 2012. +!Sample_extract_protocol_ch1 = For quantitative transcriptomes, RNAs were sequenced at LANL. +!Sample_description = UGTWcwnA2HS1 +!Sample_description = Illumina's RNA-Seq whole transcriptome analysis. +!Sample_description = mRNA +!Sample_data_processing = Illumina's proprietary software was used for basecalling. +!Sample_data_processing = The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. +!Sample_data_processing = Expression estimates were obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. +!Sample_data_processing = Genome_build: Version 4.0 assembly of the Chlamydomonas genome (http://genome.jgi-psf.org/Chlre4/Chlre4.home.html) +!Sample_data_processing = Supplementary_files_format_and_content: Processed data file corresponds to expression estimates per sample, in units of RPKMs. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02649452 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX474545 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE55253 +!Sample_data_row_count = 0 +^SAMPLE = GSM1332642 +!Sample_title = Chlamydomonas reinhardtii CC-4349 48h minus N, 4h + acetate +!Sample_geo_accession = GSM1332642 +!Sample_status = Public on Mar 09 2014 +!Sample_submission_date = Feb 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas cultured cells, CC-4349, 48 h minus nitrogen, 4h after acetate boost +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain/background: CC-4349 +!Sample_characteristics_ch1 = treatment: 48 h minus nitrogen, then acetate boost +!Sample_characteristics_ch1 = time point: 4h after acetate boost +!Sample_treatment_protocol_ch1 = Once the cultures had reached 4x10^6 cells per mL they were washed in HSM - ammonium chloride and resuspended in 2.8 l flasks to a final cell density of 2x10^6 cells per ml, final volume of 1 l. Cells for RNA preparation were sampled at the indicated timepoints. +!Sample_growth_protocol_ch1 = Cultures used for the experiments to generate RNA for RNA-sequencing were grown in 1000 ml HSM-medium in 2.8 l flasks in the light (25 µmol photons per m2 per s) under the same conditions until they had reached a cell density of 4x10^6 cells per mL. They were then processed as indicated in the treatment protocol. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was isolated at time-points indicated in the text according to a method described in Boyle et al. 2012. +!Sample_extract_protocol_ch1 = For quantitative transcriptomes, RNAs were sequenced at LANL. +!Sample_description = UGTWcwnA4HS1 +!Sample_description = Illumina's RNA-Seq whole transcriptome analysis. +!Sample_description = mRNA +!Sample_data_processing = Illumina's proprietary software was used for basecalling. +!Sample_data_processing = The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. +!Sample_data_processing = Expression estimates were obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. +!Sample_data_processing = Genome_build: Version 4.0 assembly of the Chlamydomonas genome (http://genome.jgi-psf.org/Chlre4/Chlre4.home.html) +!Sample_data_processing = Supplementary_files_format_and_content: Processed data file corresponds to expression estimates per sample, in units of RPKMs. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02649451 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX474546 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE55253 +!Sample_data_row_count = 0 +^SAMPLE = GSM1332643 +!Sample_title = Chlamydomonas reinhardtii CC-4349 48h minus N, 8h + acetate +!Sample_geo_accession = GSM1332643 +!Sample_status = Public on Mar 09 2014 +!Sample_submission_date = Feb 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas cultured cells, CC-4349, 48 h minus nitrogen, 8h after acetate boost +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain/background: CC-4349 +!Sample_characteristics_ch1 = treatment: 48 h minus nitrogen, then acetate boost +!Sample_characteristics_ch1 = time point: 8h after acetate boost +!Sample_treatment_protocol_ch1 = Once the cultures had reached 4x10^6 cells per mL they were washed in HSM - ammonium chloride and resuspended in 2.8 l flasks to a final cell density of 2x10^6 cells per ml, final volume of 1 l. Cells for RNA preparation were sampled at the indicated timepoints. +!Sample_growth_protocol_ch1 = Cultures used for the experiments to generate RNA for RNA-sequencing were grown in 1000 ml HSM-medium in 2.8 l flasks in the light (25 µmol photons per m2 per s) under the same conditions until they had reached a cell density of 4x10^6 cells per mL. They were then processed as indicated in the treatment protocol. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was isolated at time-points indicated in the text according to a method described in Boyle et al. 2012. +!Sample_extract_protocol_ch1 = For quantitative transcriptomes, RNAs were sequenced at LANL. +!Sample_description = UGTWcwnA8HS1 +!Sample_description = Illumina's RNA-Seq whole transcriptome analysis. +!Sample_description = mRNA +!Sample_data_processing = Illumina's proprietary software was used for basecalling. +!Sample_data_processing = The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. +!Sample_data_processing = Expression estimates were obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. +!Sample_data_processing = Genome_build: Version 4.0 assembly of the Chlamydomonas genome (http://genome.jgi-psf.org/Chlre4/Chlre4.home.html) +!Sample_data_processing = Supplementary_files_format_and_content: Processed data file corresponds to expression estimates per sample, in units of RPKMs. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02649456 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX474547 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE55253 +!Sample_data_row_count = 0 +^SAMPLE = GSM1332644 +!Sample_title = Chlamydomonas reinhardtii CC-4349 48h minus N, 12h + acetate +!Sample_geo_accession = GSM1332644 +!Sample_status = Public on Mar 09 2014 +!Sample_submission_date = Feb 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas cultured cells, CC-4349, 48 h minus nitrogen, 12h after acetate boost +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain/background: CC-4349 +!Sample_characteristics_ch1 = treatment: 48 h minus nitrogen, then acetate boost +!Sample_characteristics_ch1 = time point: 12h after acetate boost +!Sample_treatment_protocol_ch1 = Once the cultures had reached 4x10^6 cells per mL they were washed in HSM - ammonium chloride and resuspended in 2.8 l flasks to a final cell density of 2x10^6 cells per ml, final volume of 1 l. Cells for RNA preparation were sampled at the indicated timepoints. +!Sample_growth_protocol_ch1 = Cultures used for the experiments to generate RNA for RNA-sequencing were grown in 1000 ml HSM-medium in 2.8 l flasks in the light (25 µmol photons per m2 per s) under the same conditions until they had reached a cell density of 4x10^6 cells per mL. They were then processed as indicated in the treatment protocol. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was isolated at time-points indicated in the text according to a method described in Boyle et al. 2012. +!Sample_extract_protocol_ch1 = For quantitative transcriptomes, RNAs were sequenced at LANL. +!Sample_description = UGTWcwnA12HS1 +!Sample_description = Illumina's RNA-Seq whole transcriptome analysis. +!Sample_description = mRNA +!Sample_data_processing = Illumina's proprietary software was used for basecalling. +!Sample_data_processing = The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. +!Sample_data_processing = Expression estimates were obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. +!Sample_data_processing = Genome_build: Version 4.0 assembly of the Chlamydomonas genome (http://genome.jgi-psf.org/Chlre4/Chlre4.home.html) +!Sample_data_processing = Supplementary_files_format_and_content: Processed data file corresponds to expression estimates per sample, in units of RPKMs. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02649455 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX474548 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE55253 +!Sample_data_row_count = 0 +^SAMPLE = GSM1332645 +!Sample_title = Chlamydomonas reinhardtii CC-4349 48h minus N, 24h + acetate +!Sample_geo_accession = GSM1332645 +!Sample_status = Public on Mar 09 2014 +!Sample_submission_date = Feb 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas cultured cells, CC-4349, 48 h minus nitrogen, 24h after acetate boost +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain/background: CC-4349 +!Sample_characteristics_ch1 = treatment: 48 h minus nitrogen, then acetate boost +!Sample_characteristics_ch1 = time point: 24h after acetate boost +!Sample_treatment_protocol_ch1 = Once the cultures had reached 4x10^6 cells per mL they were washed in HSM - ammonium chloride and resuspended in 2.8 l flasks to a final cell density of 2x10^6 cells per ml, final volume of 1 l. Cells for RNA preparation were sampled at the indicated timepoints. +!Sample_growth_protocol_ch1 = Cultures used for the experiments to generate RNA for RNA-sequencing were grown in 1000 ml HSM-medium in 2.8 l flasks in the light (25 µmol photons per m2 per s) under the same conditions until they had reached a cell density of 4x10^6 cells per mL. They were then processed as indicated in the treatment protocol. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was isolated at time-points indicated in the text according to a method described in Boyle et al. 2012. +!Sample_extract_protocol_ch1 = For quantitative transcriptomes, RNAs were sequenced at LANL. +!Sample_description = UGTWcwnA24HS1 +!Sample_description = Illumina's RNA-Seq whole transcriptome analysis. +!Sample_description = mRNA +!Sample_data_processing = Illumina's proprietary software was used for basecalling. +!Sample_data_processing = The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. +!Sample_data_processing = Expression estimates were obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. +!Sample_data_processing = Genome_build: Version 4.0 assembly of the Chlamydomonas genome (http://genome.jgi-psf.org/Chlre4/Chlre4.home.html) +!Sample_data_processing = Supplementary_files_format_and_content: Processed data file corresponds to expression estimates per sample, in units of RPKMs. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02649454 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX474549 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE55253 +!Sample_data_row_count = 0 +^SAMPLE = GSM1332646 +!Sample_title = Chlamydomonas reinhardtii CC-4349 48h minus N, 48h + acetate +!Sample_geo_accession = GSM1332646 +!Sample_status = Public on Mar 09 2014 +!Sample_submission_date = Feb 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas cultured cells, CC-4349, 48 h minus nitrogen, 48h after acetate boost +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain/background: CC-4349 +!Sample_characteristics_ch1 = treatment: 48 h minus nitrogen, then acetate boost +!Sample_characteristics_ch1 = time point: 48h after acetate boost +!Sample_treatment_protocol_ch1 = Once the cultures had reached 4x10^6 cells per mL they were washed in HSM - ammonium chloride and resuspended in 2.8 l flasks to a final cell density of 2x10^6 cells per ml, final volume of 1 l. Cells for RNA preparation were sampled at the indicated timepoints. +!Sample_growth_protocol_ch1 = Cultures used for the experiments to generate RNA for RNA-sequencing were grown in 1000 ml HSM-medium in 2.8 l flasks in the light (25 µmol photons per m2 per s) under the same conditions until they had reached a cell density of 4x10^6 cells per mL. They were then processed as indicated in the treatment protocol. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was isolated at time-points indicated in the text according to a method described in Boyle et al. 2012. +!Sample_extract_protocol_ch1 = For quantitative transcriptomes, RNAs were sequenced at LANL. +!Sample_description = UGTWcwnA48HS1 +!Sample_description = Illumina's RNA-Seq whole transcriptome analysis. +!Sample_description = mRNA +!Sample_data_processing = Illumina's proprietary software was used for basecalling. +!Sample_data_processing = The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. +!Sample_data_processing = Expression estimates were obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. +!Sample_data_processing = Genome_build: Version 4.0 assembly of the Chlamydomonas genome (http://genome.jgi-psf.org/Chlre4/Chlre4.home.html) +!Sample_data_processing = Supplementary_files_format_and_content: Processed data file corresponds to expression estimates per sample, in units of RPKMs. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02649458 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX474550 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE55253 +!Sample_data_row_count = 0 +^SAMPLE = GSM1332647 +!Sample_title = Chlamydomonas reinhardtii CC-4348 sta6 minus N 0h pre-wash +!Sample_geo_accession = GSM1332647 +!Sample_status = Public on Mar 09 2014 +!Sample_submission_date = Feb 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas cultured cells, sta6 (CC-4348), minus nitrogen, pre-wash +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain/background: sta6 (CC-4348) +!Sample_characteristics_ch1 = treatment: minus nitrogen +!Sample_characteristics_ch1 = time point: pre-wash +!Sample_treatment_protocol_ch1 = Once the cultures had reached 4x10^6 cells per mL they were washed in HSM - ammonium chloride and resuspended in 2.8 l flasks to a final cell density of 2x10^6 cells per ml, final volume of 1 l. Cells for RNA preparation were sampled at the indicated timepoints. +!Sample_growth_protocol_ch1 = Cultures used for the experiments to generate RNA for RNA-sequencing were grown in 1000 ml HSM-medium in 2.8 l flasks in the light (25 µmol photons per m2 per s) under the same conditions until they had reached a cell density of 4x10^6 cells per mL. They were then processed as indicated in the treatment protocol. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was isolated at time-points indicated in the text according to a method described in Boyle et al. 2012. +!Sample_extract_protocol_ch1 = For quantitative transcriptomes, RNAs were sequenced at LANL. +!Sample_description = UGTWs6Na0aHS1 +!Sample_description = Illumina's RNA-Seq whole transcriptome analysis. +!Sample_description = mRNA +!Sample_data_processing = Illumina's proprietary software was used for basecalling. +!Sample_data_processing = The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. +!Sample_data_processing = Expression estimates were obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. +!Sample_data_processing = Genome_build: Version 4.0 assembly of the Chlamydomonas genome (http://genome.jgi-psf.org/Chlre4/Chlre4.home.html) +!Sample_data_processing = Supplementary_files_format_and_content: Processed data file corresponds to expression estimates per sample, in units of RPKMs. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02649459 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX474551 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE55253 +!Sample_data_row_count = 0 +^SAMPLE = GSM1332648 +!Sample_title = Chlamydomonas reinhardtii CC-4348 sta6 minus N 0h +!Sample_geo_accession = GSM1332648 +!Sample_status = Public on Mar 09 2014 +!Sample_submission_date = Feb 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas cultured cells, sta6 (CC-4348), minus nitrogen, 0h +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain/background: sta6 (CC-4348) +!Sample_characteristics_ch1 = treatment: minus nitrogen +!Sample_characteristics_ch1 = time point: 0h +!Sample_treatment_protocol_ch1 = Once the cultures had reached 4x10^6 cells per mL they were washed in HSM - ammonium chloride and resuspended in 2.8 l flasks to a final cell density of 2x10^6 cells per ml, final volume of 1 l. Cells for RNA preparation were sampled at the indicated timepoints. +!Sample_growth_protocol_ch1 = Cultures used for the experiments to generate RNA for RNA-sequencing were grown in 1000 ml HSM-medium in 2.8 l flasks in the light (25 µmol photons per m2 per s) under the same conditions until they had reached a cell density of 4x10^6 cells per mL. They were then processed as indicated in the treatment protocol. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was isolated at time-points indicated in the text according to a method described in Boyle et al. 2012. +!Sample_extract_protocol_ch1 = For quantitative transcriptomes, RNAs were sequenced at LANL. +!Sample_description = UGTWs6na0bHS1 +!Sample_description = Illumina's RNA-Seq whole transcriptome analysis. +!Sample_description = mRNA +!Sample_data_processing = Illumina's proprietary software was used for basecalling. +!Sample_data_processing = The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. +!Sample_data_processing = Expression estimates were obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. +!Sample_data_processing = Genome_build: Version 4.0 assembly of the Chlamydomonas genome (http://genome.jgi-psf.org/Chlre4/Chlre4.home.html) +!Sample_data_processing = Supplementary_files_format_and_content: Processed data file corresponds to expression estimates per sample, in units of RPKMs. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02649457 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX474552 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE55253 +!Sample_data_row_count = 0 +^SAMPLE = GSM1332649 +!Sample_title = Chlamydomonas reinhardtii CC-4348 sta6 minus N 0.5h +!Sample_geo_accession = GSM1332649 +!Sample_status = Public on Mar 09 2014 +!Sample_submission_date = Feb 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas cultured cells, sta6 (CC-4348), minus nitrogen, 0.5h +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain/background: sta6 (CC-4348) +!Sample_characteristics_ch1 = treatment: minus nitrogen +!Sample_characteristics_ch1 = time point: 0.5h +!Sample_treatment_protocol_ch1 = Once the cultures had reached 4x10^6 cells per mL they were washed in HSM - ammonium chloride and resuspended in 2.8 l flasks to a final cell density of 2x10^6 cells per ml, final volume of 1 l. Cells for RNA preparation were sampled at the indicated timepoints. +!Sample_growth_protocol_ch1 = Cultures used for the experiments to generate RNA for RNA-sequencing were grown in 1000 ml HSM-medium in 2.8 l flasks in the light (25 µmol photons per m2 per s) under the same conditions until they had reached a cell density of 4x10^6 cells per mL. They were then processed as indicated in the treatment protocol. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was isolated at time-points indicated in the text according to a method described in Boyle et al. 2012. +!Sample_extract_protocol_ch1 = For quantitative transcriptomes, RNAs were sequenced at LANL. +!Sample_description = UGTWs6na05HS1 +!Sample_description = Illumina's RNA-Seq whole transcriptome analysis. +!Sample_description = mRNA +!Sample_data_processing = Illumina's proprietary software was used for basecalling. +!Sample_data_processing = The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. +!Sample_data_processing = Expression estimates were obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. +!Sample_data_processing = Genome_build: Version 4.0 assembly of the Chlamydomonas genome (http://genome.jgi-psf.org/Chlre4/Chlre4.home.html) +!Sample_data_processing = Supplementary_files_format_and_content: Processed data file corresponds to expression estimates per sample, in units of RPKMs. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02649465 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX474553 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE55253 +!Sample_data_row_count = 0 +^SAMPLE = GSM1332650 +!Sample_title = Chlamydomonas reinhardtii CC-4348 sta6 minus N 2h +!Sample_geo_accession = GSM1332650 +!Sample_status = Public on Mar 09 2014 +!Sample_submission_date = Feb 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas cultured cells, sta6 (CC-4348), minus nitrogen, 2h +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain/background: sta6 (CC-4348) +!Sample_characteristics_ch1 = treatment: minus nitrogen +!Sample_characteristics_ch1 = time point: 2h +!Sample_treatment_protocol_ch1 = Once the cultures had reached 4x10^6 cells per mL they were washed in HSM - ammonium chloride and resuspended in 2.8 l flasks to a final cell density of 2x10^6 cells per ml, final volume of 1 l. Cells for RNA preparation were sampled at the indicated timepoints. +!Sample_growth_protocol_ch1 = Cultures used for the experiments to generate RNA for RNA-sequencing were grown in 1000 ml HSM-medium in 2.8 l flasks in the light (25 µmol photons per m2 per s) under the same conditions until they had reached a cell density of 4x10^6 cells per mL. They were then processed as indicated in the treatment protocol. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was isolated at time-points indicated in the text according to a method described in Boyle et al. 2012. +!Sample_extract_protocol_ch1 = For quantitative transcriptomes, RNAs were sequenced at LANL. +!Sample_description = UGTWs6na2HS1 +!Sample_description = Illumina's RNA-Seq whole transcriptome analysis. +!Sample_description = mRNA +!Sample_data_processing = Illumina's proprietary software was used for basecalling. +!Sample_data_processing = The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. +!Sample_data_processing = Expression estimates were obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. +!Sample_data_processing = Genome_build: Version 4.0 assembly of the Chlamydomonas genome (http://genome.jgi-psf.org/Chlre4/Chlre4.home.html) +!Sample_data_processing = Supplementary_files_format_and_content: Processed data file corresponds to expression estimates per sample, in units of RPKMs. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02649462 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX474554 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE55253 +!Sample_data_row_count = 0 +^SAMPLE = GSM1332651 +!Sample_title = Chlamydomonas reinhardtii CC-4348 sta6 minus N 4h +!Sample_geo_accession = GSM1332651 +!Sample_status = Public on Mar 09 2014 +!Sample_submission_date = Feb 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas cultured cells, sta6 (CC-4348), minus nitrogen, 4h +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain/background: sta6 (CC-4348) +!Sample_characteristics_ch1 = treatment: minus nitrogen +!Sample_characteristics_ch1 = time point: 4h +!Sample_treatment_protocol_ch1 = Once the cultures had reached 4x10^6 cells per mL they were washed in HSM - ammonium chloride and resuspended in 2.8 l flasks to a final cell density of 2x10^6 cells per ml, final volume of 1 l. Cells for RNA preparation were sampled at the indicated timepoints. +!Sample_growth_protocol_ch1 = Cultures used for the experiments to generate RNA for RNA-sequencing were grown in 1000 ml HSM-medium in 2.8 l flasks in the light (25 µmol photons per m2 per s) under the same conditions until they had reached a cell density of 4x10^6 cells per mL. They were then processed as indicated in the treatment protocol. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was isolated at time-points indicated in the text according to a method described in Boyle et al. 2012. +!Sample_extract_protocol_ch1 = For quantitative transcriptomes, RNAs were sequenced at LANL. +!Sample_description = UGTWs6na4HS1 +!Sample_description = Illumina's RNA-Seq whole transcriptome analysis. +!Sample_description = mRNA +!Sample_data_processing = Illumina's proprietary software was used for basecalling. +!Sample_data_processing = The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. +!Sample_data_processing = Expression estimates were obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. +!Sample_data_processing = Genome_build: Version 4.0 assembly of the Chlamydomonas genome (http://genome.jgi-psf.org/Chlre4/Chlre4.home.html) +!Sample_data_processing = Supplementary_files_format_and_content: Processed data file corresponds to expression estimates per sample, in units of RPKMs. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02649436 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX474555 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE55253 +!Sample_data_row_count = 0 +^SAMPLE = GSM1332652 +!Sample_title = Chlamydomonas reinhardtii CC-4348 sta6 minus N 8h +!Sample_geo_accession = GSM1332652 +!Sample_status = Public on Mar 09 2014 +!Sample_submission_date = Feb 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas cultured cells, sta6 (CC-4348), minus nitrogen, 8h +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain/background: sta6 (CC-4348) +!Sample_characteristics_ch1 = treatment: minus nitrogen +!Sample_characteristics_ch1 = time point: 8h +!Sample_treatment_protocol_ch1 = Once the cultures had reached 4x10^6 cells per mL they were washed in HSM - ammonium chloride and resuspended in 2.8 l flasks to a final cell density of 2x10^6 cells per ml, final volume of 1 l. Cells for RNA preparation were sampled at the indicated timepoints. +!Sample_growth_protocol_ch1 = Cultures used for the experiments to generate RNA for RNA-sequencing were grown in 1000 ml HSM-medium in 2.8 l flasks in the light (25 µmol photons per m2 per s) under the same conditions until they had reached a cell density of 4x10^6 cells per mL. They were then processed as indicated in the treatment protocol. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was isolated at time-points indicated in the text according to a method described in Boyle et al. 2012. +!Sample_extract_protocol_ch1 = For quantitative transcriptomes, RNAs were sequenced at LANL. +!Sample_description = UGTWs6na8HS1 +!Sample_description = Illumina's RNA-Seq whole transcriptome analysis. +!Sample_description = mRNA +!Sample_data_processing = Illumina's proprietary software was used for basecalling. +!Sample_data_processing = The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. +!Sample_data_processing = Expression estimates were obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. +!Sample_data_processing = Genome_build: Version 4.0 assembly of the Chlamydomonas genome (http://genome.jgi-psf.org/Chlre4/Chlre4.home.html) +!Sample_data_processing = Supplementary_files_format_and_content: Processed data file corresponds to expression estimates per sample, in units of RPKMs. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02649433 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX474556 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE55253 +!Sample_data_row_count = 0 +^SAMPLE = GSM1332653 +!Sample_title = Chlamydomonas reinhardtii CC-4348 sta6 minus N 12h +!Sample_geo_accession = GSM1332653 +!Sample_status = Public on Mar 09 2014 +!Sample_submission_date = Feb 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas cultured cells, sta6 (CC-4348), minus nitrogen, 12h +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain/background: sta6 (CC-4348) +!Sample_characteristics_ch1 = treatment: minus nitrogen +!Sample_characteristics_ch1 = time point: 12h +!Sample_treatment_protocol_ch1 = Once the cultures had reached 4x10^6 cells per mL they were washed in HSM - ammonium chloride and resuspended in 2.8 l flasks to a final cell density of 2x10^6 cells per ml, final volume of 1 l. Cells for RNA preparation were sampled at the indicated timepoints. +!Sample_growth_protocol_ch1 = Cultures used for the experiments to generate RNA for RNA-sequencing were grown in 1000 ml HSM-medium in 2.8 l flasks in the light (25 µmol photons per m2 per s) under the same conditions until they had reached a cell density of 4x10^6 cells per mL. They were then processed as indicated in the treatment protocol. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was isolated at time-points indicated in the text according to a method described in Boyle et al. 2012. +!Sample_extract_protocol_ch1 = For quantitative transcriptomes, RNAs were sequenced at LANL. +!Sample_description = UGTWs6na12HS1 +!Sample_description = Illumina's RNA-Seq whole transcriptome analysis. +!Sample_description = mRNA +!Sample_data_processing = Illumina's proprietary software was used for basecalling. +!Sample_data_processing = The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. +!Sample_data_processing = Expression estimates were obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. +!Sample_data_processing = Genome_build: Version 4.0 assembly of the Chlamydomonas genome (http://genome.jgi-psf.org/Chlre4/Chlre4.home.html) +!Sample_data_processing = Supplementary_files_format_and_content: Processed data file corresponds to expression estimates per sample, in units of RPKMs. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02649441 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX474557 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE55253 +!Sample_data_row_count = 0 +^SAMPLE = GSM1332654 +!Sample_title = Chlamydomonas reinhardtii CC-4348 sta6 minus N 24h +!Sample_geo_accession = GSM1332654 +!Sample_status = Public on Mar 09 2014 +!Sample_submission_date = Feb 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas cultured cells, sta6 (CC-4348), minus nitrogen, 24h +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain/background: sta6 (CC-4348) +!Sample_characteristics_ch1 = treatment: minus nitrogen +!Sample_characteristics_ch1 = time point: 24h +!Sample_treatment_protocol_ch1 = Once the cultures had reached 4x10^6 cells per mL they were washed in HSM - ammonium chloride and resuspended in 2.8 l flasks to a final cell density of 2x10^6 cells per ml, final volume of 1 l. Cells for RNA preparation were sampled at the indicated timepoints. +!Sample_growth_protocol_ch1 = Cultures used for the experiments to generate RNA for RNA-sequencing were grown in 1000 ml HSM-medium in 2.8 l flasks in the light (25 µmol photons per m2 per s) under the same conditions until they had reached a cell density of 4x10^6 cells per mL. They were then processed as indicated in the treatment protocol. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was isolated at time-points indicated in the text according to a method described in Boyle et al. 2012. +!Sample_extract_protocol_ch1 = For quantitative transcriptomes, RNAs were sequenced at LANL. +!Sample_description = UGTWs6na24HS1 +!Sample_description = Illumina's RNA-Seq whole transcriptome analysis. +!Sample_description = mRNA +!Sample_data_processing = Illumina's proprietary software was used for basecalling. +!Sample_data_processing = The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. +!Sample_data_processing = Expression estimates were obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. +!Sample_data_processing = Genome_build: Version 4.0 assembly of the Chlamydomonas genome (http://genome.jgi-psf.org/Chlre4/Chlre4.home.html) +!Sample_data_processing = Supplementary_files_format_and_content: Processed data file corresponds to expression estimates per sample, in units of RPKMs. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02649434 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX474558 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE55253 +!Sample_data_row_count = 0 +^SAMPLE = GSM1332655 +!Sample_title = Chlamydomonas reinhardtii CC-4348 sta6 minus N 48h +!Sample_geo_accession = GSM1332655 +!Sample_status = Public on Mar 09 2014 +!Sample_submission_date = Feb 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas cultured cells, sta6 (CC-4348), minus nitrogen, 48h +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain/background: sta6 (CC-4348) +!Sample_characteristics_ch1 = treatment: minus nitrogen +!Sample_characteristics_ch1 = time point: 48h +!Sample_treatment_protocol_ch1 = Once the cultures had reached 4x10^6 cells per mL they were washed in HSM - ammonium chloride and resuspended in 2.8 l flasks to a final cell density of 2x10^6 cells per ml, final volume of 1 l. Cells for RNA preparation were sampled at the indicated timepoints. +!Sample_growth_protocol_ch1 = Cultures used for the experiments to generate RNA for RNA-sequencing were grown in 1000 ml HSM-medium in 2.8 l flasks in the light (25 µmol photons per m2 per s) under the same conditions until they had reached a cell density of 4x10^6 cells per mL. They were then processed as indicated in the treatment protocol. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was isolated at time-points indicated in the text according to a method described in Boyle et al. 2012. +!Sample_extract_protocol_ch1 = For quantitative transcriptomes, RNAs were sequenced at LANL. +!Sample_description = UGTWs6na48HS1 +!Sample_description = Illumina's RNA-Seq whole transcriptome analysis. +!Sample_description = mRNA +!Sample_data_processing = Illumina's proprietary software was used for basecalling. +!Sample_data_processing = The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. +!Sample_data_processing = Expression estimates were obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. +!Sample_data_processing = Genome_build: Version 4.0 assembly of the Chlamydomonas genome (http://genome.jgi-psf.org/Chlre4/Chlre4.home.html) +!Sample_data_processing = Supplementary_files_format_and_content: Processed data file corresponds to expression estimates per sample, in units of RPKMs. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02649438 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX474559 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE55253 +!Sample_data_row_count = 0 +^SAMPLE = GSM1332656 +!Sample_title = Chlamydomonas reinhardtii CC-4348 sta6 48h minus N, 0h + acetate +!Sample_geo_accession = GSM1332656 +!Sample_status = Public on Mar 09 2014 +!Sample_submission_date = Feb 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas cultured cells, sta6 (CC-4348), 48 h minus nitrogen, 0h after acetate boost +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain/background: sta6 (CC-4348) +!Sample_characteristics_ch1 = treatment: 48 h minus nitrogen, then acetate boost +!Sample_characteristics_ch1 = time point: 0h after acetate boost +!Sample_treatment_protocol_ch1 = Once the cultures had reached 4x10^6 cells per mL they were washed in HSM - ammonium chloride and resuspended in 2.8 l flasks to a final cell density of 2x10^6 cells per ml, final volume of 1 l. Cells for RNA preparation were sampled at the indicated timepoints. +!Sample_growth_protocol_ch1 = Cultures used for the experiments to generate RNA for RNA-sequencing were grown in 1000 ml HSM-medium in 2.8 l flasks in the light (25 µmol photons per m2 per s) under the same conditions until they had reached a cell density of 4x10^6 cells per mL. They were then processed as indicated in the treatment protocol. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was isolated at time-points indicated in the text according to a method described in Boyle et al. 2012. +!Sample_extract_protocol_ch1 = For quantitative transcriptomes, RNAs were sequenced at LANL. +!Sample_description = UGTWs6nA0bHS1 +!Sample_description = Illumina's RNA-Seq whole transcriptome analysis. +!Sample_description = mRNA +!Sample_data_processing = Illumina's proprietary software was used for basecalling. +!Sample_data_processing = The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. +!Sample_data_processing = Expression estimates were obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. +!Sample_data_processing = Genome_build: Version 4.0 assembly of the Chlamydomonas genome (http://genome.jgi-psf.org/Chlre4/Chlre4.home.html) +!Sample_data_processing = Supplementary_files_format_and_content: Processed data file corresponds to expression estimates per sample, in units of RPKMs. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02649439 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX474560 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE55253 +!Sample_data_row_count = 0 +^SAMPLE = GSM1332657 +!Sample_title = Chlamydomonas reinhardtii CC-4348 sta6 48h minus N, 0.5h + acetate +!Sample_geo_accession = GSM1332657 +!Sample_status = Public on Mar 09 2014 +!Sample_submission_date = Feb 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas cultured cells, sta6 (CC-4348), 48 h minus nitrogen, 0.5h after acetate boost +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain/background: sta6 (CC-4348) +!Sample_characteristics_ch1 = treatment: 48 h minus nitrogen, then acetate boost +!Sample_characteristics_ch1 = time point: 0.5h after acetate boost +!Sample_treatment_protocol_ch1 = Once the cultures had reached 4x10^6 cells per mL they were washed in HSM - ammonium chloride and resuspended in 2.8 l flasks to a final cell density of 2x10^6 cells per ml, final volume of 1 l. Cells for RNA preparation were sampled at the indicated timepoints. +!Sample_growth_protocol_ch1 = Cultures used for the experiments to generate RNA for RNA-sequencing were grown in 1000 ml HSM-medium in 2.8 l flasks in the light (25 µmol photons per m2 per s) under the same conditions until they had reached a cell density of 4x10^6 cells per mL. They were then processed as indicated in the treatment protocol. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was isolated at time-points indicated in the text according to a method described in Boyle et al. 2012. +!Sample_extract_protocol_ch1 = For quantitative transcriptomes, RNAs were sequenced at LANL. +!Sample_description = UGTWs6nA05HS1 +!Sample_description = Illumina's RNA-Seq whole transcriptome analysis. +!Sample_description = mRNA +!Sample_data_processing = Illumina's proprietary software was used for basecalling. +!Sample_data_processing = The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. +!Sample_data_processing = Expression estimates were obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. +!Sample_data_processing = Genome_build: Version 4.0 assembly of the Chlamydomonas genome (http://genome.jgi-psf.org/Chlre4/Chlre4.home.html) +!Sample_data_processing = Supplementary_files_format_and_content: Processed data file corresponds to expression estimates per sample, in units of RPKMs. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02649435 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX474561 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE55253 +!Sample_data_row_count = 0 +^SAMPLE = GSM1332658 +!Sample_title = Chlamydomonas reinhardtii CC-4348 sta6 48h minus N, 2h + acetate +!Sample_geo_accession = GSM1332658 +!Sample_status = Public on Mar 09 2014 +!Sample_submission_date = Feb 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas cultured cells, sta6 (CC-4348), 48 h minus nitrogen, 2h after acetate boost +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain/background: sta6 (CC-4348) +!Sample_characteristics_ch1 = treatment: 48 h minus nitrogen, then acetate boost +!Sample_characteristics_ch1 = time point: 2h after acetate boost +!Sample_treatment_protocol_ch1 = Once the cultures had reached 4x10^6 cells per mL they were washed in HSM - ammonium chloride and resuspended in 2.8 l flasks to a final cell density of 2x10^6 cells per ml, final volume of 1 l. Cells for RNA preparation were sampled at the indicated timepoints. +!Sample_growth_protocol_ch1 = Cultures used for the experiments to generate RNA for RNA-sequencing were grown in 1000 ml HSM-medium in 2.8 l flasks in the light (25 µmol photons per m2 per s) under the same conditions until they had reached a cell density of 4x10^6 cells per mL. They were then processed as indicated in the treatment protocol. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was isolated at time-points indicated in the text according to a method described in Boyle et al. 2012. +!Sample_extract_protocol_ch1 = For quantitative transcriptomes, RNAs were sequenced at LANL. +!Sample_description = UGTWs6nA2HS1 +!Sample_description = Illumina's RNA-Seq whole transcriptome analysis. +!Sample_description = mRNA +!Sample_data_processing = Illumina's proprietary software was used for basecalling. +!Sample_data_processing = The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. +!Sample_data_processing = Expression estimates were obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. +!Sample_data_processing = Genome_build: Version 4.0 assembly of the Chlamydomonas genome (http://genome.jgi-psf.org/Chlre4/Chlre4.home.html) +!Sample_data_processing = Supplementary_files_format_and_content: Processed data file corresponds to expression estimates per sample, in units of RPKMs. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02649440 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX474562 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE55253 +!Sample_data_row_count = 0 +^SAMPLE = GSM1332659 +!Sample_title = Chlamydomonas reinhardtii CC-4348 sta6 48h minus N, 4h + acetate +!Sample_geo_accession = GSM1332659 +!Sample_status = Public on Mar 09 2014 +!Sample_submission_date = Feb 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas cultured cells, sta6 (CC-4348), 48 h minus nitrogen, 4h after acetate boost +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain/background: sta6 (CC-4348) +!Sample_characteristics_ch1 = treatment: 48 h minus nitrogen, then acetate boost +!Sample_characteristics_ch1 = time point: 4h after acetate boost +!Sample_treatment_protocol_ch1 = Once the cultures had reached 4x10^6 cells per mL they were washed in HSM - ammonium chloride and resuspended in 2.8 l flasks to a final cell density of 2x10^6 cells per ml, final volume of 1 l. Cells for RNA preparation were sampled at the indicated timepoints. +!Sample_growth_protocol_ch1 = Cultures used for the experiments to generate RNA for RNA-sequencing were grown in 1000 ml HSM-medium in 2.8 l flasks in the light (25 µmol photons per m2 per s) under the same conditions until they had reached a cell density of 4x10^6 cells per mL. They were then processed as indicated in the treatment protocol. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was isolated at time-points indicated in the text according to a method described in Boyle et al. 2012. +!Sample_extract_protocol_ch1 = For quantitative transcriptomes, RNAs were sequenced at LANL. +!Sample_description = UGTWs6nA4HS1 +!Sample_description = Illumina's RNA-Seq whole transcriptome analysis. +!Sample_description = mRNA +!Sample_data_processing = Illumina's proprietary software was used for basecalling. +!Sample_data_processing = The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. +!Sample_data_processing = Expression estimates were obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. +!Sample_data_processing = Genome_build: Version 4.0 assembly of the Chlamydomonas genome (http://genome.jgi-psf.org/Chlre4/Chlre4.home.html) +!Sample_data_processing = Supplementary_files_format_and_content: Processed data file corresponds to expression estimates per sample, in units of RPKMs. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02649460 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX474563 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE55253 +!Sample_data_row_count = 0 +^SAMPLE = GSM1332660 +!Sample_title = Chlamydomonas reinhardtii CC-4348 sta6 48h minus N, 8h + acetate +!Sample_geo_accession = GSM1332660 +!Sample_status = Public on Mar 09 2014 +!Sample_submission_date = Feb 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas cultured cells, sta6 (CC-4348), 48 h minus nitrogen, 8h after acetate boost +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain/background: sta6 (CC-4348) +!Sample_characteristics_ch1 = treatment: 48 h minus nitrogen, then acetate boost +!Sample_characteristics_ch1 = time point: 8h after acetate boost +!Sample_treatment_protocol_ch1 = Once the cultures had reached 4x10^6 cells per mL they were washed in HSM - ammonium chloride and resuspended in 2.8 l flasks to a final cell density of 2x10^6 cells per ml, final volume of 1 l. Cells for RNA preparation were sampled at the indicated timepoints. +!Sample_growth_protocol_ch1 = Cultures used for the experiments to generate RNA for RNA-sequencing were grown in 1000 ml HSM-medium in 2.8 l flasks in the light (25 µmol photons per m2 per s) under the same conditions until they had reached a cell density of 4x10^6 cells per mL. They were then processed as indicated in the treatment protocol. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was isolated at time-points indicated in the text according to a method described in Boyle et al. 2012. +!Sample_extract_protocol_ch1 = For quantitative transcriptomes, RNAs were sequenced at LANL. +!Sample_description = UGTWs6nA8HS1 +!Sample_description = Illumina's RNA-Seq whole transcriptome analysis. +!Sample_description = mRNA +!Sample_data_processing = Illumina's proprietary software was used for basecalling. +!Sample_data_processing = The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. +!Sample_data_processing = Expression estimates were obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. +!Sample_data_processing = Genome_build: Version 4.0 assembly of the Chlamydomonas genome (http://genome.jgi-psf.org/Chlre4/Chlre4.home.html) +!Sample_data_processing = Supplementary_files_format_and_content: Processed data file corresponds to expression estimates per sample, in units of RPKMs. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02649461 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX474531 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE55253 +!Sample_data_row_count = 0 +^SAMPLE = GSM1332661 +!Sample_title = Chlamydomonas reinhardtii CC-4348 sta6 48h minus N, 12h + acetate +!Sample_geo_accession = GSM1332661 +!Sample_status = Public on Mar 09 2014 +!Sample_submission_date = Feb 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas cultured cells, sta6 (CC-4348), 48 h minus nitrogen, 12h after acetate boost +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain/background: sta6 (CC-4348) +!Sample_characteristics_ch1 = treatment: 48 h minus nitrogen, then acetate boost +!Sample_characteristics_ch1 = time point: 12h after acetate boost +!Sample_treatment_protocol_ch1 = Once the cultures had reached 4x10^6 cells per mL they were washed in HSM - ammonium chloride and resuspended in 2.8 l flasks to a final cell density of 2x10^6 cells per ml, final volume of 1 l. Cells for RNA preparation were sampled at the indicated timepoints. +!Sample_growth_protocol_ch1 = Cultures used for the experiments to generate RNA for RNA-sequencing were grown in 1000 ml HSM-medium in 2.8 l flasks in the light (25 µmol photons per m2 per s) under the same conditions until they had reached a cell density of 4x10^6 cells per mL. They were then processed as indicated in the treatment protocol. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was isolated at time-points indicated in the text according to a method described in Boyle et al. 2012. +!Sample_extract_protocol_ch1 = For quantitative transcriptomes, RNAs were sequenced at LANL. +!Sample_description = UGTWs6nA12HS1 +!Sample_description = Illumina's RNA-Seq whole transcriptome analysis. +!Sample_description = mRNA +!Sample_data_processing = Illumina's proprietary software was used for basecalling. +!Sample_data_processing = The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. +!Sample_data_processing = Expression estimates were obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. +!Sample_data_processing = Genome_build: Version 4.0 assembly of the Chlamydomonas genome (http://genome.jgi-psf.org/Chlre4/Chlre4.home.html) +!Sample_data_processing = Supplementary_files_format_and_content: Processed data file corresponds to expression estimates per sample, in units of RPKMs. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02649463 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX474532 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE55253 +!Sample_data_row_count = 0 +^SAMPLE = GSM1332662 +!Sample_title = Chlamydomonas reinhardtii CC-4348 sta6 48h minus N, 24h + acetate +!Sample_geo_accession = GSM1332662 +!Sample_status = Public on Mar 09 2014 +!Sample_submission_date = Feb 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas cultured cells, sta6 (CC-4348), 48 h minus nitrogen, 24h after acetate boost +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain/background: sta6 (CC-4348) +!Sample_characteristics_ch1 = treatment: 48 h minus nitrogen, then acetate boost +!Sample_characteristics_ch1 = time point: 24h after acetate boost +!Sample_treatment_protocol_ch1 = Once the cultures had reached 4x10^6 cells per mL they were washed in HSM - ammonium chloride and resuspended in 2.8 l flasks to a final cell density of 2x10^6 cells per ml, final volume of 1 l. Cells for RNA preparation were sampled at the indicated timepoints. +!Sample_growth_protocol_ch1 = Cultures used for the experiments to generate RNA for RNA-sequencing were grown in 1000 ml HSM-medium in 2.8 l flasks in the light (25 µmol photons per m2 per s) under the same conditions until they had reached a cell density of 4x10^6 cells per mL. They were then processed as indicated in the treatment protocol. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was isolated at time-points indicated in the text according to a method described in Boyle et al. 2012. +!Sample_extract_protocol_ch1 = For quantitative transcriptomes, RNAs were sequenced at LANL. +!Sample_description = UGTWs6nA24HS1 +!Sample_description = Illumina's RNA-Seq whole transcriptome analysis. +!Sample_description = mRNA +!Sample_data_processing = Illumina's proprietary software was used for basecalling. +!Sample_data_processing = The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. +!Sample_data_processing = Expression estimates were obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. +!Sample_data_processing = Genome_build: Version 4.0 assembly of the Chlamydomonas genome (http://genome.jgi-psf.org/Chlre4/Chlre4.home.html) +!Sample_data_processing = Supplementary_files_format_and_content: Processed data file corresponds to expression estimates per sample, in units of RPKMs. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02649464 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX474533 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE55253 +!Sample_data_row_count = 0 +^SAMPLE = GSM1332663 +!Sample_title = Chlamydomonas reinhardtii CC-4348 sta6 48h minus N, 48h + acetate +!Sample_geo_accession = GSM1332663 +!Sample_status = Public on Mar 09 2014 +!Sample_submission_date = Feb 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas cultured cells, sta6 (CC-4348), 48 h minus nitrogen, 48h after acetate boost +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain/background: sta6 (CC-4348) +!Sample_characteristics_ch1 = treatment: 48 h minus nitrogen, then acetate boost +!Sample_characteristics_ch1 = time point: 48h after acetate boost +!Sample_treatment_protocol_ch1 = Once the cultures had reached 4x10^6 cells per mL they were washed in HSM - ammonium chloride and resuspended in 2.8 l flasks to a final cell density of 2x10^6 cells per ml, final volume of 1 l. Cells for RNA preparation were sampled at the indicated timepoints. +!Sample_growth_protocol_ch1 = Cultures used for the experiments to generate RNA for RNA-sequencing were grown in 1000 ml HSM-medium in 2.8 l flasks in the light (25 µmol photons per m2 per s) under the same conditions until they had reached a cell density of 4x10^6 cells per mL. They were then processed as indicated in the treatment protocol. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was isolated at time-points indicated in the text according to a method described in Boyle et al. 2012. +!Sample_extract_protocol_ch1 = For quantitative transcriptomes, RNAs were sequenced at LANL. +!Sample_description = UGTWs6nA48HS1 +!Sample_description = Illumina's RNA-Seq whole transcriptome analysis. +!Sample_description = mRNA +!Sample_data_processing = Illumina's proprietary software was used for basecalling. +!Sample_data_processing = The reads were aligned using bowtie in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome. +!Sample_data_processing = Expression estimates were obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. +!Sample_data_processing = Genome_build: Version 4.0 assembly of the Chlamydomonas genome (http://genome.jgi-psf.org/Chlre4/Chlre4.home.html) +!Sample_data_processing = Supplementary_files_format_and_content: Processed data file corresponds to expression estimates per sample, in units of RPKMs. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02649466 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX474564 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE55253 +!Sample_data_row_count = 0 +^SAMPLE = GSM1419589 +!Sample_title = SMah37ZRErKs +!Sample_geo_accession = GSM1419589 +!Sample_status = Public on Nov 01 2014 +!Sample_submission_date = Jun 24 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Zn replete - early +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: CC-4532 +!Sample_characteristics_ch1 = time point: Zn replete - early +!Sample_treatment_protocol_ch1 = Zn limitation was induced by inoculating cells from a nutrient-replete culture to a number of 10^5 cells/ml into 100 ml culture medium without supplemented Zn (“first round culture”), and then into medium without supplemented Zn (“second round culture”). ZnCl2 was resupplied at 2.5 µM to these limited cultures where described when they reached a density of 1 x 10^6 cells/ml (“t0h” of zinc resupply). +!Sample_growth_protocol_ch1 = Algae were grown from an inoculum of 1 x 10^5 cells/ml in Tris-acetate-phosphate (TAP) medium containing our revised micronutrient composition (Kropat et al., 2011) at 24°C under continuous light (~90 µmol m-2 s-1) with shaking (180 rpm). The desired lighting spectra were achieved by mixing 2 cool white fluorescent bulbs at 4100K for each 1 warm white fluorescent bulb at 3000K. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = A volume of culture containing 5 x 10^7 cells was transferred to a 15 ml Falcon tube and centrifuged at 2500 xg for 2 min at room temperature. The supernatant was immediately decanted and the pellets resuspended in 1 ml freshly made lysis buffer (50 mM Tris-HCl pH 7.5, 200 mM NaCl, 20 mM EDTA, 2% sodium dodecyl sulfate). Samples were centrifuged at 600 xg for 3 min at room temperature to pellet starch. The resulting supernatant was snap-frozen in liquid N2 and stored at -80°C for later processing. Upon thawing at room temperature, 10 ml TRIzol (Life Technologies, Carlsbad, California) was added, and the lysates were thoroughly mixed. Samples were incubated for 5 min at room temperature before being transferred to MaXtract HD (QIAgen, Hilden, Germany) tubes. 2 mL of chloroform was added and mixed again. After a 5 min incubation at room temperature, MaXtract HD tubes were centrifuged at 1500 xg for 5 min at room temperature, and the nucleic acid-containing aqueous phase was collected. To extract RNA, samples were processed using the miRNeasy Mini Kit (QIAgen, Hilden, Germany) according to manufacturer’s instructions. To remove contaminating DNA, samples were digested on-column using the RNase-Free DNase Set (QIAgen, Hilden, Germany) according to manufacturer’s instructions. RNA samples were subjected to an ethanol precipitation according to standard laboratory protocol (300 mM sodium acetate and 2.5 volumes of 100 % ethanol) to remove carry-over contaminants from the QIAgen buffers before being resuspended in 50 µL dH2O. +!Sample_extract_protocol_ch1 = We used the Illumina TruSeq Stranded mRNA Sample Prep LS kit according to the manufacturer's instructions (Protocol Rev. D from SEP-2012). +!Sample_data_processing = Basecalls performed using Illumina RTA software. +!Sample_data_processing = Basecalls and quality scores were converted to fastq format. +!Sample_data_processing = Individual libraries were demultiplexed. +!Sample_data_processing = reads filtered for adaptor sequence and low quality calls +!Sample_data_processing = alignment to genome by tophat2 +!Sample_data_processing = expression estimates by cuffdiff +!Sample_data_processing = Genome_build: v5.3.1 (Phytozome v9) available at http://genome.jgi.doe.gov/pages/dynamicOrganismDownload.jsf?organism=PhytozomeV9 +!Sample_data_processing = Supplementary_files_format_and_content: tab delimited file of expression estimate by FPKM for all genes in all samples +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sean,D.,Gallaher +!Sample_contact_laboratory = Sabeeha Merchant +!Sample_contact_department = Chem & BioChem +!Sample_contact_institute = UCLA +!Sample_contact_address = 607 Charle E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02870722 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX621638 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE58786 +!Sample_data_row_count = 0 +^SAMPLE = GSM1419590 +!Sample_title = SMah37ZRLtKs +!Sample_geo_accession = GSM1419590 +!Sample_status = Public on Nov 01 2014 +!Sample_submission_date = Jun 24 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Zn replete - late +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: CC-4532 +!Sample_characteristics_ch1 = time point: Zn replete - late +!Sample_treatment_protocol_ch1 = Zn limitation was induced by inoculating cells from a nutrient-replete culture to a number of 10^5 cells/ml into 100 ml culture medium without supplemented Zn (“first round culture”), and then into medium without supplemented Zn (“second round culture”). ZnCl2 was resupplied at 2.5 µM to these limited cultures where described when they reached a density of 1 x 10^6 cells/ml (“t0h” of zinc resupply). +!Sample_growth_protocol_ch1 = Algae were grown from an inoculum of 1 x 10^5 cells/ml in Tris-acetate-phosphate (TAP) medium containing our revised micronutrient composition (Kropat et al., 2011) at 24°C under continuous light (~90 µmol m-2 s-1) with shaking (180 rpm). The desired lighting spectra were achieved by mixing 2 cool white fluorescent bulbs at 4100K for each 1 warm white fluorescent bulb at 3000K. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = A volume of culture containing 5 x 10^7 cells was transferred to a 15 ml Falcon tube and centrifuged at 2500 xg for 2 min at room temperature. The supernatant was immediately decanted and the pellets resuspended in 1 ml freshly made lysis buffer (50 mM Tris-HCl pH 7.5, 200 mM NaCl, 20 mM EDTA, 2% sodium dodecyl sulfate). Samples were centrifuged at 600 xg for 3 min at room temperature to pellet starch. The resulting supernatant was snap-frozen in liquid N2 and stored at -80°C for later processing. Upon thawing at room temperature, 10 ml TRIzol (Life Technologies, Carlsbad, California) was added, and the lysates were thoroughly mixed. Samples were incubated for 5 min at room temperature before being transferred to MaXtract HD (QIAgen, Hilden, Germany) tubes. 2 mL of chloroform was added and mixed again. After a 5 min incubation at room temperature, MaXtract HD tubes were centrifuged at 1500 xg for 5 min at room temperature, and the nucleic acid-containing aqueous phase was collected. To extract RNA, samples were processed using the miRNeasy Mini Kit (QIAgen, Hilden, Germany) according to manufacturer’s instructions. To remove contaminating DNA, samples were digested on-column using the RNase-Free DNase Set (QIAgen, Hilden, Germany) according to manufacturer’s instructions. RNA samples were subjected to an ethanol precipitation according to standard laboratory protocol (300 mM sodium acetate and 2.5 volumes of 100 % ethanol) to remove carry-over contaminants from the QIAgen buffers before being resuspended in 50 µL dH2O. +!Sample_extract_protocol_ch1 = We used the Illumina TruSeq Stranded mRNA Sample Prep LS kit according to the manufacturer's instructions (Protocol Rev. D from SEP-2012). +!Sample_data_processing = Basecalls performed using Illumina RTA software. +!Sample_data_processing = Basecalls and quality scores were converted to fastq format. +!Sample_data_processing = Individual libraries were demultiplexed. +!Sample_data_processing = reads filtered for adaptor sequence and low quality calls +!Sample_data_processing = alignment to genome by tophat2 +!Sample_data_processing = expression estimates by cuffdiff +!Sample_data_processing = Genome_build: v5.3.1 (Phytozome v9) available at http://genome.jgi.doe.gov/pages/dynamicOrganismDownload.jsf?organism=PhytozomeV9 +!Sample_data_processing = Supplementary_files_format_and_content: tab delimited file of expression estimate by FPKM for all genes in all samples +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sean,D.,Gallaher +!Sample_contact_laboratory = Sabeeha Merchant +!Sample_contact_department = Chem & BioChem +!Sample_contact_institute = UCLA +!Sample_contact_address = 607 Charle E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02870728 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX621639 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE58786 +!Sample_data_row_count = 0 +^SAMPLE = GSM1419591 +!Sample_title = SMah37ZM00Ks +!Sample_geo_accession = GSM1419591 +!Sample_status = Public on Nov 01 2014 +!Sample_submission_date = Jun 24 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Zn minus +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: CC-4532 +!Sample_characteristics_ch1 = time point: Zn deficient - t0 +!Sample_treatment_protocol_ch1 = Zn limitation was induced by inoculating cells from a nutrient-replete culture to a number of 10^5 cells/ml into 100 ml culture medium without supplemented Zn (“first round culture”), and then into medium without supplemented Zn (“second round culture”). ZnCl2 was resupplied at 2.5 µM to these limited cultures where described when they reached a density of 1 x 10^6 cells/ml (“t0h” of zinc resupply). +!Sample_growth_protocol_ch1 = Algae were grown from an inoculum of 1 x 10^5 cells/ml in Tris-acetate-phosphate (TAP) medium containing our revised micronutrient composition (Kropat et al., 2011) at 24°C under continuous light (~90 µmol m-2 s-1) with shaking (180 rpm). The desired lighting spectra were achieved by mixing 2 cool white fluorescent bulbs at 4100K for each 1 warm white fluorescent bulb at 3000K. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = A volume of culture containing 5 x 10^7 cells was transferred to a 15 ml Falcon tube and centrifuged at 2500 xg for 2 min at room temperature. The supernatant was immediately decanted and the pellets resuspended in 1 ml freshly made lysis buffer (50 mM Tris-HCl pH 7.5, 200 mM NaCl, 20 mM EDTA, 2% sodium dodecyl sulfate). Samples were centrifuged at 600 xg for 3 min at room temperature to pellet starch. The resulting supernatant was snap-frozen in liquid N2 and stored at -80°C for later processing. Upon thawing at room temperature, 10 ml TRIzol (Life Technologies, Carlsbad, California) was added, and the lysates were thoroughly mixed. Samples were incubated for 5 min at room temperature before being transferred to MaXtract HD (QIAgen, Hilden, Germany) tubes. 2 mL of chloroform was added and mixed again. After a 5 min incubation at room temperature, MaXtract HD tubes were centrifuged at 1500 xg for 5 min at room temperature, and the nucleic acid-containing aqueous phase was collected. To extract RNA, samples were processed using the miRNeasy Mini Kit (QIAgen, Hilden, Germany) according to manufacturer’s instructions. To remove contaminating DNA, samples were digested on-column using the RNase-Free DNase Set (QIAgen, Hilden, Germany) according to manufacturer’s instructions. RNA samples were subjected to an ethanol precipitation according to standard laboratory protocol (300 mM sodium acetate and 2.5 volumes of 100 % ethanol) to remove carry-over contaminants from the QIAgen buffers before being resuspended in 50 µL dH2O. +!Sample_extract_protocol_ch1 = We used the Illumina TruSeq Stranded mRNA Sample Prep LS kit according to the manufacturer's instructions (Protocol Rev. D from SEP-2012). +!Sample_data_processing = Basecalls performed using Illumina RTA software. +!Sample_data_processing = Basecalls and quality scores were converted to fastq format. +!Sample_data_processing = Individual libraries were demultiplexed. +!Sample_data_processing = reads filtered for adaptor sequence and low quality calls +!Sample_data_processing = alignment to genome by tophat2 +!Sample_data_processing = expression estimates by cuffdiff +!Sample_data_processing = Genome_build: v5.3.1 (Phytozome v9) available at http://genome.jgi.doe.gov/pages/dynamicOrganismDownload.jsf?organism=PhytozomeV9 +!Sample_data_processing = Supplementary_files_format_and_content: tab delimited file of expression estimate by FPKM for all genes in all samples +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sean,D.,Gallaher +!Sample_contact_laboratory = Sabeeha Merchant +!Sample_contact_department = Chem & BioChem +!Sample_contact_institute = UCLA +!Sample_contact_address = 607 Charle E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02870723 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX621640 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE58786 +!Sample_data_row_count = 0 +^SAMPLE = GSM1419592 +!Sample_title = SMah37Z1.5Ks +!Sample_geo_accession = GSM1419592 +!Sample_status = Public on Nov 01 2014 +!Sample_submission_date = Jun 24 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Zn resupply - 1.5 hours +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: CC-4532 +!Sample_characteristics_ch1 = time point: 1.5h after Zn resupply +!Sample_treatment_protocol_ch1 = Zn limitation was induced by inoculating cells from a nutrient-replete culture to a number of 10^5 cells/ml into 100 ml culture medium without supplemented Zn (“first round culture”), and then into medium without supplemented Zn (“second round culture”). ZnCl2 was resupplied at 2.5 µM to these limited cultures where described when they reached a density of 1 x 10^6 cells/ml (“t0h” of zinc resupply). +!Sample_growth_protocol_ch1 = Algae were grown from an inoculum of 1 x 10^5 cells/ml in Tris-acetate-phosphate (TAP) medium containing our revised micronutrient composition (Kropat et al., 2011) at 24°C under continuous light (~90 µmol m-2 s-1) with shaking (180 rpm). The desired lighting spectra were achieved by mixing 2 cool white fluorescent bulbs at 4100K for each 1 warm white fluorescent bulb at 3000K. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = A volume of culture containing 5 x 10^7 cells was transferred to a 15 ml Falcon tube and centrifuged at 2500 xg for 2 min at room temperature. The supernatant was immediately decanted and the pellets resuspended in 1 ml freshly made lysis buffer (50 mM Tris-HCl pH 7.5, 200 mM NaCl, 20 mM EDTA, 2% sodium dodecyl sulfate). Samples were centrifuged at 600 xg for 3 min at room temperature to pellet starch. The resulting supernatant was snap-frozen in liquid N2 and stored at -80°C for later processing. Upon thawing at room temperature, 10 ml TRIzol (Life Technologies, Carlsbad, California) was added, and the lysates were thoroughly mixed. Samples were incubated for 5 min at room temperature before being transferred to MaXtract HD (QIAgen, Hilden, Germany) tubes. 2 mL of chloroform was added and mixed again. After a 5 min incubation at room temperature, MaXtract HD tubes were centrifuged at 1500 xg for 5 min at room temperature, and the nucleic acid-containing aqueous phase was collected. To extract RNA, samples were processed using the miRNeasy Mini Kit (QIAgen, Hilden, Germany) according to manufacturer’s instructions. To remove contaminating DNA, samples were digested on-column using the RNase-Free DNase Set (QIAgen, Hilden, Germany) according to manufacturer’s instructions. RNA samples were subjected to an ethanol precipitation according to standard laboratory protocol (300 mM sodium acetate and 2.5 volumes of 100 % ethanol) to remove carry-over contaminants from the QIAgen buffers before being resuspended in 50 µL dH2O. +!Sample_extract_protocol_ch1 = We used the Illumina TruSeq Stranded mRNA Sample Prep LS kit according to the manufacturer's instructions (Protocol Rev. D from SEP-2012). +!Sample_data_processing = Basecalls performed using Illumina RTA software. +!Sample_data_processing = Basecalls and quality scores were converted to fastq format. +!Sample_data_processing = Individual libraries were demultiplexed. +!Sample_data_processing = reads filtered for adaptor sequence and low quality calls +!Sample_data_processing = alignment to genome by tophat2 +!Sample_data_processing = expression estimates by cuffdiff +!Sample_data_processing = Genome_build: v5.3.1 (Phytozome v9) available at http://genome.jgi.doe.gov/pages/dynamicOrganismDownload.jsf?organism=PhytozomeV9 +!Sample_data_processing = Supplementary_files_format_and_content: tab delimited file of expression estimate by FPKM for all genes in all samples +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sean,D.,Gallaher +!Sample_contact_laboratory = Sabeeha Merchant +!Sample_contact_department = Chem & BioChem +!Sample_contact_institute = UCLA +!Sample_contact_address = 607 Charle E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02870727 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX621641 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE58786 +!Sample_data_row_count = 0 +^SAMPLE = GSM1419593 +!Sample_title = SMah37Z3.0Ks +!Sample_geo_accession = GSM1419593 +!Sample_status = Public on Nov 01 2014 +!Sample_submission_date = Jun 24 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Zn resupplly - 3.0 hours +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: CC-4532 +!Sample_characteristics_ch1 = time point: 3h after Zn resupply +!Sample_treatment_protocol_ch1 = Zn limitation was induced by inoculating cells from a nutrient-replete culture to a number of 10^5 cells/ml into 100 ml culture medium without supplemented Zn (“first round culture”), and then into medium without supplemented Zn (“second round culture”). ZnCl2 was resupplied at 2.5 µM to these limited cultures where described when they reached a density of 1 x 10^6 cells/ml (“t0h” of zinc resupply). +!Sample_growth_protocol_ch1 = Algae were grown from an inoculum of 1 x 10^5 cells/ml in Tris-acetate-phosphate (TAP) medium containing our revised micronutrient composition (Kropat et al., 2011) at 24°C under continuous light (~90 µmol m-2 s-1) with shaking (180 rpm). The desired lighting spectra were achieved by mixing 2 cool white fluorescent bulbs at 4100K for each 1 warm white fluorescent bulb at 3000K. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = A volume of culture containing 5 x 10^7 cells was transferred to a 15 ml Falcon tube and centrifuged at 2500 xg for 2 min at room temperature. The supernatant was immediately decanted and the pellets resuspended in 1 ml freshly made lysis buffer (50 mM Tris-HCl pH 7.5, 200 mM NaCl, 20 mM EDTA, 2% sodium dodecyl sulfate). Samples were centrifuged at 600 xg for 3 min at room temperature to pellet starch. The resulting supernatant was snap-frozen in liquid N2 and stored at -80°C for later processing. Upon thawing at room temperature, 10 ml TRIzol (Life Technologies, Carlsbad, California) was added, and the lysates were thoroughly mixed. Samples were incubated for 5 min at room temperature before being transferred to MaXtract HD (QIAgen, Hilden, Germany) tubes. 2 mL of chloroform was added and mixed again. After a 5 min incubation at room temperature, MaXtract HD tubes were centrifuged at 1500 xg for 5 min at room temperature, and the nucleic acid-containing aqueous phase was collected. To extract RNA, samples were processed using the miRNeasy Mini Kit (QIAgen, Hilden, Germany) according to manufacturer’s instructions. To remove contaminating DNA, samples were digested on-column using the RNase-Free DNase Set (QIAgen, Hilden, Germany) according to manufacturer’s instructions. RNA samples were subjected to an ethanol precipitation according to standard laboratory protocol (300 mM sodium acetate and 2.5 volumes of 100 % ethanol) to remove carry-over contaminants from the QIAgen buffers before being resuspended in 50 µL dH2O. +!Sample_extract_protocol_ch1 = We used the Illumina TruSeq Stranded mRNA Sample Prep LS kit according to the manufacturer's instructions (Protocol Rev. D from SEP-2012). +!Sample_data_processing = Basecalls performed using Illumina RTA software. +!Sample_data_processing = Basecalls and quality scores were converted to fastq format. +!Sample_data_processing = Individual libraries were demultiplexed. +!Sample_data_processing = reads filtered for adaptor sequence and low quality calls +!Sample_data_processing = alignment to genome by tophat2 +!Sample_data_processing = expression estimates by cuffdiff +!Sample_data_processing = Genome_build: v5.3.1 (Phytozome v9) available at http://genome.jgi.doe.gov/pages/dynamicOrganismDownload.jsf?organism=PhytozomeV9 +!Sample_data_processing = Supplementary_files_format_and_content: tab delimited file of expression estimate by FPKM for all genes in all samples +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sean,D.,Gallaher +!Sample_contact_laboratory = Sabeeha Merchant +!Sample_contact_department = Chem & BioChem +!Sample_contact_institute = UCLA +!Sample_contact_address = 607 Charle E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02870724 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX621642 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE58786 +!Sample_data_row_count = 0 +^SAMPLE = GSM1419594 +!Sample_title = SMah37Z4.5Ks +!Sample_geo_accession = GSM1419594 +!Sample_status = Public on Nov 01 2014 +!Sample_submission_date = Jun 24 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Zn resupply - 4.5 hours +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: CC-4532 +!Sample_characteristics_ch1 = time point: 4.5h after Zn resupply +!Sample_treatment_protocol_ch1 = Zn limitation was induced by inoculating cells from a nutrient-replete culture to a number of 10^5 cells/ml into 100 ml culture medium without supplemented Zn (“first round culture”), and then into medium without supplemented Zn (“second round culture”). ZnCl2 was resupplied at 2.5 µM to these limited cultures where described when they reached a density of 1 x 10^6 cells/ml (“t0h” of zinc resupply). +!Sample_growth_protocol_ch1 = Algae were grown from an inoculum of 1 x 10^5 cells/ml in Tris-acetate-phosphate (TAP) medium containing our revised micronutrient composition (Kropat et al., 2011) at 24°C under continuous light (~90 µmol m-2 s-1) with shaking (180 rpm). The desired lighting spectra were achieved by mixing 2 cool white fluorescent bulbs at 4100K for each 1 warm white fluorescent bulb at 3000K. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = A volume of culture containing 5 x 10^7 cells was transferred to a 15 ml Falcon tube and centrifuged at 2500 xg for 2 min at room temperature. The supernatant was immediately decanted and the pellets resuspended in 1 ml freshly made lysis buffer (50 mM Tris-HCl pH 7.5, 200 mM NaCl, 20 mM EDTA, 2% sodium dodecyl sulfate). Samples were centrifuged at 600 xg for 3 min at room temperature to pellet starch. The resulting supernatant was snap-frozen in liquid N2 and stored at -80°C for later processing. Upon thawing at room temperature, 10 ml TRIzol (Life Technologies, Carlsbad, California) was added, and the lysates were thoroughly mixed. Samples were incubated for 5 min at room temperature before being transferred to MaXtract HD (QIAgen, Hilden, Germany) tubes. 2 mL of chloroform was added and mixed again. After a 5 min incubation at room temperature, MaXtract HD tubes were centrifuged at 1500 xg for 5 min at room temperature, and the nucleic acid-containing aqueous phase was collected. To extract RNA, samples were processed using the miRNeasy Mini Kit (QIAgen, Hilden, Germany) according to manufacturer’s instructions. To remove contaminating DNA, samples were digested on-column using the RNase-Free DNase Set (QIAgen, Hilden, Germany) according to manufacturer’s instructions. RNA samples were subjected to an ethanol precipitation according to standard laboratory protocol (300 mM sodium acetate and 2.5 volumes of 100 % ethanol) to remove carry-over contaminants from the QIAgen buffers before being resuspended in 50 µL dH2O. +!Sample_extract_protocol_ch1 = We used the Illumina TruSeq Stranded mRNA Sample Prep LS kit according to the manufacturer's instructions (Protocol Rev. D from SEP-2012). +!Sample_data_processing = Basecalls performed using Illumina RTA software. +!Sample_data_processing = Basecalls and quality scores were converted to fastq format. +!Sample_data_processing = Individual libraries were demultiplexed. +!Sample_data_processing = reads filtered for adaptor sequence and low quality calls +!Sample_data_processing = alignment to genome by tophat2 +!Sample_data_processing = expression estimates by cuffdiff +!Sample_data_processing = Genome_build: v5.3.1 (Phytozome v9) available at http://genome.jgi.doe.gov/pages/dynamicOrganismDownload.jsf?organism=PhytozomeV9 +!Sample_data_processing = Supplementary_files_format_and_content: tab delimited file of expression estimate by FPKM for all genes in all samples +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sean,D.,Gallaher +!Sample_contact_laboratory = Sabeeha Merchant +!Sample_contact_department = Chem & BioChem +!Sample_contact_institute = UCLA +!Sample_contact_address = 607 Charle E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02870725 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX621643 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE58786 +!Sample_data_row_count = 0 +^SAMPLE = GSM1419595 +!Sample_title = SMah37Z12.Ks +!Sample_geo_accession = GSM1419595 +!Sample_status = Public on Nov 01 2014 +!Sample_submission_date = Jun 24 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Zn resupply - 12 hours +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: CC-4532 +!Sample_characteristics_ch1 = time point: 12h after Zn resupply +!Sample_treatment_protocol_ch1 = Zn limitation was induced by inoculating cells from a nutrient-replete culture to a number of 10^5 cells/ml into 100 ml culture medium without supplemented Zn (“first round culture”), and then into medium without supplemented Zn (“second round culture”). ZnCl2 was resupplied at 2.5 µM to these limited cultures where described when they reached a density of 1 x 10^6 cells/ml (“t0h” of zinc resupply). +!Sample_growth_protocol_ch1 = Algae were grown from an inoculum of 1 x 10^5 cells/ml in Tris-acetate-phosphate (TAP) medium containing our revised micronutrient composition (Kropat et al., 2011) at 24°C under continuous light (~90 µmol m-2 s-1) with shaking (180 rpm). The desired lighting spectra were achieved by mixing 2 cool white fluorescent bulbs at 4100K for each 1 warm white fluorescent bulb at 3000K. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = A volume of culture containing 5 x 10^7 cells was transferred to a 15 ml Falcon tube and centrifuged at 2500 xg for 2 min at room temperature. The supernatant was immediately decanted and the pellets resuspended in 1 ml freshly made lysis buffer (50 mM Tris-HCl pH 7.5, 200 mM NaCl, 20 mM EDTA, 2% sodium dodecyl sulfate). Samples were centrifuged at 600 xg for 3 min at room temperature to pellet starch. The resulting supernatant was snap-frozen in liquid N2 and stored at -80°C for later processing. Upon thawing at room temperature, 10 ml TRIzol (Life Technologies, Carlsbad, California) was added, and the lysates were thoroughly mixed. Samples were incubated for 5 min at room temperature before being transferred to MaXtract HD (QIAgen, Hilden, Germany) tubes. 2 mL of chloroform was added and mixed again. After a 5 min incubation at room temperature, MaXtract HD tubes were centrifuged at 1500 xg for 5 min at room temperature, and the nucleic acid-containing aqueous phase was collected. To extract RNA, samples were processed using the miRNeasy Mini Kit (QIAgen, Hilden, Germany) according to manufacturer’s instructions. To remove contaminating DNA, samples were digested on-column using the RNase-Free DNase Set (QIAgen, Hilden, Germany) according to manufacturer’s instructions. RNA samples were subjected to an ethanol precipitation according to standard laboratory protocol (300 mM sodium acetate and 2.5 volumes of 100 % ethanol) to remove carry-over contaminants from the QIAgen buffers before being resuspended in 50 µL dH2O. +!Sample_extract_protocol_ch1 = We used the Illumina TruSeq Stranded mRNA Sample Prep LS kit according to the manufacturer's instructions (Protocol Rev. D from SEP-2012). +!Sample_data_processing = Basecalls performed using Illumina RTA software. +!Sample_data_processing = Basecalls and quality scores were converted to fastq format. +!Sample_data_processing = Individual libraries were demultiplexed. +!Sample_data_processing = reads filtered for adaptor sequence and low quality calls +!Sample_data_processing = alignment to genome by tophat2 +!Sample_data_processing = expression estimates by cuffdiff +!Sample_data_processing = Genome_build: v5.3.1 (Phytozome v9) available at http://genome.jgi.doe.gov/pages/dynamicOrganismDownload.jsf?organism=PhytozomeV9 +!Sample_data_processing = Supplementary_files_format_and_content: tab delimited file of expression estimate by FPKM for all genes in all samples +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sean,D.,Gallaher +!Sample_contact_laboratory = Sabeeha Merchant +!Sample_contact_department = Chem & BioChem +!Sample_contact_institute = UCLA +!Sample_contact_address = 607 Charle E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02870729 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX621644 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE58786 +!Sample_data_row_count = 0 +^SAMPLE = GSM1419596 +!Sample_title = SMah37Z24.Ks +!Sample_geo_accession = GSM1419596 +!Sample_status = Public on Nov 01 2014 +!Sample_submission_date = Jun 24 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Zn resupply - 24 hours +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: CC-4532 +!Sample_characteristics_ch1 = time point: 24h after Zn resupply +!Sample_treatment_protocol_ch1 = Zn limitation was induced by inoculating cells from a nutrient-replete culture to a number of 10^5 cells/ml into 100 ml culture medium without supplemented Zn (“first round culture”), and then into medium without supplemented Zn (“second round culture”). ZnCl2 was resupplied at 2.5 µM to these limited cultures where described when they reached a density of 1 x 10^6 cells/ml (“t0h” of zinc resupply). +!Sample_growth_protocol_ch1 = Algae were grown from an inoculum of 1 x 10^5 cells/ml in Tris-acetate-phosphate (TAP) medium containing our revised micronutrient composition (Kropat et al., 2011) at 24°C under continuous light (~90 µmol m-2 s-1) with shaking (180 rpm). The desired lighting spectra were achieved by mixing 2 cool white fluorescent bulbs at 4100K for each 1 warm white fluorescent bulb at 3000K. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = A volume of culture containing 5 x 10^7 cells was transferred to a 15 ml Falcon tube and centrifuged at 2500 xg for 2 min at room temperature. The supernatant was immediately decanted and the pellets resuspended in 1 ml freshly made lysis buffer (50 mM Tris-HCl pH 7.5, 200 mM NaCl, 20 mM EDTA, 2% sodium dodecyl sulfate). Samples were centrifuged at 600 xg for 3 min at room temperature to pellet starch. The resulting supernatant was snap-frozen in liquid N2 and stored at -80°C for later processing. Upon thawing at room temperature, 10 ml TRIzol (Life Technologies, Carlsbad, California) was added, and the lysates were thoroughly mixed. Samples were incubated for 5 min at room temperature before being transferred to MaXtract HD (QIAgen, Hilden, Germany) tubes. 2 mL of chloroform was added and mixed again. After a 5 min incubation at room temperature, MaXtract HD tubes were centrifuged at 1500 xg for 5 min at room temperature, and the nucleic acid-containing aqueous phase was collected. To extract RNA, samples were processed using the miRNeasy Mini Kit (QIAgen, Hilden, Germany) according to manufacturer’s instructions. To remove contaminating DNA, samples were digested on-column using the RNase-Free DNase Set (QIAgen, Hilden, Germany) according to manufacturer’s instructions. RNA samples were subjected to an ethanol precipitation according to standard laboratory protocol (300 mM sodium acetate and 2.5 volumes of 100 % ethanol) to remove carry-over contaminants from the QIAgen buffers before being resuspended in 50 µL dH2O. +!Sample_extract_protocol_ch1 = We used the Illumina TruSeq Stranded mRNA Sample Prep LS kit according to the manufacturer's instructions (Protocol Rev. D from SEP-2012). +!Sample_data_processing = Basecalls performed using Illumina RTA software. +!Sample_data_processing = Basecalls and quality scores were converted to fastq format. +!Sample_data_processing = Individual libraries were demultiplexed. +!Sample_data_processing = reads filtered for adaptor sequence and low quality calls +!Sample_data_processing = alignment to genome by tophat2 +!Sample_data_processing = expression estimates by cuffdiff +!Sample_data_processing = Genome_build: v5.3.1 (Phytozome v9) available at http://genome.jgi.doe.gov/pages/dynamicOrganismDownload.jsf?organism=PhytozomeV9 +!Sample_data_processing = Supplementary_files_format_and_content: tab delimited file of expression estimate by FPKM for all genes in all samples +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sean,D.,Gallaher +!Sample_contact_laboratory = Sabeeha Merchant +!Sample_contact_department = Chem & BioChem +!Sample_contact_institute = UCLA +!Sample_contact_address = 607 Charle E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02870726 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX621645 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE58786 +!Sample_data_row_count = 0 +^SAMPLE = GSM1440761 +!Sample_title = PolyA Transcripts replicate 1 (Nitrogen starvation 0 hr; baseline) +!Sample_geo_accession = GSM1440761 +!Sample_status = Public on Jul 28 2015 +!Sample_submission_date = Jul 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = PolyA Transcripts (Nitrogen starvation 0 hr; baseline) +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 4A+ +!Sample_characteristics_ch1 = time: 0 hr +!Sample_treatment_protocol_ch1 = N-free (TAP-N) and SO42--free (TAP-S) media were prepared as described (Boyle et al., 2012; Kropat et al., 2011). For N- and S- starvation conditions, cells were grown to mid-log phase, washed twice with depleted media and re-suspended in TAP-N or TAP-S media to a density of 2x10^6 cells/ml (Boyle et al. 2012). Three acyltransferases and nitrogen-responsive regulator are implicated in nitrogen starvation-induced triacylglycerol accumulation in Chlamydomonas (The Journal of biological chemistry 287, 15811-15825; Kropat et al. 2011). A revised mineral nutrient supplement increases biomass and growth rate in Chlamydomonas reinhardtii (The Plant journal for cell and molecular biology 66, 770-780). +!Sample_growth_protocol_ch1 = C. reinhardtii wild type strain 4a+ was cultured using Tris-acetate-phosphate (TAP) medium. +!Sample_molecule_ch1 = polyA RNA +!Sample_extract_protocol_ch1 = Cells were first lysed and total RNA extracted using Trizol and cleaned up using RNeasy column (Qiagen). PolyA+ RNA was isolated from 10ug of total RNA. +!Sample_extract_protocol_ch1 = RNA was fragmented using RNA Fragmentation Reagents (Ambion). Strand-specific RNA-seq library (Parkhomchuk et al., 2009) was constructed using Illumina DNA Sample Preparation Kit (Illumina) with 10 cycles PCR amplification (Parkhomchuk et al.(2009). Nucleic acids research 37, e123). +!Sample_description = polyAND0hrR1 +!Sample_description = processed data file: master_gene_model.gtf.gz +!Sample_description = processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz +!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence and other artifacts. Trimmed reads with average quality ≥20, ≤3 Ns, and ≥32 bases were mapped to C. reinhardtii genome (Phytozome v5.3.1) using TopHat v2.0.8 with Bowtie v2.1.0. Sensitive and fusion mapping was enabled. Valid intron length was 20bp to 25 kbp and minimum distance between intra-chromosomal fusions was 1 Mbp. The library type “fr-firststrand” stated and read alignments with >3 mismatches were discarded. +!Sample_data_processing = Cufflinks v2.1.1 (modified to work on compact genomes) was used to reconstruct the transcripts guided with the Phytozome v5.3.1 reference transcriptome (See supplementary file: reference_gene_model.gtf.gz). Multi-mapped read correction was turned on and transcript composed of >50% multi-mapped reads or <25 reads were discarded. The remaining transcript assemblies from different time points were merged into a unified set of gene models, which was then compared to the annotated transcriptome. Potential noise was filtered from these predicted transcripts. Sequential steps of filtering criteria were applied as follows; 1). FPKM >0 for both replicates at least at one time point; 2) length of CDS>=50 amino acid; candidate coding regions were predicted based on transcript sequences using TransDecoder script v2013-02-25 from the Trinity package, 3) Remove “noise” transcripts of CuffDiff classes ‘E’, ‘O’ and ‘P’ and single exon transcripts of CuffDiff classes ‘.’, ‘C’ and ‘I’. +!Sample_data_processing = Illumina RTA-1.12 to 1.18 software used for basecalling depending on when library is sequenced. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii genome (Phytozome v5.3.1); C.reinhardtii_v5.3_genomic_scaffold_plastids.fasta.gz +!Sample_data_processing = Supplementary_files_format_and_content: peaks list, tab-delimited text files include FPKM values for each sample and the gene/transcript annotations +!Sample_platform_id = GPL15922 +!Sample_contact_name = Chia-Lin,,Wei +!Sample_contact_email = CWei@lbl.gov +!Sample_contact_phone = +1 (925) 927-2593 +!Sample_contact_laboratory = Sequencing Technologies +!Sample_contact_department = Genomic Technologies +!Sample_contact_institute = DOE Joint Genome Institute +!Sample_contact_address = 2800 Mitchell Drive +!Sample_contact_city = Walnut Creek +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 94598 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02928703 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX658296 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE59629 +!Sample_data_row_count = 0 +^SAMPLE = GSM1440762 +!Sample_title = PolyA Transcripts replicate 2 (Nitrogen starvation 0 hr; baseline) +!Sample_geo_accession = GSM1440762 +!Sample_status = Public on Jul 28 2015 +!Sample_submission_date = Jul 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = PolyA Transcripts (Nitrogen starvation 0 hr; baseline) +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 4A+ +!Sample_characteristics_ch1 = time: 0 hr +!Sample_treatment_protocol_ch1 = N-free (TAP-N) and SO42--free (TAP-S) media were prepared as described (Boyle et al., 2012; Kropat et al., 2011). For N- and S- starvation conditions, cells were grown to mid-log phase, washed twice with depleted media and re-suspended in TAP-N or TAP-S media to a density of 2x10^6 cells/ml (Boyle et al. 2012). Three acyltransferases and nitrogen-responsive regulator are implicated in nitrogen starvation-induced triacylglycerol accumulation in Chlamydomonas (The Journal of biological chemistry 287, 15811-15825; Kropat et al. 2011). A revised mineral nutrient supplement increases biomass and growth rate in Chlamydomonas reinhardtii (The Plant journal for cell and molecular biology 66, 770-780). +!Sample_growth_protocol_ch1 = C. reinhardtii wild type strain 4a+ was cultured using Tris-acetate-phosphate (TAP) medium. +!Sample_molecule_ch1 = polyA RNA +!Sample_extract_protocol_ch1 = Cells were first lysed and total RNA extracted using Trizol and cleaned up using RNeasy column (Qiagen). PolyA+ RNA was isolated from 10ug of total RNA. +!Sample_extract_protocol_ch1 = RNA was fragmented using RNA Fragmentation Reagents (Ambion). Strand-specific RNA-seq library (Parkhomchuk et al., 2009) was constructed using Illumina DNA Sample Preparation Kit (Illumina) with 10 cycles PCR amplification (Parkhomchuk et al.(2009). Nucleic acids research 37, e123). +!Sample_description = polyAND0hrR2 +!Sample_description = processed data file: master_gene_model.gtf.gz +!Sample_description = processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz +!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence and other artifacts. Trimmed reads with average quality ≥20, ≤3 Ns, and ≥32 bases were mapped to C. reinhardtii genome (Phytozome v5.3.1) using TopHat v2.0.8 with Bowtie v2.1.0. Sensitive and fusion mapping was enabled. Valid intron length was 20bp to 25 kbp and minimum distance between intra-chromosomal fusions was 1 Mbp. The library type “fr-firststrand” stated and read alignments with >3 mismatches were discarded. +!Sample_data_processing = Cufflinks v2.1.1 (modified to work on compact genomes) was used to reconstruct the transcripts guided with the Phytozome v5.3.1 reference transcriptome (See supplementary file: reference_gene_model.gtf.gz). Multi-mapped read correction was turned on and transcript composed of >50% multi-mapped reads or <25 reads were discarded. The remaining transcript assemblies from different time points were merged into a unified set of gene models, which was then compared to the annotated transcriptome. Potential noise was filtered from these predicted transcripts. Sequential steps of filtering criteria were applied as follows; 1). FPKM >0 for both replicates at least at one time point; 2) length of CDS>=50 amino acid; candidate coding regions were predicted based on transcript sequences using TransDecoder script v2013-02-25 from the Trinity package, 3) Remove “noise” transcripts of CuffDiff classes ‘E’, ‘O’ and ‘P’ and single exon transcripts of CuffDiff classes ‘.’, ‘C’ and ‘I’. +!Sample_data_processing = Illumina RTA-1.12 to 1.18 software used for basecalling depending on when library is sequenced. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii genome (Phytozome v5.3.1); C.reinhardtii_v5.3_genomic_scaffold_plastids.fasta.gz +!Sample_data_processing = Supplementary_files_format_and_content: peaks list, tab-delimited text files include FPKM values for each sample and the gene/transcript annotations +!Sample_platform_id = GPL15922 +!Sample_contact_name = Chia-Lin,,Wei +!Sample_contact_email = CWei@lbl.gov +!Sample_contact_phone = +1 (925) 927-2593 +!Sample_contact_laboratory = Sequencing Technologies +!Sample_contact_department = Genomic Technologies +!Sample_contact_institute = DOE Joint Genome Institute +!Sample_contact_address = 2800 Mitchell Drive +!Sample_contact_city = Walnut Creek +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 94598 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02928704 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX658297 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE59629 +!Sample_data_row_count = 0 +^SAMPLE = GSM1440763 +!Sample_title = PolyA Transcripts replicate 1 (Nitrogen starvation 10 min) +!Sample_geo_accession = GSM1440763 +!Sample_status = Public on Jul 28 2015 +!Sample_submission_date = Jul 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = PolyA Transcripts (Nitrogen starvation 10 min) +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 4A+ +!Sample_characteristics_ch1 = time: 10 min +!Sample_treatment_protocol_ch1 = N-free (TAP-N) and SO42--free (TAP-S) media were prepared as described (Boyle et al., 2012; Kropat et al., 2011). For N- and S- starvation conditions, cells were grown to mid-log phase, washed twice with depleted media and re-suspended in TAP-N or TAP-S media to a density of 2x10^6 cells/ml (Boyle et al. 2012). Three acyltransferases and nitrogen-responsive regulator are implicated in nitrogen starvation-induced triacylglycerol accumulation in Chlamydomonas (The Journal of biological chemistry 287, 15811-15825; Kropat et al. 2011). A revised mineral nutrient supplement increases biomass and growth rate in Chlamydomonas reinhardtii (The Plant journal for cell and molecular biology 66, 770-780). +!Sample_growth_protocol_ch1 = C. reinhardtii wild type strain 4a+ was cultured using Tris-acetate-phosphate (TAP) medium. +!Sample_molecule_ch1 = polyA RNA +!Sample_extract_protocol_ch1 = Cells were first lysed and total RNA extracted using Trizol and cleaned up using RNeasy column (Qiagen). PolyA+ RNA was isolated from 10ug of total RNA. +!Sample_extract_protocol_ch1 = RNA was fragmented using RNA Fragmentation Reagents (Ambion). Strand-specific RNA-seq library (Parkhomchuk et al., 2009) was constructed using Illumina DNA Sample Preparation Kit (Illumina) with 10 cycles PCR amplification (Parkhomchuk et al.(2009). Nucleic acids research 37, e123). +!Sample_description = polyAND10minR1 +!Sample_description = processed data file: master_gene_model.gtf.gz +!Sample_description = processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz +!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence and other artifacts. Trimmed reads with average quality ≥20, ≤3 Ns, and ≥32 bases were mapped to C. reinhardtii genome (Phytozome v5.3.1) using TopHat v2.0.8 with Bowtie v2.1.0. Sensitive and fusion mapping was enabled. Valid intron length was 20bp to 25 kbp and minimum distance between intra-chromosomal fusions was 1 Mbp. The library type “fr-firststrand” stated and read alignments with >3 mismatches were discarded. +!Sample_data_processing = Cufflinks v2.1.1 (modified to work on compact genomes) was used to reconstruct the transcripts guided with the Phytozome v5.3.1 reference transcriptome (See supplementary file: reference_gene_model.gtf.gz). Multi-mapped read correction was turned on and transcript composed of >50% multi-mapped reads or <25 reads were discarded. The remaining transcript assemblies from different time points were merged into a unified set of gene models, which was then compared to the annotated transcriptome. Potential noise was filtered from these predicted transcripts. Sequential steps of filtering criteria were applied as follows; 1). FPKM >0 for both replicates at least at one time point; 2) length of CDS>=50 amino acid; candidate coding regions were predicted based on transcript sequences using TransDecoder script v2013-02-25 from the Trinity package, 3) Remove “noise” transcripts of CuffDiff classes ‘E’, ‘O’ and ‘P’ and single exon transcripts of CuffDiff classes ‘.’, ‘C’ and ‘I’. +!Sample_data_processing = Illumina RTA-1.12 to 1.18 software used for basecalling depending on when library is sequenced. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii genome (Phytozome v5.3.1); C.reinhardtii_v5.3_genomic_scaffold_plastids.fasta.gz +!Sample_data_processing = Supplementary_files_format_and_content: peaks list, tab-delimited text files include FPKM values for each sample and the gene/transcript annotations +!Sample_platform_id = GPL15922 +!Sample_contact_name = Chia-Lin,,Wei +!Sample_contact_email = CWei@lbl.gov +!Sample_contact_phone = +1 (925) 927-2593 +!Sample_contact_laboratory = Sequencing Technologies +!Sample_contact_department = Genomic Technologies +!Sample_contact_institute = DOE Joint Genome Institute +!Sample_contact_address = 2800 Mitchell Drive +!Sample_contact_city = Walnut Creek +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 94598 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02928705 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX658298 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE59629 +!Sample_data_row_count = 0 +^SAMPLE = GSM1440764 +!Sample_title = PolyA Transcripts replicate 2 (Nitrogen starvation 10 min) +!Sample_geo_accession = GSM1440764 +!Sample_status = Public on Jul 28 2015 +!Sample_submission_date = Jul 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = PolyA Transcripts (Nitrogen starvation 10 min) +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 4A+ +!Sample_characteristics_ch1 = time: 10 min +!Sample_treatment_protocol_ch1 = N-free (TAP-N) and SO42--free (TAP-S) media were prepared as described (Boyle et al., 2012; Kropat et al., 2011). For N- and S- starvation conditions, cells were grown to mid-log phase, washed twice with depleted media and re-suspended in TAP-N or TAP-S media to a density of 2x10^6 cells/ml (Boyle et al. 2012). Three acyltransferases and nitrogen-responsive regulator are implicated in nitrogen starvation-induced triacylglycerol accumulation in Chlamydomonas (The Journal of biological chemistry 287, 15811-15825; Kropat et al. 2011). A revised mineral nutrient supplement increases biomass and growth rate in Chlamydomonas reinhardtii (The Plant journal for cell and molecular biology 66, 770-780). +!Sample_growth_protocol_ch1 = C. reinhardtii wild type strain 4a+ was cultured using Tris-acetate-phosphate (TAP) medium. +!Sample_molecule_ch1 = polyA RNA +!Sample_extract_protocol_ch1 = Cells were first lysed and total RNA extracted using Trizol and cleaned up using RNeasy column (Qiagen). PolyA+ RNA was isolated from 10ug of total RNA. +!Sample_extract_protocol_ch1 = RNA was fragmented using RNA Fragmentation Reagents (Ambion). Strand-specific RNA-seq library (Parkhomchuk et al., 2009) was constructed using Illumina DNA Sample Preparation Kit (Illumina) with 10 cycles PCR amplification (Parkhomchuk et al.(2009). Nucleic acids research 37, e123). +!Sample_description = polyAND10minR2 +!Sample_description = processed data file: master_gene_model.gtf.gz +!Sample_description = processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz +!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence and other artifacts. Trimmed reads with average quality ≥20, ≤3 Ns, and ≥32 bases were mapped to C. reinhardtii genome (Phytozome v5.3.1) using TopHat v2.0.8 with Bowtie v2.1.0. Sensitive and fusion mapping was enabled. Valid intron length was 20bp to 25 kbp and minimum distance between intra-chromosomal fusions was 1 Mbp. The library type “fr-firststrand” stated and read alignments with >3 mismatches were discarded. +!Sample_data_processing = Cufflinks v2.1.1 (modified to work on compact genomes) was used to reconstruct the transcripts guided with the Phytozome v5.3.1 reference transcriptome (See supplementary file: reference_gene_model.gtf.gz). Multi-mapped read correction was turned on and transcript composed of >50% multi-mapped reads or <25 reads were discarded. The remaining transcript assemblies from different time points were merged into a unified set of gene models, which was then compared to the annotated transcriptome. Potential noise was filtered from these predicted transcripts. Sequential steps of filtering criteria were applied as follows; 1). FPKM >0 for both replicates at least at one time point; 2) length of CDS>=50 amino acid; candidate coding regions were predicted based on transcript sequences using TransDecoder script v2013-02-25 from the Trinity package, 3) Remove “noise” transcripts of CuffDiff classes ‘E’, ‘O’ and ‘P’ and single exon transcripts of CuffDiff classes ‘.’, ‘C’ and ‘I’. +!Sample_data_processing = Illumina RTA-1.12 to 1.18 software used for basecalling depending on when library is sequenced. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii genome (Phytozome v5.3.1); C.reinhardtii_v5.3_genomic_scaffold_plastids.fasta.gz +!Sample_data_processing = Supplementary_files_format_and_content: peaks list, tab-delimited text files include FPKM values for each sample and the gene/transcript annotations +!Sample_platform_id = GPL15922 +!Sample_contact_name = Chia-Lin,,Wei +!Sample_contact_email = CWei@lbl.gov +!Sample_contact_phone = +1 (925) 927-2593 +!Sample_contact_laboratory = Sequencing Technologies +!Sample_contact_department = Genomic Technologies +!Sample_contact_institute = DOE Joint Genome Institute +!Sample_contact_address = 2800 Mitchell Drive +!Sample_contact_city = Walnut Creek +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 94598 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02928706 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX658299 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE59629 +!Sample_data_row_count = 0 +^SAMPLE = GSM1440765 +!Sample_title = PolyA Transcripts replicate 1 (Nitrogen starvation 30 min) +!Sample_geo_accession = GSM1440765 +!Sample_status = Public on Jul 28 2015 +!Sample_submission_date = Jul 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = PolyA Transcripts (Nitrogen starvation 30 min) +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 4A+ +!Sample_characteristics_ch1 = time: 30 min +!Sample_treatment_protocol_ch1 = N-free (TAP-N) and SO42--free (TAP-S) media were prepared as described (Boyle et al., 2012; Kropat et al., 2011). For N- and S- starvation conditions, cells were grown to mid-log phase, washed twice with depleted media and re-suspended in TAP-N or TAP-S media to a density of 2x10^6 cells/ml (Boyle et al. 2012). Three acyltransferases and nitrogen-responsive regulator are implicated in nitrogen starvation-induced triacylglycerol accumulation in Chlamydomonas (The Journal of biological chemistry 287, 15811-15825; Kropat et al. 2011). A revised mineral nutrient supplement increases biomass and growth rate in Chlamydomonas reinhardtii (The Plant journal for cell and molecular biology 66, 770-780). +!Sample_growth_protocol_ch1 = C. reinhardtii wild type strain 4a+ was cultured using Tris-acetate-phosphate (TAP) medium. +!Sample_molecule_ch1 = polyA RNA +!Sample_extract_protocol_ch1 = Cells were first lysed and total RNA extracted using Trizol and cleaned up using RNeasy column (Qiagen). PolyA+ RNA was isolated from 10ug of total RNA. +!Sample_extract_protocol_ch1 = RNA was fragmented using RNA Fragmentation Reagents (Ambion). Strand-specific RNA-seq library (Parkhomchuk et al., 2009) was constructed using Illumina DNA Sample Preparation Kit (Illumina) with 10 cycles PCR amplification (Parkhomchuk et al.(2009). Nucleic acids research 37, e123). +!Sample_description = polyAND30minR1 +!Sample_description = processed data file: master_gene_model.gtf.gz +!Sample_description = processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz +!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence and other artifacts. Trimmed reads with average quality ≥20, ≤3 Ns, and ≥32 bases were mapped to C. reinhardtii genome (Phytozome v5.3.1) using TopHat v2.0.8 with Bowtie v2.1.0. Sensitive and fusion mapping was enabled. Valid intron length was 20bp to 25 kbp and minimum distance between intra-chromosomal fusions was 1 Mbp. The library type “fr-firststrand” stated and read alignments with >3 mismatches were discarded. +!Sample_data_processing = Cufflinks v2.1.1 (modified to work on compact genomes) was used to reconstruct the transcripts guided with the Phytozome v5.3.1 reference transcriptome (See supplementary file: reference_gene_model.gtf.gz). Multi-mapped read correction was turned on and transcript composed of >50% multi-mapped reads or <25 reads were discarded. The remaining transcript assemblies from different time points were merged into a unified set of gene models, which was then compared to the annotated transcriptome. Potential noise was filtered from these predicted transcripts. Sequential steps of filtering criteria were applied as follows; 1). FPKM >0 for both replicates at least at one time point; 2) length of CDS>=50 amino acid; candidate coding regions were predicted based on transcript sequences using TransDecoder script v2013-02-25 from the Trinity package, 3) Remove “noise” transcripts of CuffDiff classes ‘E’, ‘O’ and ‘P’ and single exon transcripts of CuffDiff classes ‘.’, ‘C’ and ‘I’. +!Sample_data_processing = Illumina RTA-1.12 to 1.18 software used for basecalling depending on when library is sequenced. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii genome (Phytozome v5.3.1); C.reinhardtii_v5.3_genomic_scaffold_plastids.fasta.gz +!Sample_data_processing = Supplementary_files_format_and_content: peaks list, tab-delimited text files include FPKM values for each sample and the gene/transcript annotations +!Sample_platform_id = GPL15922 +!Sample_contact_name = Chia-Lin,,Wei +!Sample_contact_email = CWei@lbl.gov +!Sample_contact_phone = +1 (925) 927-2593 +!Sample_contact_laboratory = Sequencing Technologies +!Sample_contact_department = Genomic Technologies +!Sample_contact_institute = DOE Joint Genome Institute +!Sample_contact_address = 2800 Mitchell Drive +!Sample_contact_city = Walnut Creek +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 94598 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02928707 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX658300 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE59629 +!Sample_data_row_count = 0 +^SAMPLE = GSM1440766 +!Sample_title = PolyA Transcripts replicate 2 (Nitrogen starvation 30 min) +!Sample_geo_accession = GSM1440766 +!Sample_status = Public on Jul 28 2015 +!Sample_submission_date = Jul 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = PolyA Transcripts (Nitrogen starvation 30 min) +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 4A+ +!Sample_characteristics_ch1 = time: 30 min +!Sample_treatment_protocol_ch1 = N-free (TAP-N) and SO42--free (TAP-S) media were prepared as described (Boyle et al., 2012; Kropat et al., 2011). For N- and S- starvation conditions, cells were grown to mid-log phase, washed twice with depleted media and re-suspended in TAP-N or TAP-S media to a density of 2x10^6 cells/ml (Boyle et al. 2012). Three acyltransferases and nitrogen-responsive regulator are implicated in nitrogen starvation-induced triacylglycerol accumulation in Chlamydomonas (The Journal of biological chemistry 287, 15811-15825; Kropat et al. 2011). A revised mineral nutrient supplement increases biomass and growth rate in Chlamydomonas reinhardtii (The Plant journal for cell and molecular biology 66, 770-780). +!Sample_growth_protocol_ch1 = C. reinhardtii wild type strain 4a+ was cultured using Tris-acetate-phosphate (TAP) medium. +!Sample_molecule_ch1 = polyA RNA +!Sample_extract_protocol_ch1 = Cells were first lysed and total RNA extracted using Trizol and cleaned up using RNeasy column (Qiagen). PolyA+ RNA was isolated from 10ug of total RNA. +!Sample_extract_protocol_ch1 = RNA was fragmented using RNA Fragmentation Reagents (Ambion). Strand-specific RNA-seq library (Parkhomchuk et al., 2009) was constructed using Illumina DNA Sample Preparation Kit (Illumina) with 10 cycles PCR amplification (Parkhomchuk et al.(2009). Nucleic acids research 37, e123). +!Sample_description = polyAND30minR2 +!Sample_description = processed data file: master_gene_model.gtf.gz +!Sample_description = processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz +!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence and other artifacts. Trimmed reads with average quality ≥20, ≤3 Ns, and ≥32 bases were mapped to C. reinhardtii genome (Phytozome v5.3.1) using TopHat v2.0.8 with Bowtie v2.1.0. Sensitive and fusion mapping was enabled. Valid intron length was 20bp to 25 kbp and minimum distance between intra-chromosomal fusions was 1 Mbp. The library type “fr-firststrand” stated and read alignments with >3 mismatches were discarded. +!Sample_data_processing = Cufflinks v2.1.1 (modified to work on compact genomes) was used to reconstruct the transcripts guided with the Phytozome v5.3.1 reference transcriptome (See supplementary file: reference_gene_model.gtf.gz). Multi-mapped read correction was turned on and transcript composed of >50% multi-mapped reads or <25 reads were discarded. The remaining transcript assemblies from different time points were merged into a unified set of gene models, which was then compared to the annotated transcriptome. Potential noise was filtered from these predicted transcripts. Sequential steps of filtering criteria were applied as follows; 1). FPKM >0 for both replicates at least at one time point; 2) length of CDS>=50 amino acid; candidate coding regions were predicted based on transcript sequences using TransDecoder script v2013-02-25 from the Trinity package, 3) Remove “noise” transcripts of CuffDiff classes ‘E’, ‘O’ and ‘P’ and single exon transcripts of CuffDiff classes ‘.’, ‘C’ and ‘I’. +!Sample_data_processing = Illumina RTA-1.12 to 1.18 software used for basecalling depending on when library is sequenced. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii genome (Phytozome v5.3.1); C.reinhardtii_v5.3_genomic_scaffold_plastids.fasta.gz +!Sample_data_processing = Supplementary_files_format_and_content: peaks list, tab-delimited text files include FPKM values for each sample and the gene/transcript annotations +!Sample_platform_id = GPL15922 +!Sample_contact_name = Chia-Lin,,Wei +!Sample_contact_email = CWei@lbl.gov +!Sample_contact_phone = +1 (925) 927-2593 +!Sample_contact_laboratory = Sequencing Technologies +!Sample_contact_department = Genomic Technologies +!Sample_contact_institute = DOE Joint Genome Institute +!Sample_contact_address = 2800 Mitchell Drive +!Sample_contact_city = Walnut Creek +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 94598 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02928708 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX658301 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE59629 +!Sample_data_row_count = 0 +^SAMPLE = GSM1440767 +!Sample_title = PolyA Transcripts replicate 1 (Nitrogen starvation 1 hr) +!Sample_geo_accession = GSM1440767 +!Sample_status = Public on Jul 28 2015 +!Sample_submission_date = Jul 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = PolyA Transcripts (Nitrogen starvation 1 hr) +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 4A+ +!Sample_characteristics_ch1 = time: 1 hr +!Sample_treatment_protocol_ch1 = N-free (TAP-N) and SO42--free (TAP-S) media were prepared as described (Boyle et al., 2012; Kropat et al., 2011). For N- and S- starvation conditions, cells were grown to mid-log phase, washed twice with depleted media and re-suspended in TAP-N or TAP-S media to a density of 2x10^6 cells/ml (Boyle et al. 2012). Three acyltransferases and nitrogen-responsive regulator are implicated in nitrogen starvation-induced triacylglycerol accumulation in Chlamydomonas (The Journal of biological chemistry 287, 15811-15825; Kropat et al. 2011). A revised mineral nutrient supplement increases biomass and growth rate in Chlamydomonas reinhardtii (The Plant journal for cell and molecular biology 66, 770-780). +!Sample_growth_protocol_ch1 = C. reinhardtii wild type strain 4a+ was cultured using Tris-acetate-phosphate (TAP) medium. +!Sample_molecule_ch1 = polyA RNA +!Sample_extract_protocol_ch1 = Cells were first lysed and total RNA extracted using Trizol and cleaned up using RNeasy column (Qiagen). PolyA+ RNA was isolated from 10ug of total RNA. +!Sample_extract_protocol_ch1 = RNA was fragmented using RNA Fragmentation Reagents (Ambion). Strand-specific RNA-seq library (Parkhomchuk et al., 2009) was constructed using Illumina DNA Sample Preparation Kit (Illumina) with 10 cycles PCR amplification (Parkhomchuk et al.(2009). Nucleic acids research 37, e123). +!Sample_description = polyAND1hrR1 +!Sample_description = processed data file: master_gene_model.gtf.gz +!Sample_description = processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz +!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence and other artifacts. Trimmed reads with average quality ≥20, ≤3 Ns, and ≥32 bases were mapped to C. reinhardtii genome (Phytozome v5.3.1) using TopHat v2.0.8 with Bowtie v2.1.0. Sensitive and fusion mapping was enabled. Valid intron length was 20bp to 25 kbp and minimum distance between intra-chromosomal fusions was 1 Mbp. The library type “fr-firststrand” stated and read alignments with >3 mismatches were discarded. +!Sample_data_processing = Cufflinks v2.1.1 (modified to work on compact genomes) was used to reconstruct the transcripts guided with the Phytozome v5.3.1 reference transcriptome (See supplementary file: reference_gene_model.gtf.gz). Multi-mapped read correction was turned on and transcript composed of >50% multi-mapped reads or <25 reads were discarded. The remaining transcript assemblies from different time points were merged into a unified set of gene models, which was then compared to the annotated transcriptome. Potential noise was filtered from these predicted transcripts. Sequential steps of filtering criteria were applied as follows; 1). FPKM >0 for both replicates at least at one time point; 2) length of CDS>=50 amino acid; candidate coding regions were predicted based on transcript sequences using TransDecoder script v2013-02-25 from the Trinity package, 3) Remove “noise” transcripts of CuffDiff classes ‘E’, ‘O’ and ‘P’ and single exon transcripts of CuffDiff classes ‘.’, ‘C’ and ‘I’. +!Sample_data_processing = Illumina RTA-1.12 to 1.18 software used for basecalling depending on when library is sequenced. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii genome (Phytozome v5.3.1); C.reinhardtii_v5.3_genomic_scaffold_plastids.fasta.gz +!Sample_data_processing = Supplementary_files_format_and_content: peaks list, tab-delimited text files include FPKM values for each sample and the gene/transcript annotations +!Sample_platform_id = GPL15922 +!Sample_contact_name = Chia-Lin,,Wei +!Sample_contact_email = CWei@lbl.gov +!Sample_contact_phone = +1 (925) 927-2593 +!Sample_contact_laboratory = Sequencing Technologies +!Sample_contact_department = Genomic Technologies +!Sample_contact_institute = DOE Joint Genome Institute +!Sample_contact_address = 2800 Mitchell Drive +!Sample_contact_city = Walnut Creek +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 94598 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02928709 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX658302 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE59629 +!Sample_data_row_count = 0 +^SAMPLE = GSM1440768 +!Sample_title = PolyA Transcripts replicate 2 (Nitrogen starvation 1 hr) +!Sample_geo_accession = GSM1440768 +!Sample_status = Public on Jul 28 2015 +!Sample_submission_date = Jul 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = PolyA Transcripts (Nitrogen starvation 1 hr) +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 4A+ +!Sample_characteristics_ch1 = time: 1 hr +!Sample_treatment_protocol_ch1 = N-free (TAP-N) and SO42--free (TAP-S) media were prepared as described (Boyle et al., 2012; Kropat et al., 2011). For N- and S- starvation conditions, cells were grown to mid-log phase, washed twice with depleted media and re-suspended in TAP-N or TAP-S media to a density of 2x10^6 cells/ml (Boyle et al. 2012). Three acyltransferases and nitrogen-responsive regulator are implicated in nitrogen starvation-induced triacylglycerol accumulation in Chlamydomonas (The Journal of biological chemistry 287, 15811-15825; Kropat et al. 2011). A revised mineral nutrient supplement increases biomass and growth rate in Chlamydomonas reinhardtii (The Plant journal for cell and molecular biology 66, 770-780). +!Sample_growth_protocol_ch1 = C. reinhardtii wild type strain 4a+ was cultured using Tris-acetate-phosphate (TAP) medium. +!Sample_molecule_ch1 = polyA RNA +!Sample_extract_protocol_ch1 = Cells were first lysed and total RNA extracted using Trizol and cleaned up using RNeasy column (Qiagen). PolyA+ RNA was isolated from 10ug of total RNA. +!Sample_extract_protocol_ch1 = RNA was fragmented using RNA Fragmentation Reagents (Ambion). Strand-specific RNA-seq library (Parkhomchuk et al., 2009) was constructed using Illumina DNA Sample Preparation Kit (Illumina) with 10 cycles PCR amplification (Parkhomchuk et al.(2009). Nucleic acids research 37, e123). +!Sample_description = polyAND1hrR2 +!Sample_description = processed data file: master_gene_model.gtf.gz +!Sample_description = processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz +!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence and other artifacts. Trimmed reads with average quality ≥20, ≤3 Ns, and ≥32 bases were mapped to C. reinhardtii genome (Phytozome v5.3.1) using TopHat v2.0.8 with Bowtie v2.1.0. Sensitive and fusion mapping was enabled. Valid intron length was 20bp to 25 kbp and minimum distance between intra-chromosomal fusions was 1 Mbp. The library type “fr-firststrand” stated and read alignments with >3 mismatches were discarded. +!Sample_data_processing = Cufflinks v2.1.1 (modified to work on compact genomes) was used to reconstruct the transcripts guided with the Phytozome v5.3.1 reference transcriptome (See supplementary file: reference_gene_model.gtf.gz). Multi-mapped read correction was turned on and transcript composed of >50% multi-mapped reads or <25 reads were discarded. The remaining transcript assemblies from different time points were merged into a unified set of gene models, which was then compared to the annotated transcriptome. Potential noise was filtered from these predicted transcripts. Sequential steps of filtering criteria were applied as follows; 1). FPKM >0 for both replicates at least at one time point; 2) length of CDS>=50 amino acid; candidate coding regions were predicted based on transcript sequences using TransDecoder script v2013-02-25 from the Trinity package, 3) Remove “noise” transcripts of CuffDiff classes ‘E’, ‘O’ and ‘P’ and single exon transcripts of CuffDiff classes ‘.’, ‘C’ and ‘I’. +!Sample_data_processing = Illumina RTA-1.12 to 1.18 software used for basecalling depending on when library is sequenced. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii genome (Phytozome v5.3.1); C.reinhardtii_v5.3_genomic_scaffold_plastids.fasta.gz +!Sample_data_processing = Supplementary_files_format_and_content: peaks list, tab-delimited text files include FPKM values for each sample and the gene/transcript annotations +!Sample_platform_id = GPL15922 +!Sample_contact_name = Chia-Lin,,Wei +!Sample_contact_email = CWei@lbl.gov +!Sample_contact_phone = +1 (925) 927-2593 +!Sample_contact_laboratory = Sequencing Technologies +!Sample_contact_department = Genomic Technologies +!Sample_contact_institute = DOE Joint Genome Institute +!Sample_contact_address = 2800 Mitchell Drive +!Sample_contact_city = Walnut Creek +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 94598 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02928713 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX658303 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE59629 +!Sample_data_row_count = 0 +^SAMPLE = GSM1440769 +!Sample_title = PolyA Transcripts replicate 1 (Nitrogen starvation 2 hr) +!Sample_geo_accession = GSM1440769 +!Sample_status = Public on Jul 28 2015 +!Sample_submission_date = Jul 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = PolyA Transcripts (Nitrogen starvation 2 hr) +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 4A+ +!Sample_characteristics_ch1 = time: 2 hr +!Sample_treatment_protocol_ch1 = N-free (TAP-N) and SO42--free (TAP-S) media were prepared as described (Boyle et al., 2012; Kropat et al., 2011). For N- and S- starvation conditions, cells were grown to mid-log phase, washed twice with depleted media and re-suspended in TAP-N or TAP-S media to a density of 2x10^6 cells/ml (Boyle et al. 2012). Three acyltransferases and nitrogen-responsive regulator are implicated in nitrogen starvation-induced triacylglycerol accumulation in Chlamydomonas (The Journal of biological chemistry 287, 15811-15825; Kropat et al. 2011). A revised mineral nutrient supplement increases biomass and growth rate in Chlamydomonas reinhardtii (The Plant journal for cell and molecular biology 66, 770-780). +!Sample_growth_protocol_ch1 = C. reinhardtii wild type strain 4a+ was cultured using Tris-acetate-phosphate (TAP) medium. +!Sample_molecule_ch1 = polyA RNA +!Sample_extract_protocol_ch1 = Cells were first lysed and total RNA extracted using Trizol and cleaned up using RNeasy column (Qiagen). PolyA+ RNA was isolated from 10ug of total RNA. +!Sample_extract_protocol_ch1 = RNA was fragmented using RNA Fragmentation Reagents (Ambion). Strand-specific RNA-seq library (Parkhomchuk et al., 2009) was constructed using Illumina DNA Sample Preparation Kit (Illumina) with 10 cycles PCR amplification (Parkhomchuk et al.(2009). Nucleic acids research 37, e123). +!Sample_description = polyAND2hrR1 +!Sample_description = processed data file: master_gene_model.gtf.gz +!Sample_description = processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz +!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence and other artifacts. Trimmed reads with average quality ≥20, ≤3 Ns, and ≥32 bases were mapped to C. reinhardtii genome (Phytozome v5.3.1) using TopHat v2.0.8 with Bowtie v2.1.0. Sensitive and fusion mapping was enabled. Valid intron length was 20bp to 25 kbp and minimum distance between intra-chromosomal fusions was 1 Mbp. The library type “fr-firststrand” stated and read alignments with >3 mismatches were discarded. +!Sample_data_processing = Cufflinks v2.1.1 (modified to work on compact genomes) was used to reconstruct the transcripts guided with the Phytozome v5.3.1 reference transcriptome (See supplementary file: reference_gene_model.gtf.gz). Multi-mapped read correction was turned on and transcript composed of >50% multi-mapped reads or <25 reads were discarded. The remaining transcript assemblies from different time points were merged into a unified set of gene models, which was then compared to the annotated transcriptome. Potential noise was filtered from these predicted transcripts. Sequential steps of filtering criteria were applied as follows; 1). FPKM >0 for both replicates at least at one time point; 2) length of CDS>=50 amino acid; candidate coding regions were predicted based on transcript sequences using TransDecoder script v2013-02-25 from the Trinity package, 3) Remove “noise” transcripts of CuffDiff classes ‘E’, ‘O’ and ‘P’ and single exon transcripts of CuffDiff classes ‘.’, ‘C’ and ‘I’. +!Sample_data_processing = Illumina RTA-1.12 to 1.18 software used for basecalling depending on when library is sequenced. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii genome (Phytozome v5.3.1); C.reinhardtii_v5.3_genomic_scaffold_plastids.fasta.gz +!Sample_data_processing = Supplementary_files_format_and_content: peaks list, tab-delimited text files include FPKM values for each sample and the gene/transcript annotations +!Sample_platform_id = GPL15922 +!Sample_contact_name = Chia-Lin,,Wei +!Sample_contact_email = CWei@lbl.gov +!Sample_contact_phone = +1 (925) 927-2593 +!Sample_contact_laboratory = Sequencing Technologies +!Sample_contact_department = Genomic Technologies +!Sample_contact_institute = DOE Joint Genome Institute +!Sample_contact_address = 2800 Mitchell Drive +!Sample_contact_city = Walnut Creek +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 94598 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02928714 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX658304 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE59629 +!Sample_data_row_count = 0 +^SAMPLE = GSM1440770 +!Sample_title = PolyA Transcripts replicate 2 (Nitrogen starvation 2 hr) +!Sample_geo_accession = GSM1440770 +!Sample_status = Public on Jul 28 2015 +!Sample_submission_date = Jul 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = PolyA Transcripts (Nitrogen starvation 2 hr) +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 4A+ +!Sample_characteristics_ch1 = time: 2 hr +!Sample_treatment_protocol_ch1 = N-free (TAP-N) and SO42--free (TAP-S) media were prepared as described (Boyle et al., 2012; Kropat et al., 2011). For N- and S- starvation conditions, cells were grown to mid-log phase, washed twice with depleted media and re-suspended in TAP-N or TAP-S media to a density of 2x10^6 cells/ml (Boyle et al. 2012). Three acyltransferases and nitrogen-responsive regulator are implicated in nitrogen starvation-induced triacylglycerol accumulation in Chlamydomonas (The Journal of biological chemistry 287, 15811-15825; Kropat et al. 2011). A revised mineral nutrient supplement increases biomass and growth rate in Chlamydomonas reinhardtii (The Plant journal for cell and molecular biology 66, 770-780). +!Sample_growth_protocol_ch1 = C. reinhardtii wild type strain 4a+ was cultured using Tris-acetate-phosphate (TAP) medium. +!Sample_molecule_ch1 = polyA RNA +!Sample_extract_protocol_ch1 = Cells were first lysed and total RNA extracted using Trizol and cleaned up using RNeasy column (Qiagen). PolyA+ RNA was isolated from 10ug of total RNA. +!Sample_extract_protocol_ch1 = RNA was fragmented using RNA Fragmentation Reagents (Ambion). Strand-specific RNA-seq library (Parkhomchuk et al., 2009) was constructed using Illumina DNA Sample Preparation Kit (Illumina) with 10 cycles PCR amplification (Parkhomchuk et al.(2009). Nucleic acids research 37, e123). +!Sample_description = polyAND2hrR2 +!Sample_description = processed data file: master_gene_model.gtf.gz +!Sample_description = processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz +!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence and other artifacts. Trimmed reads with average quality ≥20, ≤3 Ns, and ≥32 bases were mapped to C. reinhardtii genome (Phytozome v5.3.1) using TopHat v2.0.8 with Bowtie v2.1.0. Sensitive and fusion mapping was enabled. Valid intron length was 20bp to 25 kbp and minimum distance between intra-chromosomal fusions was 1 Mbp. The library type “fr-firststrand” stated and read alignments with >3 mismatches were discarded. +!Sample_data_processing = Cufflinks v2.1.1 (modified to work on compact genomes) was used to reconstruct the transcripts guided with the Phytozome v5.3.1 reference transcriptome (See supplementary file: reference_gene_model.gtf.gz). Multi-mapped read correction was turned on and transcript composed of >50% multi-mapped reads or <25 reads were discarded. The remaining transcript assemblies from different time points were merged into a unified set of gene models, which was then compared to the annotated transcriptome. Potential noise was filtered from these predicted transcripts. Sequential steps of filtering criteria were applied as follows; 1). FPKM >0 for both replicates at least at one time point; 2) length of CDS>=50 amino acid; candidate coding regions were predicted based on transcript sequences using TransDecoder script v2013-02-25 from the Trinity package, 3) Remove “noise” transcripts of CuffDiff classes ‘E’, ‘O’ and ‘P’ and single exon transcripts of CuffDiff classes ‘.’, ‘C’ and ‘I’. +!Sample_data_processing = Illumina RTA-1.12 to 1.18 software used for basecalling depending on when library is sequenced. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii genome (Phytozome v5.3.1); C.reinhardtii_v5.3_genomic_scaffold_plastids.fasta.gz +!Sample_data_processing = Supplementary_files_format_and_content: peaks list, tab-delimited text files include FPKM values for each sample and the gene/transcript annotations +!Sample_platform_id = GPL15922 +!Sample_contact_name = Chia-Lin,,Wei +!Sample_contact_email = CWei@lbl.gov +!Sample_contact_phone = +1 (925) 927-2593 +!Sample_contact_laboratory = Sequencing Technologies +!Sample_contact_department = Genomic Technologies +!Sample_contact_institute = DOE Joint Genome Institute +!Sample_contact_address = 2800 Mitchell Drive +!Sample_contact_city = Walnut Creek +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 94598 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02928715 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX658305 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE59629 +!Sample_data_row_count = 0 +^SAMPLE = GSM1440771 +!Sample_title = PolyA Transcripts replicate 1 (Nitrogen starvation 6 hr) +!Sample_geo_accession = GSM1440771 +!Sample_status = Public on Jul 28 2015 +!Sample_submission_date = Jul 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = PolyA Transcripts (Nitrogen starvation 6 hr) +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 4A+ +!Sample_characteristics_ch1 = time: 6 hr +!Sample_treatment_protocol_ch1 = N-free (TAP-N) and SO42--free (TAP-S) media were prepared as described (Boyle et al., 2012; Kropat et al., 2011). For N- and S- starvation conditions, cells were grown to mid-log phase, washed twice with depleted media and re-suspended in TAP-N or TAP-S media to a density of 2x10^6 cells/ml (Boyle et al. 2012). Three acyltransferases and nitrogen-responsive regulator are implicated in nitrogen starvation-induced triacylglycerol accumulation in Chlamydomonas (The Journal of biological chemistry 287, 15811-15825; Kropat et al. 2011). A revised mineral nutrient supplement increases biomass and growth rate in Chlamydomonas reinhardtii (The Plant journal for cell and molecular biology 66, 770-780). +!Sample_growth_protocol_ch1 = C. reinhardtii wild type strain 4a+ was cultured using Tris-acetate-phosphate (TAP) medium. +!Sample_molecule_ch1 = polyA RNA +!Sample_extract_protocol_ch1 = Cells were first lysed and total RNA extracted using Trizol and cleaned up using RNeasy column (Qiagen). PolyA+ RNA was isolated from 10ug of total RNA. +!Sample_extract_protocol_ch1 = RNA was fragmented using RNA Fragmentation Reagents (Ambion). Strand-specific RNA-seq library (Parkhomchuk et al., 2009) was constructed using Illumina DNA Sample Preparation Kit (Illumina) with 10 cycles PCR amplification (Parkhomchuk et al.(2009). Nucleic acids research 37, e123). +!Sample_description = polyAND6hrR1 +!Sample_description = processed data file: master_gene_model.gtf.gz +!Sample_description = processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz +!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence and other artifacts. Trimmed reads with average quality ≥20, ≤3 Ns, and ≥32 bases were mapped to C. reinhardtii genome (Phytozome v5.3.1) using TopHat v2.0.8 with Bowtie v2.1.0. Sensitive and fusion mapping was enabled. Valid intron length was 20bp to 25 kbp and minimum distance between intra-chromosomal fusions was 1 Mbp. The library type “fr-firststrand” stated and read alignments with >3 mismatches were discarded. +!Sample_data_processing = Cufflinks v2.1.1 (modified to work on compact genomes) was used to reconstruct the transcripts guided with the Phytozome v5.3.1 reference transcriptome (See supplementary file: reference_gene_model.gtf.gz). Multi-mapped read correction was turned on and transcript composed of >50% multi-mapped reads or <25 reads were discarded. The remaining transcript assemblies from different time points were merged into a unified set of gene models, which was then compared to the annotated transcriptome. Potential noise was filtered from these predicted transcripts. Sequential steps of filtering criteria were applied as follows; 1). FPKM >0 for both replicates at least at one time point; 2) length of CDS>=50 amino acid; candidate coding regions were predicted based on transcript sequences using TransDecoder script v2013-02-25 from the Trinity package, 3) Remove “noise” transcripts of CuffDiff classes ‘E’, ‘O’ and ‘P’ and single exon transcripts of CuffDiff classes ‘.’, ‘C’ and ‘I’. +!Sample_data_processing = Illumina RTA-1.12 to 1.18 software used for basecalling depending on when library is sequenced. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii genome (Phytozome v5.3.1); C.reinhardtii_v5.3_genomic_scaffold_plastids.fasta.gz +!Sample_data_processing = Supplementary_files_format_and_content: peaks list, tab-delimited text files include FPKM values for each sample and the gene/transcript annotations +!Sample_platform_id = GPL15922 +!Sample_contact_name = Chia-Lin,,Wei +!Sample_contact_email = CWei@lbl.gov +!Sample_contact_phone = +1 (925) 927-2593 +!Sample_contact_laboratory = Sequencing Technologies +!Sample_contact_department = Genomic Technologies +!Sample_contact_institute = DOE Joint Genome Institute +!Sample_contact_address = 2800 Mitchell Drive +!Sample_contact_city = Walnut Creek +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 94598 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02928716 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX658306 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE59629 +!Sample_data_row_count = 0 +^SAMPLE = GSM1440772 +!Sample_title = PolyA Transcripts replicate 2 (Nitrogen starvation 6 hr) +!Sample_geo_accession = GSM1440772 +!Sample_status = Public on Jul 28 2015 +!Sample_submission_date = Jul 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = PolyA Transcripts (Nitrogen starvation 6 hr) +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 4A+ +!Sample_characteristics_ch1 = time: 6 hr +!Sample_treatment_protocol_ch1 = N-free (TAP-N) and SO42--free (TAP-S) media were prepared as described (Boyle et al., 2012; Kropat et al., 2011). For N- and S- starvation conditions, cells were grown to mid-log phase, washed twice with depleted media and re-suspended in TAP-N or TAP-S media to a density of 2x10^6 cells/ml (Boyle et al. 2012). Three acyltransferases and nitrogen-responsive regulator are implicated in nitrogen starvation-induced triacylglycerol accumulation in Chlamydomonas (The Journal of biological chemistry 287, 15811-15825; Kropat et al. 2011). A revised mineral nutrient supplement increases biomass and growth rate in Chlamydomonas reinhardtii (The Plant journal for cell and molecular biology 66, 770-780). +!Sample_growth_protocol_ch1 = C. reinhardtii wild type strain 4a+ was cultured using Tris-acetate-phosphate (TAP) medium. +!Sample_molecule_ch1 = polyA RNA +!Sample_extract_protocol_ch1 = Cells were first lysed and total RNA extracted using Trizol and cleaned up using RNeasy column (Qiagen). PolyA+ RNA was isolated from 10ug of total RNA. +!Sample_extract_protocol_ch1 = RNA was fragmented using RNA Fragmentation Reagents (Ambion). Strand-specific RNA-seq library (Parkhomchuk et al., 2009) was constructed using Illumina DNA Sample Preparation Kit (Illumina) with 10 cycles PCR amplification (Parkhomchuk et al.(2009). Nucleic acids research 37, e123). +!Sample_description = polyAND6hrR2 +!Sample_description = processed data file: master_gene_model.gtf.gz +!Sample_description = processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz +!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence and other artifacts. Trimmed reads with average quality ≥20, ≤3 Ns, and ≥32 bases were mapped to C. reinhardtii genome (Phytozome v5.3.1) using TopHat v2.0.8 with Bowtie v2.1.0. Sensitive and fusion mapping was enabled. Valid intron length was 20bp to 25 kbp and minimum distance between intra-chromosomal fusions was 1 Mbp. The library type “fr-firststrand” stated and read alignments with >3 mismatches were discarded. +!Sample_data_processing = Cufflinks v2.1.1 (modified to work on compact genomes) was used to reconstruct the transcripts guided with the Phytozome v5.3.1 reference transcriptome (See supplementary file: reference_gene_model.gtf.gz). Multi-mapped read correction was turned on and transcript composed of >50% multi-mapped reads or <25 reads were discarded. The remaining transcript assemblies from different time points were merged into a unified set of gene models, which was then compared to the annotated transcriptome. Potential noise was filtered from these predicted transcripts. Sequential steps of filtering criteria were applied as follows; 1). FPKM >0 for both replicates at least at one time point; 2) length of CDS>=50 amino acid; candidate coding regions were predicted based on transcript sequences using TransDecoder script v2013-02-25 from the Trinity package, 3) Remove “noise” transcripts of CuffDiff classes ‘E’, ‘O’ and ‘P’ and single exon transcripts of CuffDiff classes ‘.’, ‘C’ and ‘I’. +!Sample_data_processing = Illumina RTA-1.12 to 1.18 software used for basecalling depending on when library is sequenced. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii genome (Phytozome v5.3.1); C.reinhardtii_v5.3_genomic_scaffold_plastids.fasta.gz +!Sample_data_processing = Supplementary_files_format_and_content: peaks list, tab-delimited text files include FPKM values for each sample and the gene/transcript annotations +!Sample_platform_id = GPL15922 +!Sample_contact_name = Chia-Lin,,Wei +!Sample_contact_email = CWei@lbl.gov +!Sample_contact_phone = +1 (925) 927-2593 +!Sample_contact_laboratory = Sequencing Technologies +!Sample_contact_department = Genomic Technologies +!Sample_contact_institute = DOE Joint Genome Institute +!Sample_contact_address = 2800 Mitchell Drive +!Sample_contact_city = Walnut Creek +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 94598 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02928717 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX658307 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE59629 +!Sample_data_row_count = 0 +^SAMPLE = GSM1440773 +!Sample_title = PolyA Transcripts replicate 1 (Nitrogen starvation 8 hr) +!Sample_geo_accession = GSM1440773 +!Sample_status = Public on Jul 28 2015 +!Sample_submission_date = Jul 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = PolyA Transcripts (Nitrogen starvation 8 hr) +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 4A+ +!Sample_characteristics_ch1 = time: 8 hr +!Sample_treatment_protocol_ch1 = N-free (TAP-N) and SO42--free (TAP-S) media were prepared as described (Boyle et al., 2012; Kropat et al., 2011). For N- and S- starvation conditions, cells were grown to mid-log phase, washed twice with depleted media and re-suspended in TAP-N or TAP-S media to a density of 2x10^6 cells/ml (Boyle et al. 2012). Three acyltransferases and nitrogen-responsive regulator are implicated in nitrogen starvation-induced triacylglycerol accumulation in Chlamydomonas (The Journal of biological chemistry 287, 15811-15825; Kropat et al. 2011). A revised mineral nutrient supplement increases biomass and growth rate in Chlamydomonas reinhardtii (The Plant journal for cell and molecular biology 66, 770-780). +!Sample_growth_protocol_ch1 = C. reinhardtii wild type strain 4a+ was cultured using Tris-acetate-phosphate (TAP) medium. +!Sample_molecule_ch1 = polyA RNA +!Sample_extract_protocol_ch1 = Cells were first lysed and total RNA extracted using Trizol and cleaned up using RNeasy column (Qiagen). PolyA+ RNA was isolated from 10ug of total RNA. +!Sample_extract_protocol_ch1 = RNA was fragmented using RNA Fragmentation Reagents (Ambion). Strand-specific RNA-seq library (Parkhomchuk et al., 2009) was constructed using Illumina DNA Sample Preparation Kit (Illumina) with 10 cycles PCR amplification (Parkhomchuk et al.(2009). Nucleic acids research 37, e123). +!Sample_description = polyAND8hrR1 +!Sample_description = processed data file: master_gene_model.gtf.gz +!Sample_description = processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz +!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence and other artifacts. Trimmed reads with average quality ≥20, ≤3 Ns, and ≥32 bases were mapped to C. reinhardtii genome (Phytozome v5.3.1) using TopHat v2.0.8 with Bowtie v2.1.0. Sensitive and fusion mapping was enabled. Valid intron length was 20bp to 25 kbp and minimum distance between intra-chromosomal fusions was 1 Mbp. The library type “fr-firststrand” stated and read alignments with >3 mismatches were discarded. +!Sample_data_processing = Cufflinks v2.1.1 (modified to work on compact genomes) was used to reconstruct the transcripts guided with the Phytozome v5.3.1 reference transcriptome (See supplementary file: reference_gene_model.gtf.gz). Multi-mapped read correction was turned on and transcript composed of >50% multi-mapped reads or <25 reads were discarded. The remaining transcript assemblies from different time points were merged into a unified set of gene models, which was then compared to the annotated transcriptome. Potential noise was filtered from these predicted transcripts. Sequential steps of filtering criteria were applied as follows; 1). FPKM >0 for both replicates at least at one time point; 2) length of CDS>=50 amino acid; candidate coding regions were predicted based on transcript sequences using TransDecoder script v2013-02-25 from the Trinity package, 3) Remove “noise” transcripts of CuffDiff classes ‘E’, ‘O’ and ‘P’ and single exon transcripts of CuffDiff classes ‘.’, ‘C’ and ‘I’. +!Sample_data_processing = Illumina RTA-1.12 to 1.18 software used for basecalling depending on when library is sequenced. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii genome (Phytozome v5.3.1); C.reinhardtii_v5.3_genomic_scaffold_plastids.fasta.gz +!Sample_data_processing = Supplementary_files_format_and_content: peaks list, tab-delimited text files include FPKM values for each sample and the gene/transcript annotations +!Sample_platform_id = GPL15922 +!Sample_contact_name = Chia-Lin,,Wei +!Sample_contact_email = CWei@lbl.gov +!Sample_contact_phone = +1 (925) 927-2593 +!Sample_contact_laboratory = Sequencing Technologies +!Sample_contact_department = Genomic Technologies +!Sample_contact_institute = DOE Joint Genome Institute +!Sample_contact_address = 2800 Mitchell Drive +!Sample_contact_city = Walnut Creek +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 94598 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02928710 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX658308 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE59629 +!Sample_data_row_count = 0 +^SAMPLE = GSM1440774 +!Sample_title = PolyA Transcripts replicate 2 (Nitrogen starvation 8 hr) +!Sample_geo_accession = GSM1440774 +!Sample_status = Public on Jul 28 2015 +!Sample_submission_date = Jul 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = PolyA Transcripts (Nitrogen starvation 8 hr) +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 4A+ +!Sample_characteristics_ch1 = time: 8 hr +!Sample_treatment_protocol_ch1 = N-free (TAP-N) and SO42--free (TAP-S) media were prepared as described (Boyle et al., 2012; Kropat et al., 2011). For N- and S- starvation conditions, cells were grown to mid-log phase, washed twice with depleted media and re-suspended in TAP-N or TAP-S media to a density of 2x10^6 cells/ml (Boyle et al. 2012). Three acyltransferases and nitrogen-responsive regulator are implicated in nitrogen starvation-induced triacylglycerol accumulation in Chlamydomonas (The Journal of biological chemistry 287, 15811-15825; Kropat et al. 2011). A revised mineral nutrient supplement increases biomass and growth rate in Chlamydomonas reinhardtii (The Plant journal for cell and molecular biology 66, 770-780). +!Sample_growth_protocol_ch1 = C. reinhardtii wild type strain 4a+ was cultured using Tris-acetate-phosphate (TAP) medium. +!Sample_molecule_ch1 = polyA RNA +!Sample_extract_protocol_ch1 = Cells were first lysed and total RNA extracted using Trizol and cleaned up using RNeasy column (Qiagen). PolyA+ RNA was isolated from 10ug of total RNA. +!Sample_extract_protocol_ch1 = RNA was fragmented using RNA Fragmentation Reagents (Ambion). Strand-specific RNA-seq library (Parkhomchuk et al., 2009) was constructed using Illumina DNA Sample Preparation Kit (Illumina) with 10 cycles PCR amplification (Parkhomchuk et al.(2009). Nucleic acids research 37, e123). +!Sample_description = polyAND8hrR2 +!Sample_description = processed data file: master_gene_model.gtf.gz +!Sample_description = processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz +!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence and other artifacts. Trimmed reads with average quality ≥20, ≤3 Ns, and ≥32 bases were mapped to C. reinhardtii genome (Phytozome v5.3.1) using TopHat v2.0.8 with Bowtie v2.1.0. Sensitive and fusion mapping was enabled. Valid intron length was 20bp to 25 kbp and minimum distance between intra-chromosomal fusions was 1 Mbp. The library type “fr-firststrand” stated and read alignments with >3 mismatches were discarded. +!Sample_data_processing = Cufflinks v2.1.1 (modified to work on compact genomes) was used to reconstruct the transcripts guided with the Phytozome v5.3.1 reference transcriptome (See supplementary file: reference_gene_model.gtf.gz). Multi-mapped read correction was turned on and transcript composed of >50% multi-mapped reads or <25 reads were discarded. The remaining transcript assemblies from different time points were merged into a unified set of gene models, which was then compared to the annotated transcriptome. Potential noise was filtered from these predicted transcripts. Sequential steps of filtering criteria were applied as follows; 1). FPKM >0 for both replicates at least at one time point; 2) length of CDS>=50 amino acid; candidate coding regions were predicted based on transcript sequences using TransDecoder script v2013-02-25 from the Trinity package, 3) Remove “noise” transcripts of CuffDiff classes ‘E’, ‘O’ and ‘P’ and single exon transcripts of CuffDiff classes ‘.’, ‘C’ and ‘I’. +!Sample_data_processing = Illumina RTA-1.12 to 1.18 software used for basecalling depending on when library is sequenced. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii genome (Phytozome v5.3.1); C.reinhardtii_v5.3_genomic_scaffold_plastids.fasta.gz +!Sample_data_processing = Supplementary_files_format_and_content: peaks list, tab-delimited text files include FPKM values for each sample and the gene/transcript annotations +!Sample_platform_id = GPL15922 +!Sample_contact_name = Chia-Lin,,Wei +!Sample_contact_email = CWei@lbl.gov +!Sample_contact_phone = +1 (925) 927-2593 +!Sample_contact_laboratory = Sequencing Technologies +!Sample_contact_department = Genomic Technologies +!Sample_contact_institute = DOE Joint Genome Institute +!Sample_contact_address = 2800 Mitchell Drive +!Sample_contact_city = Walnut Creek +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 94598 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02928711 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX658309 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE59629 +!Sample_data_row_count = 0 +^SAMPLE = GSM1440775 +!Sample_title = PolyA Transcripts replicate 1 (Nitrogen starvation 24 hr) +!Sample_geo_accession = GSM1440775 +!Sample_status = Public on Jul 28 2015 +!Sample_submission_date = Jul 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = PolyA Transcripts (Nitrogen starvation 24 hr) +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 4A+ +!Sample_characteristics_ch1 = time: 24 hr +!Sample_treatment_protocol_ch1 = N-free (TAP-N) and SO42--free (TAP-S) media were prepared as described (Boyle et al., 2012; Kropat et al., 2011). For N- and S- starvation conditions, cells were grown to mid-log phase, washed twice with depleted media and re-suspended in TAP-N or TAP-S media to a density of 2x10^6 cells/ml (Boyle et al. 2012). Three acyltransferases and nitrogen-responsive regulator are implicated in nitrogen starvation-induced triacylglycerol accumulation in Chlamydomonas (The Journal of biological chemistry 287, 15811-15825; Kropat et al. 2011). A revised mineral nutrient supplement increases biomass and growth rate in Chlamydomonas reinhardtii (The Plant journal for cell and molecular biology 66, 770-780). +!Sample_growth_protocol_ch1 = C. reinhardtii wild type strain 4a+ was cultured using Tris-acetate-phosphate (TAP) medium. +!Sample_molecule_ch1 = polyA RNA +!Sample_extract_protocol_ch1 = Cells were first lysed and total RNA extracted using Trizol and cleaned up using RNeasy column (Qiagen). PolyA+ RNA was isolated from 10ug of total RNA. +!Sample_extract_protocol_ch1 = RNA was fragmented using RNA Fragmentation Reagents (Ambion). Strand-specific RNA-seq library (Parkhomchuk et al., 2009) was constructed using Illumina DNA Sample Preparation Kit (Illumina) with 10 cycles PCR amplification (Parkhomchuk et al.(2009). Nucleic acids research 37, e123). +!Sample_description = polyAND24hrR1 +!Sample_description = processed data file: master_gene_model.gtf.gz +!Sample_description = processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz +!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence and other artifacts. Trimmed reads with average quality ≥20, ≤3 Ns, and ≥32 bases were mapped to C. reinhardtii genome (Phytozome v5.3.1) using TopHat v2.0.8 with Bowtie v2.1.0. Sensitive and fusion mapping was enabled. Valid intron length was 20bp to 25 kbp and minimum distance between intra-chromosomal fusions was 1 Mbp. The library type “fr-firststrand” stated and read alignments with >3 mismatches were discarded. +!Sample_data_processing = Cufflinks v2.1.1 (modified to work on compact genomes) was used to reconstruct the transcripts guided with the Phytozome v5.3.1 reference transcriptome (See supplementary file: reference_gene_model.gtf.gz). Multi-mapped read correction was turned on and transcript composed of >50% multi-mapped reads or <25 reads were discarded. The remaining transcript assemblies from different time points were merged into a unified set of gene models, which was then compared to the annotated transcriptome. Potential noise was filtered from these predicted transcripts. Sequential steps of filtering criteria were applied as follows; 1). FPKM >0 for both replicates at least at one time point; 2) length of CDS>=50 amino acid; candidate coding regions were predicted based on transcript sequences using TransDecoder script v2013-02-25 from the Trinity package, 3) Remove “noise” transcripts of CuffDiff classes ‘E’, ‘O’ and ‘P’ and single exon transcripts of CuffDiff classes ‘.’, ‘C’ and ‘I’. +!Sample_data_processing = Illumina RTA-1.12 to 1.18 software used for basecalling depending on when library is sequenced. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii genome (Phytozome v5.3.1); C.reinhardtii_v5.3_genomic_scaffold_plastids.fasta.gz +!Sample_data_processing = Supplementary_files_format_and_content: peaks list, tab-delimited text files include FPKM values for each sample and the gene/transcript annotations +!Sample_platform_id = GPL15922 +!Sample_contact_name = Chia-Lin,,Wei +!Sample_contact_email = CWei@lbl.gov +!Sample_contact_phone = +1 (925) 927-2593 +!Sample_contact_laboratory = Sequencing Technologies +!Sample_contact_department = Genomic Technologies +!Sample_contact_institute = DOE Joint Genome Institute +!Sample_contact_address = 2800 Mitchell Drive +!Sample_contact_city = Walnut Creek +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 94598 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02928712 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX658310 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE59629 +!Sample_data_row_count = 0 +^SAMPLE = GSM1440776 +!Sample_title = PolyA Transcripts replicate 2 (Nitrogen starvation 24 hr) +!Sample_geo_accession = GSM1440776 +!Sample_status = Public on Jul 28 2015 +!Sample_submission_date = Jul 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = PolyA Transcripts (Nitrogen starvation 24 hr) +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 4A+ +!Sample_characteristics_ch1 = time: 24 hr +!Sample_treatment_protocol_ch1 = N-free (TAP-N) and SO42--free (TAP-S) media were prepared as described (Boyle et al., 2012; Kropat et al., 2011). For N- and S- starvation conditions, cells were grown to mid-log phase, washed twice with depleted media and re-suspended in TAP-N or TAP-S media to a density of 2x10^6 cells/ml (Boyle et al. 2012). Three acyltransferases and nitrogen-responsive regulator are implicated in nitrogen starvation-induced triacylglycerol accumulation in Chlamydomonas (The Journal of biological chemistry 287, 15811-15825; Kropat et al. 2011). A revised mineral nutrient supplement increases biomass and growth rate in Chlamydomonas reinhardtii (The Plant journal for cell and molecular biology 66, 770-780). +!Sample_growth_protocol_ch1 = C. reinhardtii wild type strain 4a+ was cultured using Tris-acetate-phosphate (TAP) medium. +!Sample_molecule_ch1 = polyA RNA +!Sample_extract_protocol_ch1 = Cells were first lysed and total RNA extracted using Trizol and cleaned up using RNeasy column (Qiagen). PolyA+ RNA was isolated from 10ug of total RNA. +!Sample_extract_protocol_ch1 = RNA was fragmented using RNA Fragmentation Reagents (Ambion). Strand-specific RNA-seq library (Parkhomchuk et al., 2009) was constructed using Illumina DNA Sample Preparation Kit (Illumina) with 10 cycles PCR amplification (Parkhomchuk et al.(2009). Nucleic acids research 37, e123). +!Sample_description = polyAND24hrR2 +!Sample_description = processed data file: master_gene_model.gtf.gz +!Sample_description = processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz +!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence and other artifacts. Trimmed reads with average quality ≥20, ≤3 Ns, and ≥32 bases were mapped to C. reinhardtii genome (Phytozome v5.3.1) using TopHat v2.0.8 with Bowtie v2.1.0. Sensitive and fusion mapping was enabled. Valid intron length was 20bp to 25 kbp and minimum distance between intra-chromosomal fusions was 1 Mbp. The library type “fr-firststrand” stated and read alignments with >3 mismatches were discarded. +!Sample_data_processing = Cufflinks v2.1.1 (modified to work on compact genomes) was used to reconstruct the transcripts guided with the Phytozome v5.3.1 reference transcriptome (See supplementary file: reference_gene_model.gtf.gz). Multi-mapped read correction was turned on and transcript composed of >50% multi-mapped reads or <25 reads were discarded. The remaining transcript assemblies from different time points were merged into a unified set of gene models, which was then compared to the annotated transcriptome. Potential noise was filtered from these predicted transcripts. Sequential steps of filtering criteria were applied as follows; 1). FPKM >0 for both replicates at least at one time point; 2) length of CDS>=50 amino acid; candidate coding regions were predicted based on transcript sequences using TransDecoder script v2013-02-25 from the Trinity package, 3) Remove “noise” transcripts of CuffDiff classes ‘E’, ‘O’ and ‘P’ and single exon transcripts of CuffDiff classes ‘.’, ‘C’ and ‘I’. +!Sample_data_processing = Illumina RTA-1.12 to 1.18 software used for basecalling depending on when library is sequenced. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii genome (Phytozome v5.3.1); C.reinhardtii_v5.3_genomic_scaffold_plastids.fasta.gz +!Sample_data_processing = Supplementary_files_format_and_content: peaks list, tab-delimited text files include FPKM values for each sample and the gene/transcript annotations +!Sample_platform_id = GPL15922 +!Sample_contact_name = Chia-Lin,,Wei +!Sample_contact_email = CWei@lbl.gov +!Sample_contact_phone = +1 (925) 927-2593 +!Sample_contact_laboratory = Sequencing Technologies +!Sample_contact_department = Genomic Technologies +!Sample_contact_institute = DOE Joint Genome Institute +!Sample_contact_address = 2800 Mitchell Drive +!Sample_contact_city = Walnut Creek +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 94598 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02928718 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX658311 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE59629 +!Sample_data_row_count = 0 +^SAMPLE = GSM1440777 +!Sample_title = PolyA Transcripts replicate 1 (Nitrogen starvation 48 hr) +!Sample_geo_accession = GSM1440777 +!Sample_status = Public on Jul 28 2015 +!Sample_submission_date = Jul 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = PolyA Transcripts (Nitrogen starvation 48 hr) +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 4A+ +!Sample_characteristics_ch1 = time: 48 hr +!Sample_treatment_protocol_ch1 = N-free (TAP-N) and SO42--free (TAP-S) media were prepared as described (Boyle et al., 2012; Kropat et al., 2011). For N- and S- starvation conditions, cells were grown to mid-log phase, washed twice with depleted media and re-suspended in TAP-N or TAP-S media to a density of 2x10^6 cells/ml (Boyle et al. 2012). Three acyltransferases and nitrogen-responsive regulator are implicated in nitrogen starvation-induced triacylglycerol accumulation in Chlamydomonas (The Journal of biological chemistry 287, 15811-15825; Kropat et al. 2011). A revised mineral nutrient supplement increases biomass and growth rate in Chlamydomonas reinhardtii (The Plant journal for cell and molecular biology 66, 770-780). +!Sample_growth_protocol_ch1 = C. reinhardtii wild type strain 4a+ was cultured using Tris-acetate-phosphate (TAP) medium. +!Sample_molecule_ch1 = polyA RNA +!Sample_extract_protocol_ch1 = Cells were first lysed and total RNA extracted using Trizol and cleaned up using RNeasy column (Qiagen). PolyA+ RNA was isolated from 10ug of total RNA. +!Sample_extract_protocol_ch1 = RNA was fragmented using RNA Fragmentation Reagents (Ambion). Strand-specific RNA-seq library (Parkhomchuk et al., 2009) was constructed using Illumina DNA Sample Preparation Kit (Illumina) with 10 cycles PCR amplification (Parkhomchuk et al.(2009). Nucleic acids research 37, e123). +!Sample_description = polyAND48hrR1 +!Sample_description = processed data file: master_gene_model.gtf.gz +!Sample_description = processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz +!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence and other artifacts. Trimmed reads with average quality ≥20, ≤3 Ns, and ≥32 bases were mapped to C. reinhardtii genome (Phytozome v5.3.1) using TopHat v2.0.8 with Bowtie v2.1.0. Sensitive and fusion mapping was enabled. Valid intron length was 20bp to 25 kbp and minimum distance between intra-chromosomal fusions was 1 Mbp. The library type “fr-firststrand” stated and read alignments with >3 mismatches were discarded. +!Sample_data_processing = Cufflinks v2.1.1 (modified to work on compact genomes) was used to reconstruct the transcripts guided with the Phytozome v5.3.1 reference transcriptome (See supplementary file: reference_gene_model.gtf.gz). Multi-mapped read correction was turned on and transcript composed of >50% multi-mapped reads or <25 reads were discarded. The remaining transcript assemblies from different time points were merged into a unified set of gene models, which was then compared to the annotated transcriptome. Potential noise was filtered from these predicted transcripts. Sequential steps of filtering criteria were applied as follows; 1). FPKM >0 for both replicates at least at one time point; 2) length of CDS>=50 amino acid; candidate coding regions were predicted based on transcript sequences using TransDecoder script v2013-02-25 from the Trinity package, 3) Remove “noise” transcripts of CuffDiff classes ‘E’, ‘O’ and ‘P’ and single exon transcripts of CuffDiff classes ‘.’, ‘C’ and ‘I’. +!Sample_data_processing = Illumina RTA-1.12 to 1.18 software used for basecalling depending on when library is sequenced. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii genome (Phytozome v5.3.1); C.reinhardtii_v5.3_genomic_scaffold_plastids.fasta.gz +!Sample_data_processing = Supplementary_files_format_and_content: peaks list, tab-delimited text files include FPKM values for each sample and the gene/transcript annotations +!Sample_platform_id = GPL15922 +!Sample_contact_name = Chia-Lin,,Wei +!Sample_contact_email = CWei@lbl.gov +!Sample_contact_phone = +1 (925) 927-2593 +!Sample_contact_laboratory = Sequencing Technologies +!Sample_contact_department = Genomic Technologies +!Sample_contact_institute = DOE Joint Genome Institute +!Sample_contact_address = 2800 Mitchell Drive +!Sample_contact_city = Walnut Creek +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 94598 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02928719 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX658312 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE59629 +!Sample_data_row_count = 0 +^SAMPLE = GSM1440778 +!Sample_title = PolyA Transcripts replicate 2 (Nitrogen starvation 48 hr) +!Sample_geo_accession = GSM1440778 +!Sample_status = Public on Jul 28 2015 +!Sample_submission_date = Jul 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = PolyA Transcripts (Nitrogen starvation 48 hr) +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 4A+ +!Sample_characteristics_ch1 = time: 48 hr +!Sample_treatment_protocol_ch1 = N-free (TAP-N) and SO42--free (TAP-S) media were prepared as described (Boyle et al., 2012; Kropat et al., 2011). For N- and S- starvation conditions, cells were grown to mid-log phase, washed twice with depleted media and re-suspended in TAP-N or TAP-S media to a density of 2x10^6 cells/ml (Boyle et al. 2012). Three acyltransferases and nitrogen-responsive regulator are implicated in nitrogen starvation-induced triacylglycerol accumulation in Chlamydomonas (The Journal of biological chemistry 287, 15811-15825; Kropat et al. 2011). A revised mineral nutrient supplement increases biomass and growth rate in Chlamydomonas reinhardtii (The Plant journal for cell and molecular biology 66, 770-780). +!Sample_growth_protocol_ch1 = C. reinhardtii wild type strain 4a+ was cultured using Tris-acetate-phosphate (TAP) medium. +!Sample_molecule_ch1 = polyA RNA +!Sample_extract_protocol_ch1 = Cells were first lysed and total RNA extracted using Trizol and cleaned up using RNeasy column (Qiagen). PolyA+ RNA was isolated from 10ug of total RNA. +!Sample_extract_protocol_ch1 = RNA was fragmented using RNA Fragmentation Reagents (Ambion). Strand-specific RNA-seq library (Parkhomchuk et al., 2009) was constructed using Illumina DNA Sample Preparation Kit (Illumina) with 10 cycles PCR amplification (Parkhomchuk et al.(2009). Nucleic acids research 37, e123). +!Sample_description = polyAND48hrR2 +!Sample_description = processed data file: master_gene_model.gtf.gz +!Sample_description = processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz +!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence and other artifacts. Trimmed reads with average quality ≥20, ≤3 Ns, and ≥32 bases were mapped to C. reinhardtii genome (Phytozome v5.3.1) using TopHat v2.0.8 with Bowtie v2.1.0. Sensitive and fusion mapping was enabled. Valid intron length was 20bp to 25 kbp and minimum distance between intra-chromosomal fusions was 1 Mbp. The library type “fr-firststrand” stated and read alignments with >3 mismatches were discarded. +!Sample_data_processing = Cufflinks v2.1.1 (modified to work on compact genomes) was used to reconstruct the transcripts guided with the Phytozome v5.3.1 reference transcriptome (See supplementary file: reference_gene_model.gtf.gz). Multi-mapped read correction was turned on and transcript composed of >50% multi-mapped reads or <25 reads were discarded. The remaining transcript assemblies from different time points were merged into a unified set of gene models, which was then compared to the annotated transcriptome. Potential noise was filtered from these predicted transcripts. Sequential steps of filtering criteria were applied as follows; 1). FPKM >0 for both replicates at least at one time point; 2) length of CDS>=50 amino acid; candidate coding regions were predicted based on transcript sequences using TransDecoder script v2013-02-25 from the Trinity package, 3) Remove “noise” transcripts of CuffDiff classes ‘E’, ‘O’ and ‘P’ and single exon transcripts of CuffDiff classes ‘.’, ‘C’ and ‘I’. +!Sample_data_processing = Illumina RTA-1.12 to 1.18 software used for basecalling depending on when library is sequenced. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii genome (Phytozome v5.3.1); C.reinhardtii_v5.3_genomic_scaffold_plastids.fasta.gz +!Sample_data_processing = Supplementary_files_format_and_content: peaks list, tab-delimited text files include FPKM values for each sample and the gene/transcript annotations +!Sample_platform_id = GPL15922 +!Sample_contact_name = Chia-Lin,,Wei +!Sample_contact_email = CWei@lbl.gov +!Sample_contact_phone = +1 (925) 927-2593 +!Sample_contact_laboratory = Sequencing Technologies +!Sample_contact_department = Genomic Technologies +!Sample_contact_institute = DOE Joint Genome Institute +!Sample_contact_address = 2800 Mitchell Drive +!Sample_contact_city = Walnut Creek +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 94598 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02928720 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX658313 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE59629 +!Sample_data_row_count = 0 +^SAMPLE = GSM1440779 +!Sample_title = PolyA Transcripts replicate 1 (Sulfur starvation 0 hr; baseline) +!Sample_geo_accession = GSM1440779 +!Sample_status = Public on Jul 28 2015 +!Sample_submission_date = Jul 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = PolyA Transcripts (Sulfur starvation 0 hr; baseline) +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 4A+ +!Sample_characteristics_ch1 = time: 0 hr +!Sample_treatment_protocol_ch1 = N-free (TAP-N) and SO42--free (TAP-S) media were prepared as described (Boyle et al., 2012; Kropat et al., 2011). For N- and S- starvation conditions, cells were grown to mid-log phase, washed twice with depleted media and re-suspended in TAP-N or TAP-S media to a density of 2x10^6 cells/ml (Boyle et al. 2012). Three acyltransferases and nitrogen-responsive regulator are implicated in nitrogen starvation-induced triacylglycerol accumulation in Chlamydomonas (The Journal of biological chemistry 287, 15811-15825; Kropat et al. 2011). A revised mineral nutrient supplement increases biomass and growth rate in Chlamydomonas reinhardtii (The Plant journal for cell and molecular biology 66, 770-780). +!Sample_growth_protocol_ch1 = C. reinhardtii wild type strain 4a+ was cultured using Tris-acetate-phosphate (TAP) medium. +!Sample_molecule_ch1 = polyA RNA +!Sample_extract_protocol_ch1 = Cells were first lysed and total RNA extracted using Trizol and cleaned up using RNeasy column (Qiagen). PolyA+ RNA was isolated from 5ug of total RNA. +!Sample_extract_protocol_ch1 = RNA was fragmented using RNA Fragmentation Reagents (Ambion). Strand-specific RNA-seq library (Parkhomchuk et al., 2009) was constructed using Kapa Library Amplification Kit (Kapa Biosystems) with 10 cycles PCR amplification (Parkhomchuk et al.(2009). Nucleic acids research 37, e123). +!Sample_description = polyASD0hrR1 +!Sample_description = processed data file: master_gene_model.gtf.gz +!Sample_description = processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz +!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence and other artifacts. Trimmed reads with average quality ≥20, ≤3 Ns, and ≥32 bases were mapped to C. reinhardtii genome (Phytozome v5.3.1) using TopHat v2.0.8 with Bowtie v2.1.0. Sensitive and fusion mapping was enabled. Valid intron length was 20bp to 25 kbp and minimum distance between intra-chromosomal fusions was 1 Mbp. The library type “fr-firststrand” stated and read alignments with >3 mismatches were discarded. +!Sample_data_processing = Cufflinks v2.1.1 (modified to work on compact genomes) was used to reconstruct the transcripts guided with the Phytozome v5.3.1 reference transcriptome (See supplementary file: reference_gene_model.gtf.gz). Multi-mapped read correction was turned on and transcript composed of >50% multi-mapped reads or <25 reads were discarded. The remaining transcript assemblies from different time points were merged into a unified set of gene models, which was then compared to the annotated transcriptome. Potential noise was filtered from these predicted transcripts. Sequential steps of filtering criteria were applied as follows; 1). FPKM >0 for both replicates at least at one time point; 2) length of CDS>=50 amino acid; candidate coding regions were predicted based on transcript sequences using TransDecoder script v2013-02-25 from the Trinity package, 3) Remove “noise” transcripts of CuffDiff classes ‘E’, ‘O’ and ‘P’ and single exon transcripts of CuffDiff classes ‘.’, ‘C’ and ‘I’. +!Sample_data_processing = Illumina RTA-1.12 to 1.18 software used for basecalling depending on when library is sequenced. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii genome (Phytozome v5.3.1); C.reinhardtii_v5.3_genomic_scaffold_plastids.fasta.gz +!Sample_data_processing = Supplementary_files_format_and_content: peaks list, tab-delimited text files include FPKM values for each sample and the gene/transcript annotations +!Sample_platform_id = GPL15922 +!Sample_contact_name = Chia-Lin,,Wei +!Sample_contact_email = CWei@lbl.gov +!Sample_contact_phone = +1 (925) 927-2593 +!Sample_contact_laboratory = Sequencing Technologies +!Sample_contact_department = Genomic Technologies +!Sample_contact_institute = DOE Joint Genome Institute +!Sample_contact_address = 2800 Mitchell Drive +!Sample_contact_city = Walnut Creek +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 94598 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02928721 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX658314 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE59629 +!Sample_data_row_count = 0 +^SAMPLE = GSM1440780 +!Sample_title = PolyA Transcripts replicate 2 (Sulfur starvation 0 hr; baseline) +!Sample_geo_accession = GSM1440780 +!Sample_status = Public on Jul 28 2015 +!Sample_submission_date = Jul 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = PolyA Transcripts (Sulfur starvation 0 hr; baseline) +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 4A+ +!Sample_characteristics_ch1 = time: 0 hr +!Sample_treatment_protocol_ch1 = N-free (TAP-N) and SO42--free (TAP-S) media were prepared as described (Boyle et al., 2012; Kropat et al., 2011). For N- and S- starvation conditions, cells were grown to mid-log phase, washed twice with depleted media and re-suspended in TAP-N or TAP-S media to a density of 2x10^6 cells/ml (Boyle et al. 2012). Three acyltransferases and nitrogen-responsive regulator are implicated in nitrogen starvation-induced triacylglycerol accumulation in Chlamydomonas (The Journal of biological chemistry 287, 15811-15825; Kropat et al. 2011). A revised mineral nutrient supplement increases biomass and growth rate in Chlamydomonas reinhardtii (The Plant journal for cell and molecular biology 66, 770-780). +!Sample_growth_protocol_ch1 = C. reinhardtii wild type strain 4a+ was cultured using Tris-acetate-phosphate (TAP) medium. +!Sample_molecule_ch1 = polyA RNA +!Sample_extract_protocol_ch1 = Cells were first lysed and total RNA extracted using Trizol and cleaned up using RNeasy column (Qiagen). PolyA+ RNA was isolated from 5ug of total RNA. +!Sample_extract_protocol_ch1 = RNA was fragmented using RNA Fragmentation Reagents (Ambion). Strand-specific RNA-seq library (Parkhomchuk et al., 2009) was constructed using Kapa Library Amplification Kit (Kapa Biosystems) with 10 cycles PCR amplification (Parkhomchuk et al.(2009). Nucleic acids research 37, e123). +!Sample_description = polyASD0hrR2 +!Sample_description = processed data file: master_gene_model.gtf.gz +!Sample_description = processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz +!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence and other artifacts. Trimmed reads with average quality ≥20, ≤3 Ns, and ≥32 bases were mapped to C. reinhardtii genome (Phytozome v5.3.1) using TopHat v2.0.8 with Bowtie v2.1.0. Sensitive and fusion mapping was enabled. Valid intron length was 20bp to 25 kbp and minimum distance between intra-chromosomal fusions was 1 Mbp. The library type “fr-firststrand” stated and read alignments with >3 mismatches were discarded. +!Sample_data_processing = Cufflinks v2.1.1 (modified to work on compact genomes) was used to reconstruct the transcripts guided with the Phytozome v5.3.1 reference transcriptome (See supplementary file: reference_gene_model.gtf.gz). Multi-mapped read correction was turned on and transcript composed of >50% multi-mapped reads or <25 reads were discarded. The remaining transcript assemblies from different time points were merged into a unified set of gene models, which was then compared to the annotated transcriptome. Potential noise was filtered from these predicted transcripts. Sequential steps of filtering criteria were applied as follows; 1). FPKM >0 for both replicates at least at one time point; 2) length of CDS>=50 amino acid; candidate coding regions were predicted based on transcript sequences using TransDecoder script v2013-02-25 from the Trinity package, 3) Remove “noise” transcripts of CuffDiff classes ‘E’, ‘O’ and ‘P’ and single exon transcripts of CuffDiff classes ‘.’, ‘C’ and ‘I’. +!Sample_data_processing = Illumina RTA-1.12 to 1.18 software used for basecalling depending on when library is sequenced. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii genome (Phytozome v5.3.1); C.reinhardtii_v5.3_genomic_scaffold_plastids.fasta.gz +!Sample_data_processing = Supplementary_files_format_and_content: peaks list, tab-delimited text files include FPKM values for each sample and the gene/transcript annotations +!Sample_platform_id = GPL15922 +!Sample_contact_name = Chia-Lin,,Wei +!Sample_contact_email = CWei@lbl.gov +!Sample_contact_phone = +1 (925) 927-2593 +!Sample_contact_laboratory = Sequencing Technologies +!Sample_contact_department = Genomic Technologies +!Sample_contact_institute = DOE Joint Genome Institute +!Sample_contact_address = 2800 Mitchell Drive +!Sample_contact_city = Walnut Creek +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 94598 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02928722 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX658315 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE59629 +!Sample_data_row_count = 0 +^SAMPLE = GSM1440781 +!Sample_title = PolyA Transcripts replicate 1 (Sulfur starvation 10 min) +!Sample_geo_accession = GSM1440781 +!Sample_status = Public on Jul 28 2015 +!Sample_submission_date = Jul 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = PolyA Transcripts (Sulfur starvation 10 min) +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 4A+ +!Sample_characteristics_ch1 = time: 10 min +!Sample_treatment_protocol_ch1 = N-free (TAP-N) and SO42--free (TAP-S) media were prepared as described (Boyle et al., 2012; Kropat et al., 2011). For N- and S- starvation conditions, cells were grown to mid-log phase, washed twice with depleted media and re-suspended in TAP-N or TAP-S media to a density of 2x10^6 cells/ml (Boyle et al. 2012). Three acyltransferases and nitrogen-responsive regulator are implicated in nitrogen starvation-induced triacylglycerol accumulation in Chlamydomonas (The Journal of biological chemistry 287, 15811-15825; Kropat et al. 2011). A revised mineral nutrient supplement increases biomass and growth rate in Chlamydomonas reinhardtii (The Plant journal for cell and molecular biology 66, 770-780). +!Sample_growth_protocol_ch1 = C. reinhardtii wild type strain 4a+ was cultured using Tris-acetate-phosphate (TAP) medium. +!Sample_molecule_ch1 = polyA RNA +!Sample_extract_protocol_ch1 = Cells were first lysed and total RNA extracted using Trizol and cleaned up using RNeasy column (Qiagen). PolyA+ RNA was isolated from 5ug of total RNA. +!Sample_extract_protocol_ch1 = RNA was fragmented using RNA Fragmentation Reagents (Ambion). Strand-specific RNA-seq library (Parkhomchuk et al., 2009) was constructed using Kapa Library Amplification Kit (Kapa Biosystems) with 10 cycles PCR amplification (Parkhomchuk et al.(2009). Nucleic acids research 37, e123). +!Sample_description = polyASD10minR1 +!Sample_description = processed data file: master_gene_model.gtf.gz +!Sample_description = processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz +!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence and other artifacts. Trimmed reads with average quality ≥20, ≤3 Ns, and ≥32 bases were mapped to C. reinhardtii genome (Phytozome v5.3.1) using TopHat v2.0.8 with Bowtie v2.1.0. Sensitive and fusion mapping was enabled. Valid intron length was 20bp to 25 kbp and minimum distance between intra-chromosomal fusions was 1 Mbp. The library type “fr-firststrand” stated and read alignments with >3 mismatches were discarded. +!Sample_data_processing = Cufflinks v2.1.1 (modified to work on compact genomes) was used to reconstruct the transcripts guided with the Phytozome v5.3.1 reference transcriptome (See supplementary file: reference_gene_model.gtf.gz). Multi-mapped read correction was turned on and transcript composed of >50% multi-mapped reads or <25 reads were discarded. The remaining transcript assemblies from different time points were merged into a unified set of gene models, which was then compared to the annotated transcriptome. Potential noise was filtered from these predicted transcripts. Sequential steps of filtering criteria were applied as follows; 1). FPKM >0 for both replicates at least at one time point; 2) length of CDS>=50 amino acid; candidate coding regions were predicted based on transcript sequences using TransDecoder script v2013-02-25 from the Trinity package, 3) Remove “noise” transcripts of CuffDiff classes ‘E’, ‘O’ and ‘P’ and single exon transcripts of CuffDiff classes ‘.’, ‘C’ and ‘I’. +!Sample_data_processing = Illumina RTA-1.12 to 1.18 software used for basecalling depending on when library is sequenced. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii genome (Phytozome v5.3.1); C.reinhardtii_v5.3_genomic_scaffold_plastids.fasta.gz +!Sample_data_processing = Supplementary_files_format_and_content: peaks list, tab-delimited text files include FPKM values for each sample and the gene/transcript annotations +!Sample_platform_id = GPL15922 +!Sample_contact_name = Chia-Lin,,Wei +!Sample_contact_email = CWei@lbl.gov +!Sample_contact_phone = +1 (925) 927-2593 +!Sample_contact_laboratory = Sequencing Technologies +!Sample_contact_department = Genomic Technologies +!Sample_contact_institute = DOE Joint Genome Institute +!Sample_contact_address = 2800 Mitchell Drive +!Sample_contact_city = Walnut Creek +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 94598 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02928723 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX658316 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE59629 +!Sample_data_row_count = 0 +^SAMPLE = GSM1440782 +!Sample_title = PolyA Transcripts replicate 2 (Sulfur starvation 10 min) +!Sample_geo_accession = GSM1440782 +!Sample_status = Public on Jul 28 2015 +!Sample_submission_date = Jul 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = PolyA Transcripts (Sulfur starvation 10 min) +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 4A+ +!Sample_characteristics_ch1 = time: 10 min +!Sample_treatment_protocol_ch1 = N-free (TAP-N) and SO42--free (TAP-S) media were prepared as described (Boyle et al., 2012; Kropat et al., 2011). For N- and S- starvation conditions, cells were grown to mid-log phase, washed twice with depleted media and re-suspended in TAP-N or TAP-S media to a density of 2x10^6 cells/ml (Boyle et al. 2012). Three acyltransferases and nitrogen-responsive regulator are implicated in nitrogen starvation-induced triacylglycerol accumulation in Chlamydomonas (The Journal of biological chemistry 287, 15811-15825; Kropat et al. 2011). A revised mineral nutrient supplement increases biomass and growth rate in Chlamydomonas reinhardtii (The Plant journal for cell and molecular biology 66, 770-780). +!Sample_growth_protocol_ch1 = C. reinhardtii wild type strain 4a+ was cultured using Tris-acetate-phosphate (TAP) medium. +!Sample_molecule_ch1 = polyA RNA +!Sample_extract_protocol_ch1 = Cells were first lysed and total RNA extracted using Trizol and cleaned up using RNeasy column (Qiagen). PolyA+ RNA was isolated from 5ug of total RNA. +!Sample_extract_protocol_ch1 = RNA was fragmented using RNA Fragmentation Reagents (Ambion). Strand-specific RNA-seq library (Parkhomchuk et al., 2009) was constructed using Kapa Library Amplification Kit (Kapa Biosystems) with 10 cycles PCR amplification (Parkhomchuk et al.(2009). Nucleic acids research 37, e123). +!Sample_description = polyASD10minR2 +!Sample_description = processed data file: master_gene_model.gtf.gz +!Sample_description = processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz +!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence and other artifacts. Trimmed reads with average quality ≥20, ≤3 Ns, and ≥32 bases were mapped to C. reinhardtii genome (Phytozome v5.3.1) using TopHat v2.0.8 with Bowtie v2.1.0. Sensitive and fusion mapping was enabled. Valid intron length was 20bp to 25 kbp and minimum distance between intra-chromosomal fusions was 1 Mbp. The library type “fr-firststrand” stated and read alignments with >3 mismatches were discarded. +!Sample_data_processing = Cufflinks v2.1.1 (modified to work on compact genomes) was used to reconstruct the transcripts guided with the Phytozome v5.3.1 reference transcriptome (See supplementary file: reference_gene_model.gtf.gz). Multi-mapped read correction was turned on and transcript composed of >50% multi-mapped reads or <25 reads were discarded. The remaining transcript assemblies from different time points were merged into a unified set of gene models, which was then compared to the annotated transcriptome. Potential noise was filtered from these predicted transcripts. Sequential steps of filtering criteria were applied as follows; 1). FPKM >0 for both replicates at least at one time point; 2) length of CDS>=50 amino acid; candidate coding regions were predicted based on transcript sequences using TransDecoder script v2013-02-25 from the Trinity package, 3) Remove “noise” transcripts of CuffDiff classes ‘E’, ‘O’ and ‘P’ and single exon transcripts of CuffDiff classes ‘.’, ‘C’ and ‘I’. +!Sample_data_processing = Illumina RTA-1.12 to 1.18 software used for basecalling depending on when library is sequenced. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii genome (Phytozome v5.3.1); C.reinhardtii_v5.3_genomic_scaffold_plastids.fasta.gz +!Sample_data_processing = Supplementary_files_format_and_content: peaks list, tab-delimited text files include FPKM values for each sample and the gene/transcript annotations +!Sample_platform_id = GPL15922 +!Sample_contact_name = Chia-Lin,,Wei +!Sample_contact_email = CWei@lbl.gov +!Sample_contact_phone = +1 (925) 927-2593 +!Sample_contact_laboratory = Sequencing Technologies +!Sample_contact_department = Genomic Technologies +!Sample_contact_institute = DOE Joint Genome Institute +!Sample_contact_address = 2800 Mitchell Drive +!Sample_contact_city = Walnut Creek +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 94598 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02928724 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX658317 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE59629 +!Sample_data_row_count = 0 +^SAMPLE = GSM1440783 +!Sample_title = PolyA Transcripts replicate 1 (Sulfur starvation 30 min) +!Sample_geo_accession = GSM1440783 +!Sample_status = Public on Jul 28 2015 +!Sample_submission_date = Jul 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = PolyA Transcripts (Sulfur starvation 30 min) +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 4A+ +!Sample_characteristics_ch1 = time: 30 min +!Sample_treatment_protocol_ch1 = N-free (TAP-N) and SO42--free (TAP-S) media were prepared as described (Boyle et al., 2012; Kropat et al., 2011). For N- and S- starvation conditions, cells were grown to mid-log phase, washed twice with depleted media and re-suspended in TAP-N or TAP-S media to a density of 2x10^6 cells/ml (Boyle et al. 2012). Three acyltransferases and nitrogen-responsive regulator are implicated in nitrogen starvation-induced triacylglycerol accumulation in Chlamydomonas (The Journal of biological chemistry 287, 15811-15825; Kropat et al. 2011). A revised mineral nutrient supplement increases biomass and growth rate in Chlamydomonas reinhardtii (The Plant journal for cell and molecular biology 66, 770-780). +!Sample_growth_protocol_ch1 = C. reinhardtii wild type strain 4a+ was cultured using Tris-acetate-phosphate (TAP) medium. +!Sample_molecule_ch1 = polyA RNA +!Sample_extract_protocol_ch1 = Cells were first lysed and total RNA extracted using Trizol and cleaned up using RNeasy column (Qiagen). PolyA+ RNA was isolated from 5ug of total RNA. +!Sample_extract_protocol_ch1 = RNA was fragmented using RNA Fragmentation Reagents (Ambion). Strand-specific RNA-seq library (Parkhomchuk et al., 2009) was constructed using Kapa Library Amplification Kit (Kapa Biosystems) with 10 cycles PCR amplification (Parkhomchuk et al.(2009). Nucleic acids research 37, e123). +!Sample_description = polyASD30minR1 +!Sample_description = processed data file: master_gene_model.gtf.gz +!Sample_description = processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz +!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence and other artifacts. Trimmed reads with average quality ≥20, ≤3 Ns, and ≥32 bases were mapped to C. reinhardtii genome (Phytozome v5.3.1) using TopHat v2.0.8 with Bowtie v2.1.0. Sensitive and fusion mapping was enabled. Valid intron length was 20bp to 25 kbp and minimum distance between intra-chromosomal fusions was 1 Mbp. The library type “fr-firststrand” stated and read alignments with >3 mismatches were discarded. +!Sample_data_processing = Cufflinks v2.1.1 (modified to work on compact genomes) was used to reconstruct the transcripts guided with the Phytozome v5.3.1 reference transcriptome (See supplementary file: reference_gene_model.gtf.gz). Multi-mapped read correction was turned on and transcript composed of >50% multi-mapped reads or <25 reads were discarded. The remaining transcript assemblies from different time points were merged into a unified set of gene models, which was then compared to the annotated transcriptome. Potential noise was filtered from these predicted transcripts. Sequential steps of filtering criteria were applied as follows; 1). FPKM >0 for both replicates at least at one time point; 2) length of CDS>=50 amino acid; candidate coding regions were predicted based on transcript sequences using TransDecoder script v2013-02-25 from the Trinity package, 3) Remove “noise” transcripts of CuffDiff classes ‘E’, ‘O’ and ‘P’ and single exon transcripts of CuffDiff classes ‘.’, ‘C’ and ‘I’. +!Sample_data_processing = Illumina RTA-1.12 to 1.18 software used for basecalling depending on when library is sequenced. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii genome (Phytozome v5.3.1); C.reinhardtii_v5.3_genomic_scaffold_plastids.fasta.gz +!Sample_data_processing = Supplementary_files_format_and_content: peaks list, tab-delimited text files include FPKM values for each sample and the gene/transcript annotations +!Sample_platform_id = GPL15922 +!Sample_contact_name = Chia-Lin,,Wei +!Sample_contact_email = CWei@lbl.gov +!Sample_contact_phone = +1 (925) 927-2593 +!Sample_contact_laboratory = Sequencing Technologies +!Sample_contact_department = Genomic Technologies +!Sample_contact_institute = DOE Joint Genome Institute +!Sample_contact_address = 2800 Mitchell Drive +!Sample_contact_city = Walnut Creek +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 94598 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02928725 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX658318 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE59629 +!Sample_data_row_count = 0 +^SAMPLE = GSM1440784 +!Sample_title = PolyA Transcripts replicate 2 (Sulfur starvation 30 min) +!Sample_geo_accession = GSM1440784 +!Sample_status = Public on Jul 28 2015 +!Sample_submission_date = Jul 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = PolyA Transcripts (Sulfur starvation 30 min) +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 4A+ +!Sample_characteristics_ch1 = time: 30 min +!Sample_treatment_protocol_ch1 = N-free (TAP-N) and SO42--free (TAP-S) media were prepared as described (Boyle et al., 2012; Kropat et al., 2011). For N- and S- starvation conditions, cells were grown to mid-log phase, washed twice with depleted media and re-suspended in TAP-N or TAP-S media to a density of 2x10^6 cells/ml (Boyle et al. 2012). Three acyltransferases and nitrogen-responsive regulator are implicated in nitrogen starvation-induced triacylglycerol accumulation in Chlamydomonas (The Journal of biological chemistry 287, 15811-15825; Kropat et al. 2011). A revised mineral nutrient supplement increases biomass and growth rate in Chlamydomonas reinhardtii (The Plant journal for cell and molecular biology 66, 770-780). +!Sample_growth_protocol_ch1 = C. reinhardtii wild type strain 4a+ was cultured using Tris-acetate-phosphate (TAP) medium. +!Sample_molecule_ch1 = polyA RNA +!Sample_extract_protocol_ch1 = Cells were first lysed and total RNA extracted using Trizol and cleaned up using RNeasy column (Qiagen). PolyA+ RNA was isolated from 5ug of total RNA. +!Sample_extract_protocol_ch1 = RNA was fragmented using RNA Fragmentation Reagents (Ambion). Strand-specific RNA-seq library (Parkhomchuk et al., 2009) was constructed using Kapa Library Amplification Kit (Kapa Biosystems) with 10 cycles PCR amplification (Parkhomchuk et al.(2009). Nucleic acids research 37, e123). +!Sample_description = polyASD30minR2 +!Sample_description = processed data file: master_gene_model.gtf.gz +!Sample_description = processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz +!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence and other artifacts. Trimmed reads with average quality ≥20, ≤3 Ns, and ≥32 bases were mapped to C. reinhardtii genome (Phytozome v5.3.1) using TopHat v2.0.8 with Bowtie v2.1.0. Sensitive and fusion mapping was enabled. Valid intron length was 20bp to 25 kbp and minimum distance between intra-chromosomal fusions was 1 Mbp. The library type “fr-firststrand” stated and read alignments with >3 mismatches were discarded. +!Sample_data_processing = Cufflinks v2.1.1 (modified to work on compact genomes) was used to reconstruct the transcripts guided with the Phytozome v5.3.1 reference transcriptome (See supplementary file: reference_gene_model.gtf.gz). Multi-mapped read correction was turned on and transcript composed of >50% multi-mapped reads or <25 reads were discarded. The remaining transcript assemblies from different time points were merged into a unified set of gene models, which was then compared to the annotated transcriptome. Potential noise was filtered from these predicted transcripts. Sequential steps of filtering criteria were applied as follows; 1). FPKM >0 for both replicates at least at one time point; 2) length of CDS>=50 amino acid; candidate coding regions were predicted based on transcript sequences using TransDecoder script v2013-02-25 from the Trinity package, 3) Remove “noise” transcripts of CuffDiff classes ‘E’, ‘O’ and ‘P’ and single exon transcripts of CuffDiff classes ‘.’, ‘C’ and ‘I’. +!Sample_data_processing = Illumina RTA-1.12 to 1.18 software used for basecalling depending on when library is sequenced. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii genome (Phytozome v5.3.1); C.reinhardtii_v5.3_genomic_scaffold_plastids.fasta.gz +!Sample_data_processing = Supplementary_files_format_and_content: peaks list, tab-delimited text files include FPKM values for each sample and the gene/transcript annotations +!Sample_platform_id = GPL15922 +!Sample_contact_name = Chia-Lin,,Wei +!Sample_contact_email = CWei@lbl.gov +!Sample_contact_phone = +1 (925) 927-2593 +!Sample_contact_laboratory = Sequencing Technologies +!Sample_contact_department = Genomic Technologies +!Sample_contact_institute = DOE Joint Genome Institute +!Sample_contact_address = 2800 Mitchell Drive +!Sample_contact_city = Walnut Creek +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 94598 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02928726 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX658319 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE59629 +!Sample_data_row_count = 0 +^SAMPLE = GSM1440785 +!Sample_title = PolyA Transcripts replicate 1 (Sulfur starvation 1 hr) +!Sample_geo_accession = GSM1440785 +!Sample_status = Public on Jul 28 2015 +!Sample_submission_date = Jul 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = PolyA Transcripts (Sulfur starvation 1 hr) +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 4A+ +!Sample_characteristics_ch1 = time: 1 hr +!Sample_treatment_protocol_ch1 = N-free (TAP-N) and SO42--free (TAP-S) media were prepared as described (Boyle et al., 2012; Kropat et al., 2011). For N- and S- starvation conditions, cells were grown to mid-log phase, washed twice with depleted media and re-suspended in TAP-N or TAP-S media to a density of 2x10^6 cells/ml (Boyle et al. 2012). Three acyltransferases and nitrogen-responsive regulator are implicated in nitrogen starvation-induced triacylglycerol accumulation in Chlamydomonas (The Journal of biological chemistry 287, 15811-15825; Kropat et al. 2011). A revised mineral nutrient supplement increases biomass and growth rate in Chlamydomonas reinhardtii (The Plant journal for cell and molecular biology 66, 770-780). +!Sample_growth_protocol_ch1 = C. reinhardtii wild type strain 4a+ was cultured using Tris-acetate-phosphate (TAP) medium. +!Sample_molecule_ch1 = polyA RNA +!Sample_extract_protocol_ch1 = Cells were first lysed and total RNA extracted using Trizol and cleaned up using RNeasy column (Qiagen). PolyA+ RNA was isolated from 5ug of total RNA. +!Sample_extract_protocol_ch1 = RNA was fragmented using RNA Fragmentation Reagents (Ambion). Strand-specific RNA-seq library (Parkhomchuk et al., 2009) was constructed using Kapa Library Amplification Kit (Kapa Biosystems) with 10 cycles PCR amplification (Parkhomchuk et al.(2009). Nucleic acids research 37, e123). +!Sample_description = polyASD1hrR1 +!Sample_description = processed data file: master_gene_model.gtf.gz +!Sample_description = processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz +!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence and other artifacts. Trimmed reads with average quality ≥20, ≤3 Ns, and ≥32 bases were mapped to C. reinhardtii genome (Phytozome v5.3.1) using TopHat v2.0.8 with Bowtie v2.1.0. Sensitive and fusion mapping was enabled. Valid intron length was 20bp to 25 kbp and minimum distance between intra-chromosomal fusions was 1 Mbp. The library type “fr-firststrand” stated and read alignments with >3 mismatches were discarded. +!Sample_data_processing = Cufflinks v2.1.1 (modified to work on compact genomes) was used to reconstruct the transcripts guided with the Phytozome v5.3.1 reference transcriptome (See supplementary file: reference_gene_model.gtf.gz). Multi-mapped read correction was turned on and transcript composed of >50% multi-mapped reads or <25 reads were discarded. The remaining transcript assemblies from different time points were merged into a unified set of gene models, which was then compared to the annotated transcriptome. Potential noise was filtered from these predicted transcripts. Sequential steps of filtering criteria were applied as follows; 1). FPKM >0 for both replicates at least at one time point; 2) length of CDS>=50 amino acid; candidate coding regions were predicted based on transcript sequences using TransDecoder script v2013-02-25 from the Trinity package, 3) Remove “noise” transcripts of CuffDiff classes ‘E’, ‘O’ and ‘P’ and single exon transcripts of CuffDiff classes ‘.’, ‘C’ and ‘I’. +!Sample_data_processing = Illumina RTA-1.12 to 1.18 software used for basecalling depending on when library is sequenced. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii genome (Phytozome v5.3.1); C.reinhardtii_v5.3_genomic_scaffold_plastids.fasta.gz +!Sample_data_processing = Supplementary_files_format_and_content: peaks list, tab-delimited text files include FPKM values for each sample and the gene/transcript annotations +!Sample_platform_id = GPL15922 +!Sample_contact_name = Chia-Lin,,Wei +!Sample_contact_email = CWei@lbl.gov +!Sample_contact_phone = +1 (925) 927-2593 +!Sample_contact_laboratory = Sequencing Technologies +!Sample_contact_department = Genomic Technologies +!Sample_contact_institute = DOE Joint Genome Institute +!Sample_contact_address = 2800 Mitchell Drive +!Sample_contact_city = Walnut Creek +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 94598 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02928727 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX658320 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE59629 +!Sample_data_row_count = 0 +^SAMPLE = GSM1440786 +!Sample_title = PolyA Transcripts replicate 2 (Sulfur starvation 1 hr) +!Sample_geo_accession = GSM1440786 +!Sample_status = Public on Jul 28 2015 +!Sample_submission_date = Jul 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = PolyA Transcripts (Sulfur starvation 1 hr) +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 4A+ +!Sample_characteristics_ch1 = time: 1 hr +!Sample_treatment_protocol_ch1 = N-free (TAP-N) and SO42--free (TAP-S) media were prepared as described (Boyle et al., 2012; Kropat et al., 2011). For N- and S- starvation conditions, cells were grown to mid-log phase, washed twice with depleted media and re-suspended in TAP-N or TAP-S media to a density of 2x10^6 cells/ml (Boyle et al. 2012). Three acyltransferases and nitrogen-responsive regulator are implicated in nitrogen starvation-induced triacylglycerol accumulation in Chlamydomonas (The Journal of biological chemistry 287, 15811-15825; Kropat et al. 2011). A revised mineral nutrient supplement increases biomass and growth rate in Chlamydomonas reinhardtii (The Plant journal for cell and molecular biology 66, 770-780). +!Sample_growth_protocol_ch1 = C. reinhardtii wild type strain 4a+ was cultured using Tris-acetate-phosphate (TAP) medium. +!Sample_molecule_ch1 = polyA RNA +!Sample_extract_protocol_ch1 = Cells were first lysed and total RNA extracted using Trizol and cleaned up using RNeasy column (Qiagen). PolyA+ RNA was isolated from 5ug of total RNA. +!Sample_extract_protocol_ch1 = RNA was fragmented using RNA Fragmentation Reagents (Ambion). Strand-specific RNA-seq library (Parkhomchuk et al., 2009) was constructed using Kapa Library Amplification Kit (Kapa Biosystems) with 10 cycles PCR amplification (Parkhomchuk et al.(2009). Nucleic acids research 37, e123). +!Sample_description = polyASD1hrR2 +!Sample_description = processed data file: master_gene_model.gtf.gz +!Sample_description = processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz +!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence and other artifacts. Trimmed reads with average quality ≥20, ≤3 Ns, and ≥32 bases were mapped to C. reinhardtii genome (Phytozome v5.3.1) using TopHat v2.0.8 with Bowtie v2.1.0. Sensitive and fusion mapping was enabled. Valid intron length was 20bp to 25 kbp and minimum distance between intra-chromosomal fusions was 1 Mbp. The library type “fr-firststrand” stated and read alignments with >3 mismatches were discarded. +!Sample_data_processing = Cufflinks v2.1.1 (modified to work on compact genomes) was used to reconstruct the transcripts guided with the Phytozome v5.3.1 reference transcriptome (See supplementary file: reference_gene_model.gtf.gz). Multi-mapped read correction was turned on and transcript composed of >50% multi-mapped reads or <25 reads were discarded. The remaining transcript assemblies from different time points were merged into a unified set of gene models, which was then compared to the annotated transcriptome. Potential noise was filtered from these predicted transcripts. Sequential steps of filtering criteria were applied as follows; 1). FPKM >0 for both replicates at least at one time point; 2) length of CDS>=50 amino acid; candidate coding regions were predicted based on transcript sequences using TransDecoder script v2013-02-25 from the Trinity package, 3) Remove “noise” transcripts of CuffDiff classes ‘E’, ‘O’ and ‘P’ and single exon transcripts of CuffDiff classes ‘.’, ‘C’ and ‘I’. +!Sample_data_processing = Illumina RTA-1.12 to 1.18 software used for basecalling depending on when library is sequenced. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii genome (Phytozome v5.3.1); C.reinhardtii_v5.3_genomic_scaffold_plastids.fasta.gz +!Sample_data_processing = Supplementary_files_format_and_content: peaks list, tab-delimited text files include FPKM values for each sample and the gene/transcript annotations +!Sample_platform_id = GPL15922 +!Sample_contact_name = Chia-Lin,,Wei +!Sample_contact_email = CWei@lbl.gov +!Sample_contact_phone = +1 (925) 927-2593 +!Sample_contact_laboratory = Sequencing Technologies +!Sample_contact_department = Genomic Technologies +!Sample_contact_institute = DOE Joint Genome Institute +!Sample_contact_address = 2800 Mitchell Drive +!Sample_contact_city = Walnut Creek +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 94598 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02928728 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX658321 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE59629 +!Sample_data_row_count = 0 +^SAMPLE = GSM1440787 +!Sample_title = PolyA Transcripts replicate 1 (Sulfur starvation 2 hr) +!Sample_geo_accession = GSM1440787 +!Sample_status = Public on Jul 28 2015 +!Sample_submission_date = Jul 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = PolyA Transcripts (Sulfur starvation 2 hr) +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 4A+ +!Sample_characteristics_ch1 = time: 2 hr +!Sample_treatment_protocol_ch1 = N-free (TAP-N) and SO42--free (TAP-S) media were prepared as described (Boyle et al., 2012; Kropat et al., 2011). For N- and S- starvation conditions, cells were grown to mid-log phase, washed twice with depleted media and re-suspended in TAP-N or TAP-S media to a density of 2x10^6 cells/ml (Boyle et al. 2012). Three acyltransferases and nitrogen-responsive regulator are implicated in nitrogen starvation-induced triacylglycerol accumulation in Chlamydomonas (The Journal of biological chemistry 287, 15811-15825; Kropat et al. 2011). A revised mineral nutrient supplement increases biomass and growth rate in Chlamydomonas reinhardtii (The Plant journal for cell and molecular biology 66, 770-780). +!Sample_growth_protocol_ch1 = C. reinhardtii wild type strain 4a+ was cultured using Tris-acetate-phosphate (TAP) medium. +!Sample_molecule_ch1 = polyA RNA +!Sample_extract_protocol_ch1 = Cells were first lysed and total RNA extracted using Trizol and cleaned up using RNeasy column (Qiagen). PolyA+ RNA was isolated from 5ug of total RNA. +!Sample_extract_protocol_ch1 = RNA was fragmented using RNA Fragmentation Reagents (Ambion). Strand-specific RNA-seq library (Parkhomchuk et al., 2009) was constructed using Kapa Library Amplification Kit (Kapa Biosystems) with 10 cycles PCR amplification (Parkhomchuk et al.(2009). Nucleic acids research 37, e123). +!Sample_description = polyASD2hrR1 +!Sample_description = processed data file: master_gene_model.gtf.gz +!Sample_description = processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz +!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence and other artifacts. Trimmed reads with average quality ≥20, ≤3 Ns, and ≥32 bases were mapped to C. reinhardtii genome (Phytozome v5.3.1) using TopHat v2.0.8 with Bowtie v2.1.0. Sensitive and fusion mapping was enabled. Valid intron length was 20bp to 25 kbp and minimum distance between intra-chromosomal fusions was 1 Mbp. The library type “fr-firststrand” stated and read alignments with >3 mismatches were discarded. +!Sample_data_processing = Cufflinks v2.1.1 (modified to work on compact genomes) was used to reconstruct the transcripts guided with the Phytozome v5.3.1 reference transcriptome (See supplementary file: reference_gene_model.gtf.gz). Multi-mapped read correction was turned on and transcript composed of >50% multi-mapped reads or <25 reads were discarded. The remaining transcript assemblies from different time points were merged into a unified set of gene models, which was then compared to the annotated transcriptome. Potential noise was filtered from these predicted transcripts. Sequential steps of filtering criteria were applied as follows; 1). FPKM >0 for both replicates at least at one time point; 2) length of CDS>=50 amino acid; candidate coding regions were predicted based on transcript sequences using TransDecoder script v2013-02-25 from the Trinity package, 3) Remove “noise” transcripts of CuffDiff classes ‘E’, ‘O’ and ‘P’ and single exon transcripts of CuffDiff classes ‘.’, ‘C’ and ‘I’. +!Sample_data_processing = Illumina RTA-1.12 to 1.18 software used for basecalling depending on when library is sequenced. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii genome (Phytozome v5.3.1); C.reinhardtii_v5.3_genomic_scaffold_plastids.fasta.gz +!Sample_data_processing = Supplementary_files_format_and_content: peaks list, tab-delimited text files include FPKM values for each sample and the gene/transcript annotations +!Sample_platform_id = GPL15922 +!Sample_contact_name = Chia-Lin,,Wei +!Sample_contact_email = CWei@lbl.gov +!Sample_contact_phone = +1 (925) 927-2593 +!Sample_contact_laboratory = Sequencing Technologies +!Sample_contact_department = Genomic Technologies +!Sample_contact_institute = DOE Joint Genome Institute +!Sample_contact_address = 2800 Mitchell Drive +!Sample_contact_city = Walnut Creek +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 94598 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02928729 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX658322 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE59629 +!Sample_data_row_count = 0 +^SAMPLE = GSM1440788 +!Sample_title = PolyA Transcripts replicate 2 (Sulfur starvation 2 hr) +!Sample_geo_accession = GSM1440788 +!Sample_status = Public on Jul 28 2015 +!Sample_submission_date = Jul 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = PolyA Transcripts (Sulfur starvation 2 hr) +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 4A+ +!Sample_characteristics_ch1 = time: 2 hr +!Sample_treatment_protocol_ch1 = N-free (TAP-N) and SO42--free (TAP-S) media were prepared as described (Boyle et al., 2012; Kropat et al., 2011). For N- and S- starvation conditions, cells were grown to mid-log phase, washed twice with depleted media and re-suspended in TAP-N or TAP-S media to a density of 2x10^6 cells/ml (Boyle et al. 2012). Three acyltransferases and nitrogen-responsive regulator are implicated in nitrogen starvation-induced triacylglycerol accumulation in Chlamydomonas (The Journal of biological chemistry 287, 15811-15825; Kropat et al. 2011). A revised mineral nutrient supplement increases biomass and growth rate in Chlamydomonas reinhardtii (The Plant journal for cell and molecular biology 66, 770-780). +!Sample_growth_protocol_ch1 = C. reinhardtii wild type strain 4a+ was cultured using Tris-acetate-phosphate (TAP) medium. +!Sample_molecule_ch1 = polyA RNA +!Sample_extract_protocol_ch1 = Cells were first lysed and total RNA extracted using Trizol and cleaned up using RNeasy column (Qiagen). PolyA+ RNA was isolated from 5ug of total RNA. +!Sample_extract_protocol_ch1 = RNA was fragmented using RNA Fragmentation Reagents (Ambion). Strand-specific RNA-seq library (Parkhomchuk et al., 2009) was constructed using Kapa Library Amplification Kit (Kapa Biosystems) with 10 cycles PCR amplification (Parkhomchuk et al.(2009). Nucleic acids research 37, e123). +!Sample_description = polyASD2hrR2 +!Sample_description = processed data file: master_gene_model.gtf.gz +!Sample_description = processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz +!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence and other artifacts. Trimmed reads with average quality ≥20, ≤3 Ns, and ≥32 bases were mapped to C. reinhardtii genome (Phytozome v5.3.1) using TopHat v2.0.8 with Bowtie v2.1.0. Sensitive and fusion mapping was enabled. Valid intron length was 20bp to 25 kbp and minimum distance between intra-chromosomal fusions was 1 Mbp. The library type “fr-firststrand” stated and read alignments with >3 mismatches were discarded. +!Sample_data_processing = Cufflinks v2.1.1 (modified to work on compact genomes) was used to reconstruct the transcripts guided with the Phytozome v5.3.1 reference transcriptome (See supplementary file: reference_gene_model.gtf.gz). Multi-mapped read correction was turned on and transcript composed of >50% multi-mapped reads or <25 reads were discarded. The remaining transcript assemblies from different time points were merged into a unified set of gene models, which was then compared to the annotated transcriptome. Potential noise was filtered from these predicted transcripts. Sequential steps of filtering criteria were applied as follows; 1). FPKM >0 for both replicates at least at one time point; 2) length of CDS>=50 amino acid; candidate coding regions were predicted based on transcript sequences using TransDecoder script v2013-02-25 from the Trinity package, 3) Remove “noise” transcripts of CuffDiff classes ‘E’, ‘O’ and ‘P’ and single exon transcripts of CuffDiff classes ‘.’, ‘C’ and ‘I’. +!Sample_data_processing = Illumina RTA-1.12 to 1.18 software used for basecalling depending on when library is sequenced. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii genome (Phytozome v5.3.1); C.reinhardtii_v5.3_genomic_scaffold_plastids.fasta.gz +!Sample_data_processing = Supplementary_files_format_and_content: peaks list, tab-delimited text files include FPKM values for each sample and the gene/transcript annotations +!Sample_platform_id = GPL15922 +!Sample_contact_name = Chia-Lin,,Wei +!Sample_contact_email = CWei@lbl.gov +!Sample_contact_phone = +1 (925) 927-2593 +!Sample_contact_laboratory = Sequencing Technologies +!Sample_contact_department = Genomic Technologies +!Sample_contact_institute = DOE Joint Genome Institute +!Sample_contact_address = 2800 Mitchell Drive +!Sample_contact_city = Walnut Creek +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 94598 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02928730 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX658323 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE59629 +!Sample_data_row_count = 0 +^SAMPLE = GSM1440789 +!Sample_title = PolyA Transcripts replicate 1 (Sulfur starvation 6 hr) +!Sample_geo_accession = GSM1440789 +!Sample_status = Public on Jul 28 2015 +!Sample_submission_date = Jul 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = PolyA Transcripts (Sulfur starvation 6 hr) +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 4A+ +!Sample_characteristics_ch1 = time: 6 hr +!Sample_treatment_protocol_ch1 = N-free (TAP-N) and SO42--free (TAP-S) media were prepared as described (Boyle et al., 2012; Kropat et al., 2011). For N- and S- starvation conditions, cells were grown to mid-log phase, washed twice with depleted media and re-suspended in TAP-N or TAP-S media to a density of 2x10^6 cells/ml (Boyle et al. 2012). Three acyltransferases and nitrogen-responsive regulator are implicated in nitrogen starvation-induced triacylglycerol accumulation in Chlamydomonas (The Journal of biological chemistry 287, 15811-15825; Kropat et al. 2011). A revised mineral nutrient supplement increases biomass and growth rate in Chlamydomonas reinhardtii (The Plant journal for cell and molecular biology 66, 770-780). +!Sample_growth_protocol_ch1 = C. reinhardtii wild type strain 4a+ was cultured using Tris-acetate-phosphate (TAP) medium. +!Sample_molecule_ch1 = polyA RNA +!Sample_extract_protocol_ch1 = Cells were first lysed and total RNA extracted using Trizol and cleaned up using RNeasy column (Qiagen). PolyA+ RNA was isolated from 5ug of total RNA. +!Sample_extract_protocol_ch1 = RNA was fragmented using RNA Fragmentation Reagents (Ambion). Strand-specific RNA-seq library (Parkhomchuk et al., 2009) was constructed using Kapa Library Amplification Kit (Kapa Biosystems) with 10 cycles PCR amplification (Parkhomchuk et al.(2009). Nucleic acids research 37, e123). +!Sample_description = polyASD6hrR1 +!Sample_description = processed data file: master_gene_model.gtf.gz +!Sample_description = processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz +!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence and other artifacts. Trimmed reads with average quality ≥20, ≤3 Ns, and ≥32 bases were mapped to C. reinhardtii genome (Phytozome v5.3.1) using TopHat v2.0.8 with Bowtie v2.1.0. Sensitive and fusion mapping was enabled. Valid intron length was 20bp to 25 kbp and minimum distance between intra-chromosomal fusions was 1 Mbp. The library type “fr-firststrand” stated and read alignments with >3 mismatches were discarded. +!Sample_data_processing = Cufflinks v2.1.1 (modified to work on compact genomes) was used to reconstruct the transcripts guided with the Phytozome v5.3.1 reference transcriptome (See supplementary file: reference_gene_model.gtf.gz). Multi-mapped read correction was turned on and transcript composed of >50% multi-mapped reads or <25 reads were discarded. The remaining transcript assemblies from different time points were merged into a unified set of gene models, which was then compared to the annotated transcriptome. Potential noise was filtered from these predicted transcripts. Sequential steps of filtering criteria were applied as follows; 1). FPKM >0 for both replicates at least at one time point; 2) length of CDS>=50 amino acid; candidate coding regions were predicted based on transcript sequences using TransDecoder script v2013-02-25 from the Trinity package, 3) Remove “noise” transcripts of CuffDiff classes ‘E’, ‘O’ and ‘P’ and single exon transcripts of CuffDiff classes ‘.’, ‘C’ and ‘I’. +!Sample_data_processing = Illumina RTA-1.12 to 1.18 software used for basecalling depending on when library is sequenced. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii genome (Phytozome v5.3.1); C.reinhardtii_v5.3_genomic_scaffold_plastids.fasta.gz +!Sample_data_processing = Supplementary_files_format_and_content: peaks list, tab-delimited text files include FPKM values for each sample and the gene/transcript annotations +!Sample_platform_id = GPL15922 +!Sample_contact_name = Chia-Lin,,Wei +!Sample_contact_email = CWei@lbl.gov +!Sample_contact_phone = +1 (925) 927-2593 +!Sample_contact_laboratory = Sequencing Technologies +!Sample_contact_department = Genomic Technologies +!Sample_contact_institute = DOE Joint Genome Institute +!Sample_contact_address = 2800 Mitchell Drive +!Sample_contact_city = Walnut Creek +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 94598 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02928731 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX658324 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE59629 +!Sample_data_row_count = 0 +^SAMPLE = GSM1440790 +!Sample_title = PolyA Transcripts replicate 2 (Sulfur starvation 6 hr) +!Sample_geo_accession = GSM1440790 +!Sample_status = Public on Jul 28 2015 +!Sample_submission_date = Jul 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = PolyA Transcripts (Sulfur starvation 6 hr) +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 4A+ +!Sample_characteristics_ch1 = time: 6 hr +!Sample_treatment_protocol_ch1 = N-free (TAP-N) and SO42--free (TAP-S) media were prepared as described (Boyle et al., 2012; Kropat et al., 2011). For N- and S- starvation conditions, cells were grown to mid-log phase, washed twice with depleted media and re-suspended in TAP-N or TAP-S media to a density of 2x10^6 cells/ml (Boyle et al. 2012). Three acyltransferases and nitrogen-responsive regulator are implicated in nitrogen starvation-induced triacylglycerol accumulation in Chlamydomonas (The Journal of biological chemistry 287, 15811-15825; Kropat et al. 2011). A revised mineral nutrient supplement increases biomass and growth rate in Chlamydomonas reinhardtii (The Plant journal for cell and molecular biology 66, 770-780). +!Sample_growth_protocol_ch1 = C. reinhardtii wild type strain 4a+ was cultured using Tris-acetate-phosphate (TAP) medium. +!Sample_molecule_ch1 = polyA RNA +!Sample_extract_protocol_ch1 = Cells were first lysed and total RNA extracted using Trizol and cleaned up using RNeasy column (Qiagen). PolyA+ RNA was isolated from 5ug of total RNA. +!Sample_extract_protocol_ch1 = RNA was fragmented using RNA Fragmentation Reagents (Ambion). Strand-specific RNA-seq library (Parkhomchuk et al., 2009) was constructed using Kapa Library Amplification Kit (Kapa Biosystems) with 10 cycles PCR amplification (Parkhomchuk et al.(2009). Nucleic acids research 37, e123). +!Sample_description = polyASD6hrR2 +!Sample_description = processed data file: master_gene_model.gtf.gz +!Sample_description = processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz +!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence and other artifacts. Trimmed reads with average quality ≥20, ≤3 Ns, and ≥32 bases were mapped to C. reinhardtii genome (Phytozome v5.3.1) using TopHat v2.0.8 with Bowtie v2.1.0. Sensitive and fusion mapping was enabled. Valid intron length was 20bp to 25 kbp and minimum distance between intra-chromosomal fusions was 1 Mbp. The library type “fr-firststrand” stated and read alignments with >3 mismatches were discarded. +!Sample_data_processing = Cufflinks v2.1.1 (modified to work on compact genomes) was used to reconstruct the transcripts guided with the Phytozome v5.3.1 reference transcriptome (See supplementary file: reference_gene_model.gtf.gz). Multi-mapped read correction was turned on and transcript composed of >50% multi-mapped reads or <25 reads were discarded. The remaining transcript assemblies from different time points were merged into a unified set of gene models, which was then compared to the annotated transcriptome. Potential noise was filtered from these predicted transcripts. Sequential steps of filtering criteria were applied as follows; 1). FPKM >0 for both replicates at least at one time point; 2) length of CDS>=50 amino acid; candidate coding regions were predicted based on transcript sequences using TransDecoder script v2013-02-25 from the Trinity package, 3) Remove “noise” transcripts of CuffDiff classes ‘E’, ‘O’ and ‘P’ and single exon transcripts of CuffDiff classes ‘.’, ‘C’ and ‘I’. +!Sample_data_processing = Illumina RTA-1.12 to 1.18 software used for basecalling depending on when library is sequenced. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii genome (Phytozome v5.3.1); C.reinhardtii_v5.3_genomic_scaffold_plastids.fasta.gz +!Sample_data_processing = Supplementary_files_format_and_content: peaks list, tab-delimited text files include FPKM values for each sample and the gene/transcript annotations +!Sample_platform_id = GPL15922 +!Sample_contact_name = Chia-Lin,,Wei +!Sample_contact_email = CWei@lbl.gov +!Sample_contact_phone = +1 (925) 927-2593 +!Sample_contact_laboratory = Sequencing Technologies +!Sample_contact_department = Genomic Technologies +!Sample_contact_institute = DOE Joint Genome Institute +!Sample_contact_address = 2800 Mitchell Drive +!Sample_contact_city = Walnut Creek +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 94598 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02928732 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX658325 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE59629 +!Sample_data_row_count = 0 +^SAMPLE = GSM1440791 +!Sample_title = PolyA Transcripts replicate 1 (Sulfur starvation 8 hr) +!Sample_geo_accession = GSM1440791 +!Sample_status = Public on Jul 28 2015 +!Sample_submission_date = Jul 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = PolyA Transcripts (Sulfur starvation 8 hr) +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 4A+ +!Sample_characteristics_ch1 = time: 8 hr +!Sample_treatment_protocol_ch1 = N-free (TAP-N) and SO42--free (TAP-S) media were prepared as described (Boyle et al., 2012; Kropat et al., 2011). For N- and S- starvation conditions, cells were grown to mid-log phase, washed twice with depleted media and re-suspended in TAP-N or TAP-S media to a density of 2x10^6 cells/ml (Boyle et al. 2012). Three acyltransferases and nitrogen-responsive regulator are implicated in nitrogen starvation-induced triacylglycerol accumulation in Chlamydomonas (The Journal of biological chemistry 287, 15811-15825; Kropat et al. 2011). A revised mineral nutrient supplement increases biomass and growth rate in Chlamydomonas reinhardtii (The Plant journal for cell and molecular biology 66, 770-780). +!Sample_growth_protocol_ch1 = C. reinhardtii wild type strain 4a+ was cultured using Tris-acetate-phosphate (TAP) medium. +!Sample_molecule_ch1 = polyA RNA +!Sample_extract_protocol_ch1 = Cells were first lysed and total RNA extracted using Trizol and cleaned up using RNeasy column (Qiagen). PolyA+ RNA was isolated from 5ug of total RNA. +!Sample_extract_protocol_ch1 = RNA was fragmented using RNA Fragmentation Reagents (Ambion). Strand-specific RNA-seq library (Parkhomchuk et al., 2009) was constructed using Kapa Library Amplification Kit (Kapa Biosystems) with 10 cycles PCR amplification (Parkhomchuk et al.(2009). Nucleic acids research 37, e123). +!Sample_description = polyASD8hrR1 +!Sample_description = processed data file: master_gene_model.gtf.gz +!Sample_description = processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz +!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence and other artifacts. Trimmed reads with average quality ≥20, ≤3 Ns, and ≥32 bases were mapped to C. reinhardtii genome (Phytozome v5.3.1) using TopHat v2.0.8 with Bowtie v2.1.0. Sensitive and fusion mapping was enabled. Valid intron length was 20bp to 25 kbp and minimum distance between intra-chromosomal fusions was 1 Mbp. The library type “fr-firststrand” stated and read alignments with >3 mismatches were discarded. +!Sample_data_processing = Cufflinks v2.1.1 (modified to work on compact genomes) was used to reconstruct the transcripts guided with the Phytozome v5.3.1 reference transcriptome (See supplementary file: reference_gene_model.gtf.gz). Multi-mapped read correction was turned on and transcript composed of >50% multi-mapped reads or <25 reads were discarded. The remaining transcript assemblies from different time points were merged into a unified set of gene models, which was then compared to the annotated transcriptome. Potential noise was filtered from these predicted transcripts. Sequential steps of filtering criteria were applied as follows; 1). FPKM >0 for both replicates at least at one time point; 2) length of CDS>=50 amino acid; candidate coding regions were predicted based on transcript sequences using TransDecoder script v2013-02-25 from the Trinity package, 3) Remove “noise” transcripts of CuffDiff classes ‘E’, ‘O’ and ‘P’ and single exon transcripts of CuffDiff classes ‘.’, ‘C’ and ‘I’. +!Sample_data_processing = Illumina RTA-1.12 to 1.18 software used for basecalling depending on when library is sequenced. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii genome (Phytozome v5.3.1); C.reinhardtii_v5.3_genomic_scaffold_plastids.fasta.gz +!Sample_data_processing = Supplementary_files_format_and_content: peaks list, tab-delimited text files include FPKM values for each sample and the gene/transcript annotations +!Sample_platform_id = GPL15922 +!Sample_contact_name = Chia-Lin,,Wei +!Sample_contact_email = CWei@lbl.gov +!Sample_contact_phone = +1 (925) 927-2593 +!Sample_contact_laboratory = Sequencing Technologies +!Sample_contact_department = Genomic Technologies +!Sample_contact_institute = DOE Joint Genome Institute +!Sample_contact_address = 2800 Mitchell Drive +!Sample_contact_city = Walnut Creek +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 94598 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02928733 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX658326 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE59629 +!Sample_data_row_count = 0 +^SAMPLE = GSM1440792 +!Sample_title = PolyA Transcripts replicate 2 (Sulfur starvation 8 hr) +!Sample_geo_accession = GSM1440792 +!Sample_status = Public on Jul 28 2015 +!Sample_submission_date = Jul 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = PolyA Transcripts (Sulfur starvation 8 hr) +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 4A+ +!Sample_characteristics_ch1 = time: 8 hr +!Sample_treatment_protocol_ch1 = N-free (TAP-N) and SO42--free (TAP-S) media were prepared as described (Boyle et al., 2012; Kropat et al., 2011). For N- and S- starvation conditions, cells were grown to mid-log phase, washed twice with depleted media and re-suspended in TAP-N or TAP-S media to a density of 2x10^6 cells/ml (Boyle et al. 2012). Three acyltransferases and nitrogen-responsive regulator are implicated in nitrogen starvation-induced triacylglycerol accumulation in Chlamydomonas (The Journal of biological chemistry 287, 15811-15825; Kropat et al. 2011). A revised mineral nutrient supplement increases biomass and growth rate in Chlamydomonas reinhardtii (The Plant journal for cell and molecular biology 66, 770-780). +!Sample_growth_protocol_ch1 = C. reinhardtii wild type strain 4a+ was cultured using Tris-acetate-phosphate (TAP) medium. +!Sample_molecule_ch1 = polyA RNA +!Sample_extract_protocol_ch1 = Cells were first lysed and total RNA extracted using Trizol and cleaned up using RNeasy column (Qiagen). PolyA+ RNA was isolated from 5ug of total RNA. +!Sample_extract_protocol_ch1 = RNA was fragmented using RNA Fragmentation Reagents (Ambion). Strand-specific RNA-seq library (Parkhomchuk et al., 2009) was constructed using Kapa Library Amplification Kit (Kapa Biosystems) with 10 cycles PCR amplification (Parkhomchuk et al.(2009). Nucleic acids research 37, e123). +!Sample_description = polyASD8hrR2 +!Sample_description = processed data file: master_gene_model.gtf.gz +!Sample_description = processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz +!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence and other artifacts. Trimmed reads with average quality ≥20, ≤3 Ns, and ≥32 bases were mapped to C. reinhardtii genome (Phytozome v5.3.1) using TopHat v2.0.8 with Bowtie v2.1.0. Sensitive and fusion mapping was enabled. Valid intron length was 20bp to 25 kbp and minimum distance between intra-chromosomal fusions was 1 Mbp. The library type “fr-firststrand” stated and read alignments with >3 mismatches were discarded. +!Sample_data_processing = Cufflinks v2.1.1 (modified to work on compact genomes) was used to reconstruct the transcripts guided with the Phytozome v5.3.1 reference transcriptome (See supplementary file: reference_gene_model.gtf.gz). Multi-mapped read correction was turned on and transcript composed of >50% multi-mapped reads or <25 reads were discarded. The remaining transcript assemblies from different time points were merged into a unified set of gene models, which was then compared to the annotated transcriptome. Potential noise was filtered from these predicted transcripts. Sequential steps of filtering criteria were applied as follows; 1). FPKM >0 for both replicates at least at one time point; 2) length of CDS>=50 amino acid; candidate coding regions were predicted based on transcript sequences using TransDecoder script v2013-02-25 from the Trinity package, 3) Remove “noise” transcripts of CuffDiff classes ‘E’, ‘O’ and ‘P’ and single exon transcripts of CuffDiff classes ‘.’, ‘C’ and ‘I’. +!Sample_data_processing = Illumina RTA-1.12 to 1.18 software used for basecalling depending on when library is sequenced. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii genome (Phytozome v5.3.1); C.reinhardtii_v5.3_genomic_scaffold_plastids.fasta.gz +!Sample_data_processing = Supplementary_files_format_and_content: peaks list, tab-delimited text files include FPKM values for each sample and the gene/transcript annotations +!Sample_platform_id = GPL15922 +!Sample_contact_name = Chia-Lin,,Wei +!Sample_contact_email = CWei@lbl.gov +!Sample_contact_phone = +1 (925) 927-2593 +!Sample_contact_laboratory = Sequencing Technologies +!Sample_contact_department = Genomic Technologies +!Sample_contact_institute = DOE Joint Genome Institute +!Sample_contact_address = 2800 Mitchell Drive +!Sample_contact_city = Walnut Creek +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 94598 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02928734 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX658327 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE59629 +!Sample_data_row_count = 0 +^SAMPLE = GSM1440793 +!Sample_title = PolyA Transcripts replicate 1 (Sulfur starvation 24 hr) +!Sample_geo_accession = GSM1440793 +!Sample_status = Public on Jul 28 2015 +!Sample_submission_date = Jul 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = PolyA Transcripts (Sulfur starvation 24 hr) +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 4A+ +!Sample_characteristics_ch1 = time: 24 hr +!Sample_treatment_protocol_ch1 = N-free (TAP-N) and SO42--free (TAP-S) media were prepared as described (Boyle et al., 2012; Kropat et al., 2011). For N- and S- starvation conditions, cells were grown to mid-log phase, washed twice with depleted media and re-suspended in TAP-N or TAP-S media to a density of 2x10^6 cells/ml (Boyle et al. 2012). Three acyltransferases and nitrogen-responsive regulator are implicated in nitrogen starvation-induced triacylglycerol accumulation in Chlamydomonas (The Journal of biological chemistry 287, 15811-15825; Kropat et al. 2011). A revised mineral nutrient supplement increases biomass and growth rate in Chlamydomonas reinhardtii (The Plant journal for cell and molecular biology 66, 770-780). +!Sample_growth_protocol_ch1 = C. reinhardtii wild type strain 4a+ was cultured using Tris-acetate-phosphate (TAP) medium. +!Sample_molecule_ch1 = polyA RNA +!Sample_extract_protocol_ch1 = Cells were first lysed and total RNA extracted using Trizol and cleaned up using RNeasy column (Qiagen). PolyA+ RNA was isolated from 5ug of total RNA. +!Sample_extract_protocol_ch1 = RNA was fragmented using RNA Fragmentation Reagents (Ambion). Strand-specific RNA-seq library (Parkhomchuk et al., 2009) was constructed using Kapa Library Amplification Kit (Kapa Biosystems) with 10 cycles PCR amplification (Parkhomchuk et al.(2009). Nucleic acids research 37, e123). +!Sample_description = polyASD24hrR1 +!Sample_description = processed data file: master_gene_model.gtf.gz +!Sample_description = processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz +!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence and other artifacts. Trimmed reads with average quality ≥20, ≤3 Ns, and ≥32 bases were mapped to C. reinhardtii genome (Phytozome v5.3.1) using TopHat v2.0.8 with Bowtie v2.1.0. Sensitive and fusion mapping was enabled. Valid intron length was 20bp to 25 kbp and minimum distance between intra-chromosomal fusions was 1 Mbp. The library type “fr-firststrand” stated and read alignments with >3 mismatches were discarded. +!Sample_data_processing = Cufflinks v2.1.1 (modified to work on compact genomes) was used to reconstruct the transcripts guided with the Phytozome v5.3.1 reference transcriptome (See supplementary file: reference_gene_model.gtf.gz). Multi-mapped read correction was turned on and transcript composed of >50% multi-mapped reads or <25 reads were discarded. The remaining transcript assemblies from different time points were merged into a unified set of gene models, which was then compared to the annotated transcriptome. Potential noise was filtered from these predicted transcripts. Sequential steps of filtering criteria were applied as follows; 1). FPKM >0 for both replicates at least at one time point; 2) length of CDS>=50 amino acid; candidate coding regions were predicted based on transcript sequences using TransDecoder script v2013-02-25 from the Trinity package, 3) Remove “noise” transcripts of CuffDiff classes ‘E’, ‘O’ and ‘P’ and single exon transcripts of CuffDiff classes ‘.’, ‘C’ and ‘I’. +!Sample_data_processing = Illumina RTA-1.12 to 1.18 software used for basecalling depending on when library is sequenced. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii genome (Phytozome v5.3.1); C.reinhardtii_v5.3_genomic_scaffold_plastids.fasta.gz +!Sample_data_processing = Supplementary_files_format_and_content: peaks list, tab-delimited text files include FPKM values for each sample and the gene/transcript annotations +!Sample_platform_id = GPL15922 +!Sample_contact_name = Chia-Lin,,Wei +!Sample_contact_email = CWei@lbl.gov +!Sample_contact_phone = +1 (925) 927-2593 +!Sample_contact_laboratory = Sequencing Technologies +!Sample_contact_department = Genomic Technologies +!Sample_contact_institute = DOE Joint Genome Institute +!Sample_contact_address = 2800 Mitchell Drive +!Sample_contact_city = Walnut Creek +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 94598 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02928735 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX658328 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE59629 +!Sample_data_row_count = 0 +^SAMPLE = GSM1440794 +!Sample_title = PolyA Transcripts replicate 2 (Sulfur starvation 24 hr) +!Sample_geo_accession = GSM1440794 +!Sample_status = Public on Jul 28 2015 +!Sample_submission_date = Jul 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = PolyA Transcripts (Sulfur starvation 24 hr) +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 4A+ +!Sample_characteristics_ch1 = time: 24 hr +!Sample_treatment_protocol_ch1 = N-free (TAP-N) and SO42--free (TAP-S) media were prepared as described (Boyle et al., 2012; Kropat et al., 2011). For N- and S- starvation conditions, cells were grown to mid-log phase, washed twice with depleted media and re-suspended in TAP-N or TAP-S media to a density of 2x10^6 cells/ml (Boyle et al. 2012). Three acyltransferases and nitrogen-responsive regulator are implicated in nitrogen starvation-induced triacylglycerol accumulation in Chlamydomonas (The Journal of biological chemistry 287, 15811-15825; Kropat et al. 2011). A revised mineral nutrient supplement increases biomass and growth rate in Chlamydomonas reinhardtii (The Plant journal for cell and molecular biology 66, 770-780). +!Sample_growth_protocol_ch1 = C. reinhardtii wild type strain 4a+ was cultured using Tris-acetate-phosphate (TAP) medium. +!Sample_molecule_ch1 = polyA RNA +!Sample_extract_protocol_ch1 = Cells were first lysed and total RNA extracted using Trizol and cleaned up using RNeasy column (Qiagen). PolyA+ RNA was isolated from 5ug of total RNA. +!Sample_extract_protocol_ch1 = RNA was fragmented using RNA Fragmentation Reagents (Ambion). Strand-specific RNA-seq library (Parkhomchuk et al., 2009) was constructed using Kapa Library Amplification Kit (Kapa Biosystems) with 10 cycles PCR amplification (Parkhomchuk et al.(2009). Nucleic acids research 37, e123). +!Sample_description = polyASD24hrR2 +!Sample_description = processed data file: master_gene_model.gtf.gz +!Sample_description = processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz +!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence and other artifacts. Trimmed reads with average quality ≥20, ≤3 Ns, and ≥32 bases were mapped to C. reinhardtii genome (Phytozome v5.3.1) using TopHat v2.0.8 with Bowtie v2.1.0. Sensitive and fusion mapping was enabled. Valid intron length was 20bp to 25 kbp and minimum distance between intra-chromosomal fusions was 1 Mbp. The library type “fr-firststrand” stated and read alignments with >3 mismatches were discarded. +!Sample_data_processing = Cufflinks v2.1.1 (modified to work on compact genomes) was used to reconstruct the transcripts guided with the Phytozome v5.3.1 reference transcriptome (See supplementary file: reference_gene_model.gtf.gz). Multi-mapped read correction was turned on and transcript composed of >50% multi-mapped reads or <25 reads were discarded. The remaining transcript assemblies from different time points were merged into a unified set of gene models, which was then compared to the annotated transcriptome. Potential noise was filtered from these predicted transcripts. Sequential steps of filtering criteria were applied as follows; 1). FPKM >0 for both replicates at least at one time point; 2) length of CDS>=50 amino acid; candidate coding regions were predicted based on transcript sequences using TransDecoder script v2013-02-25 from the Trinity package, 3) Remove “noise” transcripts of CuffDiff classes ‘E’, ‘O’ and ‘P’ and single exon transcripts of CuffDiff classes ‘.’, ‘C’ and ‘I’. +!Sample_data_processing = Illumina RTA-1.12 to 1.18 software used for basecalling depending on when library is sequenced. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii genome (Phytozome v5.3.1); C.reinhardtii_v5.3_genomic_scaffold_plastids.fasta.gz +!Sample_data_processing = Supplementary_files_format_and_content: peaks list, tab-delimited text files include FPKM values for each sample and the gene/transcript annotations +!Sample_platform_id = GPL15922 +!Sample_contact_name = Chia-Lin,,Wei +!Sample_contact_email = CWei@lbl.gov +!Sample_contact_phone = +1 (925) 927-2593 +!Sample_contact_laboratory = Sequencing Technologies +!Sample_contact_department = Genomic Technologies +!Sample_contact_institute = DOE Joint Genome Institute +!Sample_contact_address = 2800 Mitchell Drive +!Sample_contact_city = Walnut Creek +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 94598 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02928736 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX658329 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE59629 +!Sample_data_row_count = 0 +^SAMPLE = GSM1440795 +!Sample_title = PolyA Transcripts replicate 1 (Sulfur starvation 48 hr) +!Sample_geo_accession = GSM1440795 +!Sample_status = Public on Jul 28 2015 +!Sample_submission_date = Jul 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = PolyA Transcripts (Sulfur starvation 48 hr) +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 4A+ +!Sample_characteristics_ch1 = time: 48 hr +!Sample_treatment_protocol_ch1 = N-free (TAP-N) and SO42--free (TAP-S) media were prepared as described (Boyle et al., 2012; Kropat et al., 2011). For N- and S- starvation conditions, cells were grown to mid-log phase, washed twice with depleted media and re-suspended in TAP-N or TAP-S media to a density of 2x10^6 cells/ml (Boyle et al. 2012). Three acyltransferases and nitrogen-responsive regulator are implicated in nitrogen starvation-induced triacylglycerol accumulation in Chlamydomonas (The Journal of biological chemistry 287, 15811-15825; Kropat et al. 2011). A revised mineral nutrient supplement increases biomass and growth rate in Chlamydomonas reinhardtii (The Plant journal for cell and molecular biology 66, 770-780). +!Sample_growth_protocol_ch1 = C. reinhardtii wild type strain 4a+ was cultured using Tris-acetate-phosphate (TAP) medium. +!Sample_molecule_ch1 = polyA RNA +!Sample_extract_protocol_ch1 = Cells were first lysed and total RNA extracted using Trizol and cleaned up using RNeasy column (Qiagen). PolyA+ RNA was isolated from 5ug of total RNA. +!Sample_extract_protocol_ch1 = RNA was fragmented using RNA Fragmentation Reagents (Ambion). Strand-specific RNA-seq library (Parkhomchuk et al., 2009) was constructed using Kapa Library Amplification Kit (Kapa Biosystems) with 10 cycles PCR amplification (Parkhomchuk et al.(2009). Nucleic acids research 37, e123). +!Sample_description = polyASD48hrR1 +!Sample_description = processed data file: master_gene_model.gtf.gz +!Sample_description = processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz +!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence and other artifacts. Trimmed reads with average quality ≥20, ≤3 Ns, and ≥32 bases were mapped to C. reinhardtii genome (Phytozome v5.3.1) using TopHat v2.0.8 with Bowtie v2.1.0. Sensitive and fusion mapping was enabled. Valid intron length was 20bp to 25 kbp and minimum distance between intra-chromosomal fusions was 1 Mbp. The library type “fr-firststrand” stated and read alignments with >3 mismatches were discarded. +!Sample_data_processing = Cufflinks v2.1.1 (modified to work on compact genomes) was used to reconstruct the transcripts guided with the Phytozome v5.3.1 reference transcriptome (See supplementary file: reference_gene_model.gtf.gz). Multi-mapped read correction was turned on and transcript composed of >50% multi-mapped reads or <25 reads were discarded. The remaining transcript assemblies from different time points were merged into a unified set of gene models, which was then compared to the annotated transcriptome. Potential noise was filtered from these predicted transcripts. Sequential steps of filtering criteria were applied as follows; 1). FPKM >0 for both replicates at least at one time point; 2) length of CDS>=50 amino acid; candidate coding regions were predicted based on transcript sequences using TransDecoder script v2013-02-25 from the Trinity package, 3) Remove “noise” transcripts of CuffDiff classes ‘E’, ‘O’ and ‘P’ and single exon transcripts of CuffDiff classes ‘.’, ‘C’ and ‘I’. +!Sample_data_processing = Illumina RTA-1.12 to 1.18 software used for basecalling depending on when library is sequenced. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii genome (Phytozome v5.3.1); C.reinhardtii_v5.3_genomic_scaffold_plastids.fasta.gz +!Sample_data_processing = Supplementary_files_format_and_content: peaks list, tab-delimited text files include FPKM values for each sample and the gene/transcript annotations +!Sample_platform_id = GPL15922 +!Sample_contact_name = Chia-Lin,,Wei +!Sample_contact_email = CWei@lbl.gov +!Sample_contact_phone = +1 (925) 927-2593 +!Sample_contact_laboratory = Sequencing Technologies +!Sample_contact_department = Genomic Technologies +!Sample_contact_institute = DOE Joint Genome Institute +!Sample_contact_address = 2800 Mitchell Drive +!Sample_contact_city = Walnut Creek +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 94598 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02928737 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX658330 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE59629 +!Sample_data_row_count = 0 +^SAMPLE = GSM1440796 +!Sample_title = PolyA Transcripts replicate 2 (Sulfur starvation 48 hr) +!Sample_geo_accession = GSM1440796 +!Sample_status = Public on Jul 28 2015 +!Sample_submission_date = Jul 21 2014 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = PolyA Transcripts (Sulfur starvation 48 hr) +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 4A+ +!Sample_characteristics_ch1 = time: 48 hr +!Sample_treatment_protocol_ch1 = N-free (TAP-N) and SO42--free (TAP-S) media were prepared as described (Boyle et al., 2012; Kropat et al., 2011). For N- and S- starvation conditions, cells were grown to mid-log phase, washed twice with depleted media and re-suspended in TAP-N or TAP-S media to a density of 2x10^6 cells/ml (Boyle et al. 2012). Three acyltransferases and nitrogen-responsive regulator are implicated in nitrogen starvation-induced triacylglycerol accumulation in Chlamydomonas (The Journal of biological chemistry 287, 15811-15825; Kropat et al. 2011). A revised mineral nutrient supplement increases biomass and growth rate in Chlamydomonas reinhardtii (The Plant journal for cell and molecular biology 66, 770-780). +!Sample_growth_protocol_ch1 = C. reinhardtii wild type strain 4a+ was cultured using Tris-acetate-phosphate (TAP) medium. +!Sample_molecule_ch1 = polyA RNA +!Sample_extract_protocol_ch1 = Cells were first lysed and total RNA extracted using Trizol and cleaned up using RNeasy column (Qiagen). PolyA+ RNA was isolated from 5ug of total RNA. +!Sample_extract_protocol_ch1 = RNA was fragmented using RNA Fragmentation Reagents (Ambion). Strand-specific RNA-seq library (Parkhomchuk et al., 2009) was constructed using Kapa Library Amplification Kit (Kapa Biosystems) with 10 cycles PCR amplification (Parkhomchuk et al.(2009). Nucleic acids research 37, e123). +!Sample_description = polyASD48hrR2 +!Sample_description = processed data file: master_gene_model.gtf.gz +!Sample_description = processed data file: RNA-Seq_Transcripts_and_Annotation.txt.gz +!Sample_data_processing = Sequenced reads were trimmed for adaptor sequence and other artifacts. Trimmed reads with average quality ≥20, ≤3 Ns, and ≥32 bases were mapped to C. reinhardtii genome (Phytozome v5.3.1) using TopHat v2.0.8 with Bowtie v2.1.0. Sensitive and fusion mapping was enabled. Valid intron length was 20bp to 25 kbp and minimum distance between intra-chromosomal fusions was 1 Mbp. The library type “fr-firststrand” stated and read alignments with >3 mismatches were discarded. +!Sample_data_processing = Cufflinks v2.1.1 (modified to work on compact genomes) was used to reconstruct the transcripts guided with the Phytozome v5.3.1 reference transcriptome (See supplementary file: reference_gene_model.gtf.gz). Multi-mapped read correction was turned on and transcript composed of >50% multi-mapped reads or <25 reads were discarded. The remaining transcript assemblies from different time points were merged into a unified set of gene models, which was then compared to the annotated transcriptome. Potential noise was filtered from these predicted transcripts. Sequential steps of filtering criteria were applied as follows; 1). FPKM >0 for both replicates at least at one time point; 2) length of CDS>=50 amino acid; candidate coding regions were predicted based on transcript sequences using TransDecoder script v2013-02-25 from the Trinity package, 3) Remove “noise” transcripts of CuffDiff classes ‘E’, ‘O’ and ‘P’ and single exon transcripts of CuffDiff classes ‘.’, ‘C’ and ‘I’. +!Sample_data_processing = Illumina RTA-1.12 to 1.18 software used for basecalling depending on when library is sequenced. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii genome (Phytozome v5.3.1); C.reinhardtii_v5.3_genomic_scaffold_plastids.fasta.gz +!Sample_data_processing = Supplementary_files_format_and_content: peaks list, tab-delimited text files include FPKM values for each sample and the gene/transcript annotations +!Sample_platform_id = GPL15922 +!Sample_contact_name = Chia-Lin,,Wei +!Sample_contact_email = CWei@lbl.gov +!Sample_contact_phone = +1 (925) 927-2593 +!Sample_contact_laboratory = Sequencing Technologies +!Sample_contact_department = Genomic Technologies +!Sample_contact_institute = DOE Joint Genome Institute +!Sample_contact_address = 2800 Mitchell Drive +!Sample_contact_city = Walnut Creek +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 94598 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN02928738 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX658331 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE59629 +!Sample_data_row_count = 0 +^SAMPLE = GSM1666091 +!Sample_title = m6A-IP-light-1 +!Sample_geo_accession = GSM1666091 +!Sample_status = Public on Apr 30 2015 +!Sample_submission_date = Apr 24 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Algae cultured in constant light +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = culture media: Tris-Acetate-Phosphate (TAP) +!Sample_characteristics_ch1 = antibody: m6A antibody, rabbit polyclonal (SYSY, 202003, lot 202003/32) +!Sample_characteristics_ch1 = strain: CC 1609 +!Sample_growth_protocol_ch1 = Wild type Chlamydomonas strain CC 1609, wild type, mt+ (also called 21gr+) was grown in standard Tris-Acetate-Phosphate (TAP) medium in at 25 ºC with 220 rpm shaking and constant light. +!Sample_molecule_ch1 = genomic DNA +!Sample_extract_protocol_ch1 = Genomic DNA was isolated using phenol-chloroform-isoamyl alcohol with overnight RNase A treatment. For MeDIP, genomic DNA is sonicated to 200-400 bp segments, then m6A antibody is used to pull down DNA pieces containing m6A modification which is subject for standard Illumina DNA library construction. +!Sample_extract_protocol_ch1 = Standard DNA sequencing and Stranded RNA-seq protocol from Illumina +!Sample_data_processing = After adaptor trimming and quality control, 50 bp sequence reads were mapped to the Chlamydomonas genome Cre4 (JGI 9) using Bowtie v1.0.1 +!Sample_data_processing = Then MACS2 was introduced to find enriched regions which we called m6A peaks by comparing the reads from IP sample with input sample. FDR cutoff was set to 0.01. +!Sample_data_processing = For enzyme-treated samples, 100 bp paired-end reads are mapped by Bowtie V1.0.1,Reads ends are compared with CATG or GATC map in genome-wide. +!Sample_data_processing = Methylation ratios are determined by the the reads ends information. +!Sample_data_processing = Genome_build: Cre4 +!Sample_data_processing = Supplementary_files_format_and_content: tdf files are generated by samtools and IGVTools. They can be directly loaded into IGV genome browser to visualize the reads distribution of each sequencing sample. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Guan-Zheng,,Luo +!Sample_contact_department = Chemistry +!Sample_contact_institute = UChicago +!Sample_contact_address = 929 E 57th St +!Sample_contact_city = Chicago +!Sample_contact_state = IL +!Sample_contact_zip/postal_code = 60637 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = 5-methylcytidine antibody +!Sample_library_source = genomic +!Sample_library_strategy = MeDIP-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03567036 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1008135 +!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1666nnn/GSM1666091/suppl/GSM1666091_m6A-IP-light-R1.tdf +!Sample_series_id = GSE62690 +!Sample_data_row_count = 0 +^SAMPLE = GSM1666092 +!Sample_title = m6A-IP-light-2 +!Sample_geo_accession = GSM1666092 +!Sample_status = Public on Apr 30 2015 +!Sample_submission_date = Apr 24 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Algae cultured in constant light +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = culture media: Tris-Acetate-Phosphate (TAP) +!Sample_characteristics_ch1 = antibody: m6A antibody, rabbit polyclonal (SYSY, 202003, lot 202003/32) +!Sample_characteristics_ch1 = strain: CC 1609 +!Sample_growth_protocol_ch1 = Wild type Chlamydomonas strain CC 1609, wild type, mt+ (also called 21gr+) was grown in standard Tris-Acetate-Phosphate (TAP) medium in at 25 ºC with 220 rpm shaking and constant light. +!Sample_molecule_ch1 = genomic DNA +!Sample_extract_protocol_ch1 = Genomic DNA was isolated using phenol-chloroform-isoamyl alcohol with overnight RNase A treatment. For MeDIP, genomic DNA is sonicated to 200-400 bp segments, then m6A antibody is used to pull down DNA pieces containing m6A modification which is subject for standard Illumina DNA library construction. +!Sample_extract_protocol_ch1 = Standard DNA sequencing and Stranded RNA-seq protocol from Illumina +!Sample_data_processing = After adaptor trimming and quality control, 50 bp sequence reads were mapped to the Chlamydomonas genome Cre4 (JGI 9) using Bowtie v1.0.1 +!Sample_data_processing = Then MACS2 was introduced to find enriched regions which we called m6A peaks by comparing the reads from IP sample with input sample. FDR cutoff was set to 0.01. +!Sample_data_processing = For enzyme-treated samples, 100 bp paired-end reads are mapped by Bowtie V1.0.1,Reads ends are compared with CATG or GATC map in genome-wide. +!Sample_data_processing = Methylation ratios are determined by the the reads ends information. +!Sample_data_processing = Genome_build: Cre4 +!Sample_data_processing = Supplementary_files_format_and_content: tdf files are generated by samtools and IGVTools. They can be directly loaded into IGV genome browser to visualize the reads distribution of each sequencing sample. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Guan-Zheng,,Luo +!Sample_contact_department = Chemistry +!Sample_contact_institute = UChicago +!Sample_contact_address = 929 E 57th St +!Sample_contact_city = Chicago +!Sample_contact_state = IL +!Sample_contact_zip/postal_code = 60637 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = 5-methylcytidine antibody +!Sample_library_source = genomic +!Sample_library_strategy = MeDIP-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03567037 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1008136 +!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1666nnn/GSM1666092/suppl/GSM1666092_m6A-IP-light-R2.tdf +!Sample_series_id = GSE62690 +!Sample_data_row_count = 0 +^SAMPLE = GSM1666093 +!Sample_title = m6A-IP-dark +!Sample_geo_accession = GSM1666093 +!Sample_status = Public on Apr 30 2015 +!Sample_submission_date = Apr 24 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Algae cultured in constant dark +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = culture media: Tris-Acetate-Phosphate (TAP) +!Sample_characteristics_ch1 = antibody: m6A antibody, rabbit polyclonal (SYSY, 202003, lot 202003/33) +!Sample_characteristics_ch1 = strain: CC 1609 +!Sample_growth_protocol_ch1 = Wild type Chlamydomonas strain CC 1609, wild type, mt+ (also called 21gr+) was grown in standard Tris-Acetate-Phosphate (TAP) medium in at 25 ºC with 220 rpm shaking and constant light. +!Sample_molecule_ch1 = genomic DNA +!Sample_extract_protocol_ch1 = Genomic DNA was isolated using phenol-chloroform-isoamyl alcohol with overnight RNase A treatment. For MeDIP, genomic DNA is sonicated to 200-400 bp segments, then m6A antibody is used to pull down DNA pieces containing m6A modification which is subject for standard Illumina DNA library construction. +!Sample_extract_protocol_ch1 = Standard DNA sequencing and Stranded RNA-seq protocol from Illumina +!Sample_data_processing = After adaptor trimming and quality control, 50 bp sequence reads were mapped to the Chlamydomonas genome Cre4 (JGI 9) using Bowtie v1.0.1 +!Sample_data_processing = Then MACS2 was introduced to find enriched regions which we called m6A peaks by comparing the reads from IP sample with input sample. FDR cutoff was set to 0.01. +!Sample_data_processing = For enzyme-treated samples, 100 bp paired-end reads are mapped by Bowtie V1.0.1,Reads ends are compared with CATG or GATC map in genome-wide. +!Sample_data_processing = Methylation ratios are determined by the the reads ends information. +!Sample_data_processing = Genome_build: Cre4 +!Sample_data_processing = Supplementary_files_format_and_content: tdf files are generated by samtools and IGVTools. They can be directly loaded into IGV genome browser to visualize the reads distribution of each sequencing sample. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Guan-Zheng,,Luo +!Sample_contact_department = Chemistry +!Sample_contact_institute = UChicago +!Sample_contact_address = 929 E 57th St +!Sample_contact_city = Chicago +!Sample_contact_state = IL +!Sample_contact_zip/postal_code = 60637 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = 5-methylcytidine antibody +!Sample_library_source = genomic +!Sample_library_strategy = MeDIP-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03567038 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1008137 +!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1666nnn/GSM1666093/suppl/GSM1666093_m6A-IP-dark.tdf +!Sample_series_id = GSE62690 +!Sample_data_row_count = 0 +^SAMPLE = GSM1666094 +!Sample_title = m6A-Input-light +!Sample_geo_accession = GSM1666094 +!Sample_status = Public on Apr 30 2015 +!Sample_submission_date = Apr 24 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Algae cultured in constant light +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = culture media: Tris-Acetate-Phosphate (TAP) +!Sample_characteristics_ch1 = strain: CC 1609 +!Sample_growth_protocol_ch1 = Wild type Chlamydomonas strain CC 1609, wild type, mt+ (also called 21gr+) was grown in standard Tris-Acetate-Phosphate (TAP) medium in at 25 ºC with 220 rpm shaking and constant light. +!Sample_molecule_ch1 = genomic DNA +!Sample_extract_protocol_ch1 = Genomic DNA was isolated using phenol-chloroform-isoamyl alcohol with overnight RNase A treatment. For MeDIP, genomic DNA is sonicated to 200-400 bp segments, then m6A antibody is used to pull down DNA pieces containing m6A modification which is subject for standard Illumina DNA library construction. +!Sample_extract_protocol_ch1 = Standard DNA sequencing and Stranded RNA-seq protocol from Illumina +!Sample_data_processing = After adaptor trimming and quality control, 50 bp sequence reads were mapped to the Chlamydomonas genome Cre4 (JGI 9) using Bowtie v1.0.1 +!Sample_data_processing = Then MACS2 was introduced to find enriched regions which we called m6A peaks by comparing the reads from IP sample with input sample. FDR cutoff was set to 0.01. +!Sample_data_processing = For enzyme-treated samples, 100 bp paired-end reads are mapped by Bowtie V1.0.1,Reads ends are compared with CATG or GATC map in genome-wide. +!Sample_data_processing = Methylation ratios are determined by the the reads ends information. +!Sample_data_processing = Genome_build: Cre4 +!Sample_data_processing = Supplementary_files_format_and_content: tdf files are generated by samtools and IGVTools. They can be directly loaded into IGV genome browser to visualize the reads distribution of each sequencing sample. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Guan-Zheng,,Luo +!Sample_contact_department = Chemistry +!Sample_contact_institute = UChicago +!Sample_contact_address = 929 E 57th St +!Sample_contact_city = Chicago +!Sample_contact_state = IL +!Sample_contact_zip/postal_code = 60637 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = 5-methylcytidine antibody +!Sample_library_source = genomic +!Sample_library_strategy = MeDIP-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03567039 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1008138 +!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1666nnn/GSM1666094/suppl/GSM1666094_m6A-Input-light.tdf +!Sample_series_id = GSE62690 +!Sample_data_row_count = 0 +^SAMPLE = GSM1666095 +!Sample_title = m6A-Input-dark +!Sample_geo_accession = GSM1666095 +!Sample_status = Public on Apr 30 2015 +!Sample_submission_date = Apr 24 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Algae cultured in constant dark +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = culture media: Tris-Acetate-Phosphate (TAP) +!Sample_characteristics_ch1 = strain: CC 1609 +!Sample_growth_protocol_ch1 = Wild type Chlamydomonas strain CC 1609, wild type, mt+ (also called 21gr+) was grown in standard Tris-Acetate-Phosphate (TAP) medium in at 25 ºC with 220 rpm shaking and constant light. +!Sample_molecule_ch1 = genomic DNA +!Sample_extract_protocol_ch1 = Genomic DNA was isolated using phenol-chloroform-isoamyl alcohol with overnight RNase A treatment. For MeDIP, genomic DNA is sonicated to 200-400 bp segments, then m6A antibody is used to pull down DNA pieces containing m6A modification which is subject for standard Illumina DNA library construction. +!Sample_extract_protocol_ch1 = Standard DNA sequencing and Stranded RNA-seq protocol from Illumina +!Sample_data_processing = After adaptor trimming and quality control, 50 bp sequence reads were mapped to the Chlamydomonas genome Cre4 (JGI 9) using Bowtie v1.0.1 +!Sample_data_processing = Then MACS2 was introduced to find enriched regions which we called m6A peaks by comparing the reads from IP sample with input sample. FDR cutoff was set to 0.01. +!Sample_data_processing = For enzyme-treated samples, 100 bp paired-end reads are mapped by Bowtie V1.0.1,Reads ends are compared with CATG or GATC map in genome-wide. +!Sample_data_processing = Methylation ratios are determined by the the reads ends information. +!Sample_data_processing = Genome_build: Cre4 +!Sample_data_processing = Supplementary_files_format_and_content: tdf files are generated by samtools and IGVTools. They can be directly loaded into IGV genome browser to visualize the reads distribution of each sequencing sample. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Guan-Zheng,,Luo +!Sample_contact_department = Chemistry +!Sample_contact_institute = UChicago +!Sample_contact_address = 929 E 57th St +!Sample_contact_city = Chicago +!Sample_contact_state = IL +!Sample_contact_zip/postal_code = 60637 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = 5-methylcytidine antibody +!Sample_library_source = genomic +!Sample_library_strategy = MeDIP-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03567040 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1008139 +!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1666nnn/GSM1666095/suppl/GSM1666095_m6A-Input-dark.tdf +!Sample_series_id = GSE62690 +!Sample_data_row_count = 0 +^SAMPLE = GSM1666096 +!Sample_title = m6A-DpnII-light +!Sample_geo_accession = GSM1666096 +!Sample_status = Public on Apr 30 2015 +!Sample_submission_date = Apr 24 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Algae cultured in constant light +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = culture media: Tris-Acetate-Phosphate (TAP) +!Sample_characteristics_ch1 = strain: CC 1609 +!Sample_growth_protocol_ch1 = Wild type Chlamydomonas strain CC 1609, wild type, mt+ (also called 21gr+) was grown in standard Tris-Acetate-Phosphate (TAP) medium in at 25 ºC with 220 rpm shaking and constant light. +!Sample_molecule_ch1 = genomic DNA +!Sample_extract_protocol_ch1 = For enzyme digested samples, CviAII or DpnII are added to 10 U/ug and incubated overnight. Digested DNA is sonicated to ~500 bp segments which is subject to DNA library construction. +!Sample_extract_protocol_ch1 = Standard DNA sequencing and Stranded RNA-seq protocol from Illumina +!Sample_description = enzyme-treated +!Sample_data_processing = After adaptor trimming and quality control, 50 bp sequence reads were mapped to the Chlamydomonas genome Cre4 (JGI 9) using Bowtie v1.0.1 +!Sample_data_processing = Then MACS2 was introduced to find enriched regions which we called m6A peaks by comparing the reads from IP sample with input sample. FDR cutoff was set to 0.01. +!Sample_data_processing = For enzyme-treated samples, 100 bp paired-end reads are mapped by Bowtie V1.0.1,Reads ends are compared with CATG or GATC map in genome-wide. +!Sample_data_processing = Methylation ratios are determined by the the reads ends information. +!Sample_data_processing = Genome_build: Cre4 +!Sample_data_processing = Supplementary_files_format_and_content: tdf files are generated by samtools and IGVTools. They can be directly loaded into IGV genome browser to visualize the reads distribution of each sequencing sample. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Guan-Zheng,,Luo +!Sample_contact_department = Chemistry +!Sample_contact_institute = UChicago +!Sample_contact_address = 929 E 57th St +!Sample_contact_city = Chicago +!Sample_contact_state = IL +!Sample_contact_zip/postal_code = 60637 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = other +!Sample_library_source = genomic +!Sample_library_strategy = OTHER +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03567041 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1008140 +!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1666nnn/GSM1666096/suppl/GSM1666096_m6A-DpnII-light.tdf +!Sample_series_id = GSE62690 +!Sample_data_row_count = 0 +^SAMPLE = GSM1666097 +!Sample_title = m6A-DpnII-dark +!Sample_geo_accession = GSM1666097 +!Sample_status = Public on Apr 30 2015 +!Sample_submission_date = Apr 24 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Algae cultured in constant dark +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = culture media: Tris-Acetate-Phosphate (TAP) +!Sample_characteristics_ch1 = strain: CC 1609 +!Sample_growth_protocol_ch1 = Wild type Chlamydomonas strain CC 1609, wild type, mt+ (also called 21gr+) was grown in standard Tris-Acetate-Phosphate (TAP) medium in at 25 ºC with 220 rpm shaking and constant light. +!Sample_molecule_ch1 = genomic DNA +!Sample_extract_protocol_ch1 = For enzyme digested samples, CviAII or DpnII are added to 10 U/ug and incubated overnight. Digested DNA is sonicated to ~500 bp segments which is subject to DNA library construction. +!Sample_extract_protocol_ch1 = Standard DNA sequencing and Stranded RNA-seq protocol from Illumina +!Sample_description = enzyme-treated +!Sample_data_processing = After adaptor trimming and quality control, 50 bp sequence reads were mapped to the Chlamydomonas genome Cre4 (JGI 9) using Bowtie v1.0.1 +!Sample_data_processing = Then MACS2 was introduced to find enriched regions which we called m6A peaks by comparing the reads from IP sample with input sample. FDR cutoff was set to 0.01. +!Sample_data_processing = For enzyme-treated samples, 100 bp paired-end reads are mapped by Bowtie V1.0.1,Reads ends are compared with CATG or GATC map in genome-wide. +!Sample_data_processing = Methylation ratios are determined by the the reads ends information. +!Sample_data_processing = Genome_build: Cre4 +!Sample_data_processing = Supplementary_files_format_and_content: tdf files are generated by samtools and IGVTools. They can be directly loaded into IGV genome browser to visualize the reads distribution of each sequencing sample. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Guan-Zheng,,Luo +!Sample_contact_department = Chemistry +!Sample_contact_institute = UChicago +!Sample_contact_address = 929 E 57th St +!Sample_contact_city = Chicago +!Sample_contact_state = IL +!Sample_contact_zip/postal_code = 60637 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = other +!Sample_library_source = genomic +!Sample_library_strategy = OTHER +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03567042 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1008141 +!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1666nnn/GSM1666097/suppl/GSM1666097_m6A-DpnII-dark.tdf +!Sample_series_id = GSE62690 +!Sample_data_row_count = 0 +^SAMPLE = GSM1666098 +!Sample_title = m6A-CviAII-light +!Sample_geo_accession = GSM1666098 +!Sample_status = Public on Apr 30 2015 +!Sample_submission_date = Apr 24 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Algae cultured in constant light +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = culture media: Tris-Acetate-Phosphate (TAP) +!Sample_characteristics_ch1 = strain: CC 1609 +!Sample_growth_protocol_ch1 = Wild type Chlamydomonas strain CC 1609, wild type, mt+ (also called 21gr+) was grown in standard Tris-Acetate-Phosphate (TAP) medium in at 25 ºC with 220 rpm shaking and constant light. +!Sample_molecule_ch1 = genomic DNA +!Sample_extract_protocol_ch1 = For enzyme digested samples, CviAII or DpnII are added to 10 U/ug and incubated overnight. Digested DNA is sonicated to ~500 bp segments which is subject to DNA library construction. +!Sample_extract_protocol_ch1 = Standard DNA sequencing and Stranded RNA-seq protocol from Illumina +!Sample_description = enzyme-treated +!Sample_data_processing = After adaptor trimming and quality control, 50 bp sequence reads were mapped to the Chlamydomonas genome Cre4 (JGI 9) using Bowtie v1.0.1 +!Sample_data_processing = Then MACS2 was introduced to find enriched regions which we called m6A peaks by comparing the reads from IP sample with input sample. FDR cutoff was set to 0.01. +!Sample_data_processing = For enzyme-treated samples, 100 bp paired-end reads are mapped by Bowtie V1.0.1,Reads ends are compared with CATG or GATC map in genome-wide. +!Sample_data_processing = Methylation ratios are determined by the the reads ends information. +!Sample_data_processing = Genome_build: Cre4 +!Sample_data_processing = Supplementary_files_format_and_content: tdf files are generated by samtools and IGVTools. They can be directly loaded into IGV genome browser to visualize the reads distribution of each sequencing sample. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Guan-Zheng,,Luo +!Sample_contact_department = Chemistry +!Sample_contact_institute = UChicago +!Sample_contact_address = 929 E 57th St +!Sample_contact_city = Chicago +!Sample_contact_state = IL +!Sample_contact_zip/postal_code = 60637 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = other +!Sample_library_source = genomic +!Sample_library_strategy = OTHER +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03567043 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1008142 +!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1666nnn/GSM1666098/suppl/GSM1666098_m6A-CviAII-light.tdf +!Sample_series_id = GSE62690 +!Sample_data_row_count = 0 +^SAMPLE = GSM1666099 +!Sample_title = m6A-CviAII-dark +!Sample_geo_accession = GSM1666099 +!Sample_status = Public on Apr 30 2015 +!Sample_submission_date = Apr 24 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Algae cultured in constant dark +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = culture media: Tris-Acetate-Phosphate (TAP) +!Sample_characteristics_ch1 = strain: CC 1609 +!Sample_growth_protocol_ch1 = Wild type Chlamydomonas strain CC 1609, wild type, mt+ (also called 21gr+) was grown in standard Tris-Acetate-Phosphate (TAP) medium in at 25 ºC with 220 rpm shaking and constant light. +!Sample_molecule_ch1 = genomic DNA +!Sample_extract_protocol_ch1 = For enzyme digested samples, CviAII or DpnII are added to 10 U/ug and incubated overnight. Digested DNA is sonicated to ~500 bp segments which is subject to DNA library construction. +!Sample_extract_protocol_ch1 = Standard DNA sequencing and Stranded RNA-seq protocol from Illumina +!Sample_description = enzyme-treated +!Sample_data_processing = After adaptor trimming and quality control, 50 bp sequence reads were mapped to the Chlamydomonas genome Cre4 (JGI 9) using Bowtie v1.0.1 +!Sample_data_processing = Then MACS2 was introduced to find enriched regions which we called m6A peaks by comparing the reads from IP sample with input sample. FDR cutoff was set to 0.01. +!Sample_data_processing = For enzyme-treated samples, 100 bp paired-end reads are mapped by Bowtie V1.0.1,Reads ends are compared with CATG or GATC map in genome-wide. +!Sample_data_processing = Methylation ratios are determined by the the reads ends information. +!Sample_data_processing = Genome_build: Cre4 +!Sample_data_processing = Supplementary_files_format_and_content: tdf files are generated by samtools and IGVTools. They can be directly loaded into IGV genome browser to visualize the reads distribution of each sequencing sample. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Guan-Zheng,,Luo +!Sample_contact_department = Chemistry +!Sample_contact_institute = UChicago +!Sample_contact_address = 929 E 57th St +!Sample_contact_city = Chicago +!Sample_contact_state = IL +!Sample_contact_zip/postal_code = 60637 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = other +!Sample_library_source = genomic +!Sample_library_strategy = OTHER +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03567044 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1008143 +!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1666nnn/GSM1666099/suppl/GSM1666099_m6A-CviAII-dark.tdf +!Sample_series_id = GSE62690 +!Sample_data_row_count = 0 +^SAMPLE = GSM1666100 +!Sample_title = MNase-seq +!Sample_geo_accession = GSM1666100 +!Sample_status = Public on Apr 30 2015 +!Sample_submission_date = Apr 24 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Algae cultured in constant light +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = culture media: Tris-Acetate-Phosphate (TAP) +!Sample_characteristics_ch1 = strain: CC 1609 +!Sample_growth_protocol_ch1 = Wild type Chlamydomonas strain CC 1609, wild type, mt+ (also called 21gr+) was grown in standard Tris-Acetate-Phosphate (TAP) medium in at 25 ºC with 220 rpm shaking and constant light. +!Sample_molecule_ch1 = genomic DNA +!Sample_extract_protocol_ch1 = For nucleosome profiling, nuclei is extracted and digested by Mnase for 12 minutes. After agarose gel electrophoresis, 150 bp band is cutted and purifiled for standard illumina DNA library construction. +!Sample_extract_protocol_ch1 = Standard DNA sequencing and Stranded RNA-seq protocol from Illumina +!Sample_data_processing = After adaptor trimming and quality control, 50 bp sequence reads were mapped to the Chlamydomonas genome Cre4 (JGI 9) using Bowtie v1.0.1 +!Sample_data_processing = Then MACS2 was introduced to find enriched regions which we called m6A peaks by comparing the reads from IP sample with input sample. FDR cutoff was set to 0.01. +!Sample_data_processing = For enzyme-treated samples, 100 bp paired-end reads are mapped by Bowtie V1.0.1,Reads ends are compared with CATG or GATC map in genome-wide. +!Sample_data_processing = Methylation ratios are determined by the the reads ends information. +!Sample_data_processing = Genome_build: Cre4 +!Sample_data_processing = Supplementary_files_format_and_content: tdf files are generated by samtools and IGVTools. They can be directly loaded into IGV genome browser to visualize the reads distribution of each sequencing sample. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Guan-Zheng,,Luo +!Sample_contact_department = Chemistry +!Sample_contact_institute = UChicago +!Sample_contact_address = 929 E 57th St +!Sample_contact_city = Chicago +!Sample_contact_state = IL +!Sample_contact_zip/postal_code = 60637 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = MNase +!Sample_library_source = genomic +!Sample_library_strategy = MNase-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03567045 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1008144 +!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1666nnn/GSM1666100/suppl/GSM1666100_Mnase-seq.tdf +!Sample_series_id = GSE62690 +!Sample_data_row_count = 0 +^SAMPLE = GSM1666101 +!Sample_title = RNA-light-1 +!Sample_geo_accession = GSM1666101 +!Sample_status = Public on Apr 30 2015 +!Sample_submission_date = Apr 24 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Algae cultured in constant light +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = culture media: Tris-Acetate-Phosphate (TAP) +!Sample_characteristics_ch1 = strain: CC 1609 +!Sample_growth_protocol_ch1 = Wild type Chlamydomonas strain CC 1609, wild type, mt+ (also called 21gr+) was grown in standard Tris-Acetate-Phosphate (TAP) medium in at 25 ºC with 220 rpm shaking and constant light. +!Sample_molecule_ch1 = polyA RNA +!Sample_extract_protocol_ch1 = For RNA samples, poly-A tailed RNA is extracted by Oligo(dT)/Magnetic Capture Method. Then Stranded RNA library is constructed by the instruction of Illumina. +!Sample_extract_protocol_ch1 = Standard DNA sequencing and Stranded RNA-seq protocol from Illumina +!Sample_data_processing = After adaptor trimming and quality control, 50 bp sequence reads were mapped to the Chlamydomonas genome Cre4 (JGI 9) using Bowtie v1.0.1 +!Sample_data_processing = Then MACS2 was introduced to find enriched regions which we called m6A peaks by comparing the reads from IP sample with input sample. FDR cutoff was set to 0.01. +!Sample_data_processing = For enzyme-treated samples, 100 bp paired-end reads are mapped by Bowtie V1.0.1,Reads ends are compared with CATG or GATC map in genome-wide. +!Sample_data_processing = Methylation ratios are determined by the the reads ends information. +!Sample_data_processing = Genome_build: Cre4 +!Sample_data_processing = Supplementary_files_format_and_content: tdf files are generated by samtools and IGVTools. They can be directly loaded into IGV genome browser to visualize the reads distribution of each sequencing sample. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Guan-Zheng,,Luo +!Sample_contact_department = Chemistry +!Sample_contact_institute = UChicago +!Sample_contact_address = 929 E 57th St +!Sample_contact_city = Chicago +!Sample_contact_state = IL +!Sample_contact_zip/postal_code = 60637 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03567046 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1008145 +!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1666nnn/GSM1666101/suppl/GSM1666101_RNAseq-light-R1.tdf +!Sample_series_id = GSE62690 +!Sample_data_row_count = 0 +^SAMPLE = GSM1666102 +!Sample_title = RNA-light-2 +!Sample_geo_accession = GSM1666102 +!Sample_status = Public on Apr 30 2015 +!Sample_submission_date = Apr 24 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Algae cultured in constant light +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = culture media: Tris-Acetate-Phosphate (TAP) +!Sample_characteristics_ch1 = strain: CC 1609 +!Sample_growth_protocol_ch1 = Wild type Chlamydomonas strain CC 1609, wild type, mt+ (also called 21gr+) was grown in standard Tris-Acetate-Phosphate (TAP) medium in at 25 ºC with 220 rpm shaking and constant light. +!Sample_molecule_ch1 = polyA RNA +!Sample_extract_protocol_ch1 = For RNA samples, poly-A tailed RNA is extracted by Oligo(dT)/Magnetic Capture Method. Then Stranded RNA library is constructed by the instruction of Illumina. +!Sample_extract_protocol_ch1 = Standard DNA sequencing and Stranded RNA-seq protocol from Illumina +!Sample_data_processing = After adaptor trimming and quality control, 50 bp sequence reads were mapped to the Chlamydomonas genome Cre4 (JGI 9) using Bowtie v1.0.1 +!Sample_data_processing = Then MACS2 was introduced to find enriched regions which we called m6A peaks by comparing the reads from IP sample with input sample. FDR cutoff was set to 0.01. +!Sample_data_processing = For enzyme-treated samples, 100 bp paired-end reads are mapped by Bowtie V1.0.1,Reads ends are compared with CATG or GATC map in genome-wide. +!Sample_data_processing = Methylation ratios are determined by the the reads ends information. +!Sample_data_processing = Genome_build: Cre4 +!Sample_data_processing = Supplementary_files_format_and_content: tdf files are generated by samtools and IGVTools. They can be directly loaded into IGV genome browser to visualize the reads distribution of each sequencing sample. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Guan-Zheng,,Luo +!Sample_contact_department = Chemistry +!Sample_contact_institute = UChicago +!Sample_contact_address = 929 E 57th St +!Sample_contact_city = Chicago +!Sample_contact_state = IL +!Sample_contact_zip/postal_code = 60637 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03567047 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1008146 +!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1666nnn/GSM1666102/suppl/GSM1666102_RNAseq-light-R2.tdf +!Sample_series_id = GSE62690 +!Sample_data_row_count = 0 +^SAMPLE = GSM1666103 +!Sample_title = RNA-dark-1 +!Sample_geo_accession = GSM1666103 +!Sample_status = Public on Apr 30 2015 +!Sample_submission_date = Apr 24 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Algae cultured in constant dark +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = culture media: Tris-Acetate-Phosphate (TAP) +!Sample_characteristics_ch1 = strain: CC 1609 +!Sample_growth_protocol_ch1 = Wild type Chlamydomonas strain CC 1609, wild type, mt+ (also called 21gr+) was grown in standard Tris-Acetate-Phosphate (TAP) medium in at 25 ºC with 220 rpm shaking and constant light. +!Sample_molecule_ch1 = polyA RNA +!Sample_extract_protocol_ch1 = For RNA samples, poly-A tailed RNA is extracted by Oligo(dT)/Magnetic Capture Method. Then Stranded RNA library is constructed by the instruction of Illumina. +!Sample_extract_protocol_ch1 = Standard DNA sequencing and Stranded RNA-seq protocol from Illumina +!Sample_data_processing = After adaptor trimming and quality control, 50 bp sequence reads were mapped to the Chlamydomonas genome Cre4 (JGI 9) using Bowtie v1.0.1 +!Sample_data_processing = Then MACS2 was introduced to find enriched regions which we called m6A peaks by comparing the reads from IP sample with input sample. FDR cutoff was set to 0.01. +!Sample_data_processing = For enzyme-treated samples, 100 bp paired-end reads are mapped by Bowtie V1.0.1,Reads ends are compared with CATG or GATC map in genome-wide. +!Sample_data_processing = Methylation ratios are determined by the the reads ends information. +!Sample_data_processing = Genome_build: Cre4 +!Sample_data_processing = Supplementary_files_format_and_content: tdf files are generated by samtools and IGVTools. They can be directly loaded into IGV genome browser to visualize the reads distribution of each sequencing sample. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Guan-Zheng,,Luo +!Sample_contact_department = Chemistry +!Sample_contact_institute = UChicago +!Sample_contact_address = 929 E 57th St +!Sample_contact_city = Chicago +!Sample_contact_state = IL +!Sample_contact_zip/postal_code = 60637 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03567048 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1008147 +!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1666nnn/GSM1666103/suppl/GSM1666103_RNAseq-dark-R1.tdf +!Sample_series_id = GSE62690 +!Sample_data_row_count = 0 +^SAMPLE = GSM1666104 +!Sample_title = RNA-dark-2 +!Sample_geo_accession = GSM1666104 +!Sample_status = Public on Apr 30 2015 +!Sample_submission_date = Apr 24 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Algae cultured in constant dark +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = culture media: Tris-Acetate-Phosphate (TAP) +!Sample_characteristics_ch1 = strain: CC 1609 +!Sample_growth_protocol_ch1 = Wild type Chlamydomonas strain CC 1609, wild type, mt+ (also called 21gr+) was grown in standard Tris-Acetate-Phosphate (TAP) medium in at 25 ºC with 220 rpm shaking and constant light. +!Sample_molecule_ch1 = polyA RNA +!Sample_extract_protocol_ch1 = For RNA samples, poly-A tailed RNA is extracted by Oligo(dT)/Magnetic Capture Method. Then Stranded RNA library is constructed by the instruction of Illumina. +!Sample_extract_protocol_ch1 = Standard DNA sequencing and Stranded RNA-seq protocol from Illumina +!Sample_data_processing = After adaptor trimming and quality control, 50 bp sequence reads were mapped to the Chlamydomonas genome Cre4 (JGI 9) using Bowtie v1.0.1 +!Sample_data_processing = Then MACS2 was introduced to find enriched regions which we called m6A peaks by comparing the reads from IP sample with input sample. FDR cutoff was set to 0.01. +!Sample_data_processing = For enzyme-treated samples, 100 bp paired-end reads are mapped by Bowtie V1.0.1,Reads ends are compared with CATG or GATC map in genome-wide. +!Sample_data_processing = Methylation ratios are determined by the the reads ends information. +!Sample_data_processing = Genome_build: Cre4 +!Sample_data_processing = Supplementary_files_format_and_content: tdf files are generated by samtools and IGVTools. They can be directly loaded into IGV genome browser to visualize the reads distribution of each sequencing sample. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Guan-Zheng,,Luo +!Sample_contact_department = Chemistry +!Sample_contact_institute = UChicago +!Sample_contact_address = 929 E 57th St +!Sample_contact_city = Chicago +!Sample_contact_state = IL +!Sample_contact_zip/postal_code = 60637 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03567049 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1008148 +!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1666nnn/GSM1666104/suppl/GSM1666104_RNAseq-dark-R2.tdf +!Sample_series_id = GSE62690 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835200 +!Sample_title = 1_1 +!Sample_geo_accession = GSM1835200 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 1 +!Sample_characteristics_ch1 = protocol: light +!Sample_characteristics_ch1 = time (zeitgeber): ZT1 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941585 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122839 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835201 +!Sample_title = 2_1 +!Sample_geo_accession = GSM1835201 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 1 +!Sample_characteristics_ch1 = protocol: light +!Sample_characteristics_ch1 = time (zeitgeber): ZT2 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941586 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122840 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835202 +!Sample_title = 3_1 +!Sample_geo_accession = GSM1835202 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 1 +!Sample_characteristics_ch1 = protocol: light +!Sample_characteristics_ch1 = time (zeitgeber): ZT3 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941587 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122841 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835203 +!Sample_title = 4_1 +!Sample_geo_accession = GSM1835203 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 1 +!Sample_characteristics_ch1 = protocol: light +!Sample_characteristics_ch1 = time (zeitgeber): ZT4 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941588 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122842 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835204 +!Sample_title = 5_1 +!Sample_geo_accession = GSM1835204 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 1 +!Sample_characteristics_ch1 = protocol: light +!Sample_characteristics_ch1 = time (zeitgeber): ZT5 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941589 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122843 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835205 +!Sample_title = 6_1 +!Sample_geo_accession = GSM1835205 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 1 +!Sample_characteristics_ch1 = protocol: light +!Sample_characteristics_ch1 = time (zeitgeber): ZT6 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941590 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122844 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835206 +!Sample_title = 7_1 +!Sample_geo_accession = GSM1835206 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 1 +!Sample_characteristics_ch1 = protocol: light +!Sample_characteristics_ch1 = time (zeitgeber): ZT7 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941591 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122845 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835207 +!Sample_title = 8_1 +!Sample_geo_accession = GSM1835207 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 1 +!Sample_characteristics_ch1 = protocol: light +!Sample_characteristics_ch1 = time (zeitgeber): ZT8 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941592 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122846 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835208 +!Sample_title = 9_1 +!Sample_geo_accession = GSM1835208 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 1 +!Sample_characteristics_ch1 = protocol: light +!Sample_characteristics_ch1 = time (zeitgeber): ZT9 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941593 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122847 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835209 +!Sample_title = 10_1 +!Sample_geo_accession = GSM1835209 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 1 +!Sample_characteristics_ch1 = protocol: light +!Sample_characteristics_ch1 = time (zeitgeber): ZT10 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941594 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122848 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835210 +!Sample_title = 11_1 +!Sample_geo_accession = GSM1835210 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 1 +!Sample_characteristics_ch1 = protocol: light +!Sample_characteristics_ch1 = time (zeitgeber): ZT11 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941595 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122849 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835211 +!Sample_title = 11.5_1 +!Sample_geo_accession = GSM1835211 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 1 +!Sample_characteristics_ch1 = protocol: light +!Sample_characteristics_ch1 = time (zeitgeber): ZT11.5 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941596 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122850 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835212 +!Sample_title = 12_1 +!Sample_geo_accession = GSM1835212 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 1 +!Sample_characteristics_ch1 = protocol: light +!Sample_characteristics_ch1 = time (zeitgeber): ZT12 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941597 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122851 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835213 +!Sample_title = 12.5_1 +!Sample_geo_accession = GSM1835213 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 1 +!Sample_characteristics_ch1 = protocol: dark +!Sample_characteristics_ch1 = time (zeitgeber): ZT12.5 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941598 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122852 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835214 +!Sample_title = 13_1 +!Sample_geo_accession = GSM1835214 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 1 +!Sample_characteristics_ch1 = protocol: dark +!Sample_characteristics_ch1 = time (zeitgeber): ZT13 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941599 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122853 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835215 +!Sample_title = 13.5_1 +!Sample_geo_accession = GSM1835215 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 1 +!Sample_characteristics_ch1 = protocol: dark +!Sample_characteristics_ch1 = time (zeitgeber): ZT13.5 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941600 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122854 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835216 +!Sample_title = 14_1 +!Sample_geo_accession = GSM1835216 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 1 +!Sample_characteristics_ch1 = protocol: dark +!Sample_characteristics_ch1 = time (zeitgeber): ZT14 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941601 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122855 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835217 +!Sample_title = 14.5_1 +!Sample_geo_accession = GSM1835217 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 1 +!Sample_characteristics_ch1 = protocol: dark +!Sample_characteristics_ch1 = time (zeitgeber): ZT14.5 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941602 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122856 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835218 +!Sample_title = 15_1 +!Sample_geo_accession = GSM1835218 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 1 +!Sample_characteristics_ch1 = protocol: dark +!Sample_characteristics_ch1 = time (zeitgeber): ZT15 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941603 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122857 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835219 +!Sample_title = 16_1 +!Sample_geo_accession = GSM1835219 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 1 +!Sample_characteristics_ch1 = protocol: dark +!Sample_characteristics_ch1 = time (zeitgeber): ZT16 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941604 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122858 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835220 +!Sample_title = 17_1 +!Sample_geo_accession = GSM1835220 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 1 +!Sample_characteristics_ch1 = protocol: dark +!Sample_characteristics_ch1 = time (zeitgeber): ZT17 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941605 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122859 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835221 +!Sample_title = 18_1 +!Sample_geo_accession = GSM1835221 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 1 +!Sample_characteristics_ch1 = protocol: dark +!Sample_characteristics_ch1 = time (zeitgeber): ZT18 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941606 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122860 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835222 +!Sample_title = 19_1 +!Sample_geo_accession = GSM1835222 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 1 +!Sample_characteristics_ch1 = protocol: dark +!Sample_characteristics_ch1 = time (zeitgeber): ZT19 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941607 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122861 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835223 +!Sample_title = 20_1 +!Sample_geo_accession = GSM1835223 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 1 +!Sample_characteristics_ch1 = protocol: dark +!Sample_characteristics_ch1 = time (zeitgeber): ZT20 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941608 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122862 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835224 +!Sample_title = 21_1 +!Sample_geo_accession = GSM1835224 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 1 +!Sample_characteristics_ch1 = protocol: dark +!Sample_characteristics_ch1 = time (zeitgeber): ZT21 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941609 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122863 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835225 +!Sample_title = 22_1 +!Sample_geo_accession = GSM1835225 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 1 +!Sample_characteristics_ch1 = protocol: dark +!Sample_characteristics_ch1 = time (zeitgeber): ZT22 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941610 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122864 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835226 +!Sample_title = 23_1 +!Sample_geo_accession = GSM1835226 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 1 +!Sample_characteristics_ch1 = protocol: dark +!Sample_characteristics_ch1 = time (zeitgeber): ZT23 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941611 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122865 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835227 +!Sample_title = 24_1 +!Sample_geo_accession = GSM1835227 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 1 +!Sample_characteristics_ch1 = protocol: dark +!Sample_characteristics_ch1 = time (zeitgeber): ZT24 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941612 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122866 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835228 +!Sample_title = 1_2 +!Sample_geo_accession = GSM1835228 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 2 +!Sample_characteristics_ch1 = protocol: light +!Sample_characteristics_ch1 = time (zeitgeber): ZT1 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941613 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122867 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835229 +!Sample_title = 2_2 +!Sample_geo_accession = GSM1835229 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 2 +!Sample_characteristics_ch1 = protocol: light +!Sample_characteristics_ch1 = time (zeitgeber): ZT2 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941614 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122868 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835230 +!Sample_title = 3_2 +!Sample_geo_accession = GSM1835230 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 2 +!Sample_characteristics_ch1 = protocol: light +!Sample_characteristics_ch1 = time (zeitgeber): ZT3 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941616 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122869 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835231 +!Sample_title = 4_2 +!Sample_geo_accession = GSM1835231 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 2 +!Sample_characteristics_ch1 = protocol: light +!Sample_characteristics_ch1 = time (zeitgeber): ZT4 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941617 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122870 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835232 +!Sample_title = 5_2 +!Sample_geo_accession = GSM1835232 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 2 +!Sample_characteristics_ch1 = protocol: light +!Sample_characteristics_ch1 = time (zeitgeber): ZT5 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941618 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122871 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835233 +!Sample_title = 6_2 +!Sample_geo_accession = GSM1835233 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 2 +!Sample_characteristics_ch1 = protocol: light +!Sample_characteristics_ch1 = time (zeitgeber): ZT6 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941619 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122872 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835234 +!Sample_title = 7_2 +!Sample_geo_accession = GSM1835234 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 2 +!Sample_characteristics_ch1 = protocol: light +!Sample_characteristics_ch1 = time (zeitgeber): ZT7 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941620 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122873 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835235 +!Sample_title = 8_2 +!Sample_geo_accession = GSM1835235 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 2 +!Sample_characteristics_ch1 = protocol: light +!Sample_characteristics_ch1 = time (zeitgeber): ZT8 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941621 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122874 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835236 +!Sample_title = 9_2 +!Sample_geo_accession = GSM1835236 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 2 +!Sample_characteristics_ch1 = protocol: light +!Sample_characteristics_ch1 = time (zeitgeber): ZT9 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941622 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122875 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835237 +!Sample_title = 10_2 +!Sample_geo_accession = GSM1835237 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 2 +!Sample_characteristics_ch1 = protocol: light +!Sample_characteristics_ch1 = time (zeitgeber): ZT10 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941615 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122876 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835238 +!Sample_title = 11_2 +!Sample_geo_accession = GSM1835238 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 2 +!Sample_characteristics_ch1 = protocol: light +!Sample_characteristics_ch1 = time (zeitgeber): ZT11 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941623 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122877 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835239 +!Sample_title = 11.5_2 +!Sample_geo_accession = GSM1835239 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 2 +!Sample_characteristics_ch1 = protocol: light +!Sample_characteristics_ch1 = time (zeitgeber): ZT11.5 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941624 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122878 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835240 +!Sample_title = 12_2 +!Sample_geo_accession = GSM1835240 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 2 +!Sample_characteristics_ch1 = protocol: light +!Sample_characteristics_ch1 = time (zeitgeber): ZT12 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941625 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122879 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835241 +!Sample_title = 12.5_2 +!Sample_geo_accession = GSM1835241 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 2 +!Sample_characteristics_ch1 = protocol: dark +!Sample_characteristics_ch1 = time (zeitgeber): ZT12.5 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941626 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122880 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835242 +!Sample_title = 13_2 +!Sample_geo_accession = GSM1835242 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 2 +!Sample_characteristics_ch1 = protocol: dark +!Sample_characteristics_ch1 = time (zeitgeber): ZT13 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941627 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122881 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835243 +!Sample_title = 13.5_2 +!Sample_geo_accession = GSM1835243 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 2 +!Sample_characteristics_ch1 = protocol: dark +!Sample_characteristics_ch1 = time (zeitgeber): ZT13.5 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941628 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122882 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835244 +!Sample_title = 14_2 +!Sample_geo_accession = GSM1835244 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 2 +!Sample_characteristics_ch1 = protocol: dark +!Sample_characteristics_ch1 = time (zeitgeber): ZT14 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941629 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122883 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835245 +!Sample_title = 14.5_2 +!Sample_geo_accession = GSM1835245 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 2 +!Sample_characteristics_ch1 = protocol: dark +!Sample_characteristics_ch1 = time (zeitgeber): ZT14.5 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941630 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122884 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835246 +!Sample_title = 15_2 +!Sample_geo_accession = GSM1835246 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 2 +!Sample_characteristics_ch1 = protocol: dark +!Sample_characteristics_ch1 = time (zeitgeber): ZT15 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941631 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122885 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835247 +!Sample_title = 16_2 +!Sample_geo_accession = GSM1835247 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 2 +!Sample_characteristics_ch1 = protocol: dark +!Sample_characteristics_ch1 = time (zeitgeber): ZT16 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941632 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122886 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835248 +!Sample_title = 17_2 +!Sample_geo_accession = GSM1835248 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 2 +!Sample_characteristics_ch1 = protocol: dark +!Sample_characteristics_ch1 = time (zeitgeber): ZT17 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941633 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122887 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835249 +!Sample_title = 18_2 +!Sample_geo_accession = GSM1835249 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 2 +!Sample_characteristics_ch1 = protocol: dark +!Sample_characteristics_ch1 = time (zeitgeber): ZT18 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941634 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122888 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835250 +!Sample_title = 19_2 +!Sample_geo_accession = GSM1835250 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 2 +!Sample_characteristics_ch1 = protocol: dark +!Sample_characteristics_ch1 = time (zeitgeber): ZT19 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941635 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122889 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835251 +!Sample_title = 20_2 +!Sample_geo_accession = GSM1835251 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 2 +!Sample_characteristics_ch1 = protocol: dark +!Sample_characteristics_ch1 = time (zeitgeber): ZT20 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941636 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122890 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835252 +!Sample_title = 21_2 +!Sample_geo_accession = GSM1835252 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 2 +!Sample_characteristics_ch1 = protocol: dark +!Sample_characteristics_ch1 = time (zeitgeber): ZT21 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941637 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122891 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835253 +!Sample_title = 22_2 +!Sample_geo_accession = GSM1835253 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 2 +!Sample_characteristics_ch1 = protocol: dark +!Sample_characteristics_ch1 = time (zeitgeber): ZT22 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941638 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122892 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835254 +!Sample_title = 23_2 +!Sample_geo_accession = GSM1835254 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 2 +!Sample_characteristics_ch1 = protocol: dark +!Sample_characteristics_ch1 = time (zeitgeber): ZT23 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941639 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122893 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835255 +!Sample_title = 24_2 +!Sample_geo_accession = GSM1835255 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 2 +!Sample_characteristics_ch1 = protocol: dark +!Sample_characteristics_ch1 = time (zeitgeber): ZT24 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941640 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122894 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM2051194 +!Sample_title = JLDD4ANT4 Biological Replicate #1 +!Sample_geo_accession = GSM2051194 +!Sample_status = Public on Jan 24 2019 +!Sample_submission_date = Jan 29 2016 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas reinhardtii 4A+ wild-type +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 4A+ +!Sample_characteristics_ch1 = treatment: 0 mM +!Sample_characteristics_ch1 = light: 4h white light +!Sample_treatment_protocol_ch1 = Cells (4A+, hmox1, ho1C1 or ho1C2) were innoculated in TAP medium (containing 0.5% v/v methanol with or without 0.1 mM BV IXα) at 5×104 cells/ml and grown in the dark at 22 C until the cell density reached ~2×106 cells/ml and then illuminated with white light (150 µmol photons m-2 s-1) for 30 minutes. Cells were harvested before and after light treatment and total RNA was extracted with Trizol and Qiagen RNeasy mini kit. +!Sample_growth_protocol_ch1 = All strains were maintained on TAP (Tris-Acetate-Phosphate) plates with modified recipe of trace metal elements {Kropat, 2011} at room temperature (22 C) under continuous illumination (30 μmol photons m−2 s−1). Liquid cultures were grown on a gyratory shaker (~100 rpm) heterotrophically on TAP medium in darkness. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was prepared as described previously {Castruita, 2011} and RNA quality was assessed by an Agilent 2100 Bioanalyzer at the UC Davis Genome Center. RNA-Seq libraries were sequenced as single-end 100mers using the HiSeq platform from Illumina. +!Sample_description = Illumina's RNA-Seq whole transcriptome analysis +!Sample_data_processing = Illumina Casava1.8 software used for basecalling. +!Sample_data_processing = The STAR aligner (v2.3.0) was used to generate the genome index and perform alignments in single-end mode. Reads were aligned to a genome index that included both the genome sequence (Chlamydomonas reinhardtii v5.5 assembly) and the exon/intron structure of known gene models (Augustus 11). Relevant alignment parameters included: multimapping score range=0.66, minimum alignment length=75%. +!Sample_data_processing = Alignment files were used to generate gene-level count summaries with HTSeq (unique hits and “intersection-strict” mode for version v0.6.1p2). +!Sample_data_processing = Genome_build: version 5.5 assembly of the Chlamydomonas genome +!Sample_data_processing = Supplementary_files_format_and_content: Per-library expression estimates in units of FPKMs. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN04448186 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1553139 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE77388 +!Sample_data_row_count = 0 +^SAMPLE = GSM2051195 +!Sample_title = JLDD4ANT4 Biological Replicate #2 +!Sample_geo_accession = GSM2051195 +!Sample_status = Public on Jan 24 2019 +!Sample_submission_date = Jan 29 2016 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas reinhardtii 4A+ wild-type +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 4A+ +!Sample_characteristics_ch1 = treatment: 0 mM +!Sample_characteristics_ch1 = light: 4h white light +!Sample_treatment_protocol_ch1 = Cells (4A+, hmox1, ho1C1 or ho1C2) were innoculated in TAP medium (containing 0.5% v/v methanol with or without 0.1 mM BV IXα) at 5×104 cells/ml and grown in the dark at 22 C until the cell density reached ~2×106 cells/ml and then illuminated with white light (150 µmol photons m-2 s-1) for 30 minutes. Cells were harvested before and after light treatment and total RNA was extracted with Trizol and Qiagen RNeasy mini kit. +!Sample_growth_protocol_ch1 = All strains were maintained on TAP (Tris-Acetate-Phosphate) plates with modified recipe of trace metal elements {Kropat, 2011} at room temperature (22 C) under continuous illumination (30 μmol photons m−2 s−1). Liquid cultures were grown on a gyratory shaker (~100 rpm) heterotrophically on TAP medium in darkness. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was prepared as described previously {Castruita, 2011} and RNA quality was assessed by an Agilent 2100 Bioanalyzer at the UC Davis Genome Center. RNA-Seq libraries were sequenced as single-end 100mers using the HiSeq platform from Illumina. +!Sample_description = Illumina's RNA-Seq whole transcriptome analysis +!Sample_data_processing = Illumina Casava1.8 software used for basecalling. +!Sample_data_processing = The STAR aligner (v2.3.0) was used to generate the genome index and perform alignments in single-end mode. Reads were aligned to a genome index that included both the genome sequence (Chlamydomonas reinhardtii v5.5 assembly) and the exon/intron structure of known gene models (Augustus 11). Relevant alignment parameters included: multimapping score range=0.66, minimum alignment length=75%. +!Sample_data_processing = Alignment files were used to generate gene-level count summaries with HTSeq (unique hits and “intersection-strict” mode for version v0.6.1p2). +!Sample_data_processing = Genome_build: version 5.5 assembly of the Chlamydomonas genome +!Sample_data_processing = Supplementary_files_format_and_content: Per-library expression estimates in units of FPKMs. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN04448187 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1553140 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE77388 +!Sample_data_row_count = 0 +^SAMPLE = GSM2051196 +!Sample_title = JLDD4ABV4 Biological Replicate #1 +!Sample_geo_accession = GSM2051196 +!Sample_status = Public on Jan 24 2019 +!Sample_submission_date = Jan 29 2016 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas reinhardtii 4A+ wild-type +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 4A+ +!Sample_characteristics_ch1 = treatment: 0.1 mM +!Sample_characteristics_ch1 = light: 4h white light +!Sample_treatment_protocol_ch1 = Cells (4A+, hmox1, ho1C1 or ho1C2) were innoculated in TAP medium (containing 0.5% v/v methanol with or without 0.1 mM BV IXα) at 5×104 cells/ml and grown in the dark at 22 C until the cell density reached ~2×106 cells/ml and then illuminated with white light (150 µmol photons m-2 s-1) for 30 minutes. Cells were harvested before and after light treatment and total RNA was extracted with Trizol and Qiagen RNeasy mini kit. +!Sample_growth_protocol_ch1 = All strains were maintained on TAP (Tris-Acetate-Phosphate) plates with modified recipe of trace metal elements {Kropat, 2011} at room temperature (22 C) under continuous illumination (30 μmol photons m−2 s−1). Liquid cultures were grown on a gyratory shaker (~100 rpm) heterotrophically on TAP medium in darkness. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was prepared as described previously {Castruita, 2011} and RNA quality was assessed by an Agilent 2100 Bioanalyzer at the UC Davis Genome Center. RNA-Seq libraries were sequenced as single-end 100mers using the HiSeq platform from Illumina. +!Sample_description = Illumina's RNA-Seq whole transcriptome analysis +!Sample_data_processing = Illumina Casava1.8 software used for basecalling. +!Sample_data_processing = The STAR aligner (v2.3.0) was used to generate the genome index and perform alignments in single-end mode. Reads were aligned to a genome index that included both the genome sequence (Chlamydomonas reinhardtii v5.5 assembly) and the exon/intron structure of known gene models (Augustus 11). Relevant alignment parameters included: multimapping score range=0.66, minimum alignment length=75%. +!Sample_data_processing = Alignment files were used to generate gene-level count summaries with HTSeq (unique hits and “intersection-strict” mode for version v0.6.1p2). +!Sample_data_processing = Genome_build: version 5.5 assembly of the Chlamydomonas genome +!Sample_data_processing = Supplementary_files_format_and_content: Per-library expression estimates in units of FPKMs. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN04448188 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1553141 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE77388 +!Sample_data_row_count = 0 +^SAMPLE = GSM2051197 +!Sample_title = JLDD4ABV4 Biological Replicate #2 +!Sample_geo_accession = GSM2051197 +!Sample_status = Public on Jan 24 2019 +!Sample_submission_date = Jan 29 2016 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas reinhardtii 4A+ wild-type +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 4A+ +!Sample_characteristics_ch1 = treatment: 0.1 mM +!Sample_characteristics_ch1 = light: 4h white light +!Sample_treatment_protocol_ch1 = Cells (4A+, hmox1, ho1C1 or ho1C2) were innoculated in TAP medium (containing 0.5% v/v methanol with or without 0.1 mM BV IXα) at 5×104 cells/ml and grown in the dark at 22 C until the cell density reached ~2×106 cells/ml and then illuminated with white light (150 µmol photons m-2 s-1) for 30 minutes. Cells were harvested before and after light treatment and total RNA was extracted with Trizol and Qiagen RNeasy mini kit. +!Sample_growth_protocol_ch1 = All strains were maintained on TAP (Tris-Acetate-Phosphate) plates with modified recipe of trace metal elements {Kropat, 2011} at room temperature (22 C) under continuous illumination (30 μmol photons m−2 s−1). Liquid cultures were grown on a gyratory shaker (~100 rpm) heterotrophically on TAP medium in darkness. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was prepared as described previously {Castruita, 2011} and RNA quality was assessed by an Agilent 2100 Bioanalyzer at the UC Davis Genome Center. RNA-Seq libraries were sequenced as single-end 100mers using the HiSeq platform from Illumina. +!Sample_description = Illumina's RNA-Seq whole transcriptome analysis +!Sample_data_processing = Illumina Casava1.8 software used for basecalling. +!Sample_data_processing = The STAR aligner (v2.3.0) was used to generate the genome index and perform alignments in single-end mode. Reads were aligned to a genome index that included both the genome sequence (Chlamydomonas reinhardtii v5.5 assembly) and the exon/intron structure of known gene models (Augustus 11). Relevant alignment parameters included: multimapping score range=0.66, minimum alignment length=75%. +!Sample_data_processing = Alignment files were used to generate gene-level count summaries with HTSeq (unique hits and “intersection-strict” mode for version v0.6.1p2). +!Sample_data_processing = Genome_build: version 5.5 assembly of the Chlamydomonas genome +!Sample_data_processing = Supplementary_files_format_and_content: Per-library expression estimates in units of FPKMs. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN04448189 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1553142 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE77388 +!Sample_data_row_count = 0 +^SAMPLE = GSM2051198 +!Sample_title = JLDDhoNT4 Biological Replicate #1 +!Sample_geo_accession = GSM2051198 +!Sample_status = Public on Jan 24 2019 +!Sample_submission_date = Jan 29 2016 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas reinhardtii hmox1 mutant +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: hmox1 +!Sample_characteristics_ch1 = treatment: 0 mM +!Sample_characteristics_ch1 = light: 4h white light +!Sample_treatment_protocol_ch1 = Cells (4A+, hmox1, ho1C1 or ho1C2) were innoculated in TAP medium (containing 0.5% v/v methanol with or without 0.1 mM BV IXα) at 5×104 cells/ml and grown in the dark at 22 C until the cell density reached ~2×106 cells/ml and then illuminated with white light (150 µmol photons m-2 s-1) for 30 minutes. Cells were harvested before and after light treatment and total RNA was extracted with Trizol and Qiagen RNeasy mini kit. +!Sample_growth_protocol_ch1 = All strains were maintained on TAP (Tris-Acetate-Phosphate) plates with modified recipe of trace metal elements {Kropat, 2011} at room temperature (22 C) under continuous illumination (30 μmol photons m−2 s−1). Liquid cultures were grown on a gyratory shaker (~100 rpm) heterotrophically on TAP medium in darkness. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was prepared as described previously {Castruita, 2011} and RNA quality was assessed by an Agilent 2100 Bioanalyzer at the UC Davis Genome Center. RNA-Seq libraries were sequenced as single-end 100mers using the HiSeq platform from Illumina. +!Sample_description = Illumina's RNA-Seq whole transcriptome analysis +!Sample_data_processing = Illumina Casava1.8 software used for basecalling. +!Sample_data_processing = The STAR aligner (v2.3.0) was used to generate the genome index and perform alignments in single-end mode. Reads were aligned to a genome index that included both the genome sequence (Chlamydomonas reinhardtii v5.5 assembly) and the exon/intron structure of known gene models (Augustus 11). Relevant alignment parameters included: multimapping score range=0.66, minimum alignment length=75%. +!Sample_data_processing = Alignment files were used to generate gene-level count summaries with HTSeq (unique hits and “intersection-strict” mode for version v0.6.1p2). +!Sample_data_processing = Genome_build: version 5.5 assembly of the Chlamydomonas genome +!Sample_data_processing = Supplementary_files_format_and_content: Per-library expression estimates in units of FPKMs. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN04448190 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1553143 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE77388 +!Sample_data_row_count = 0 +^SAMPLE = GSM2051199 +!Sample_title = JLDDhoNT4 Biological Replicate #2 +!Sample_geo_accession = GSM2051199 +!Sample_status = Public on Jan 24 2019 +!Sample_submission_date = Jan 29 2016 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas reinhardtii hmox1 mutant +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: hmox1 +!Sample_characteristics_ch1 = treatment: 0 mM +!Sample_characteristics_ch1 = light: 4h white light +!Sample_treatment_protocol_ch1 = Cells (4A+, hmox1, ho1C1 or ho1C2) were innoculated in TAP medium (containing 0.5% v/v methanol with or without 0.1 mM BV IXα) at 5×104 cells/ml and grown in the dark at 22 C until the cell density reached ~2×106 cells/ml and then illuminated with white light (150 µmol photons m-2 s-1) for 30 minutes. Cells were harvested before and after light treatment and total RNA was extracted with Trizol and Qiagen RNeasy mini kit. +!Sample_growth_protocol_ch1 = All strains were maintained on TAP (Tris-Acetate-Phosphate) plates with modified recipe of trace metal elements {Kropat, 2011} at room temperature (22 C) under continuous illumination (30 μmol photons m−2 s−1). Liquid cultures were grown on a gyratory shaker (~100 rpm) heterotrophically on TAP medium in darkness. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was prepared as described previously {Castruita, 2011} and RNA quality was assessed by an Agilent 2100 Bioanalyzer at the UC Davis Genome Center. RNA-Seq libraries were sequenced as single-end 100mers using the HiSeq platform from Illumina. +!Sample_description = Illumina's RNA-Seq whole transcriptome analysis +!Sample_data_processing = Illumina Casava1.8 software used for basecalling. +!Sample_data_processing = The STAR aligner (v2.3.0) was used to generate the genome index and perform alignments in single-end mode. Reads were aligned to a genome index that included both the genome sequence (Chlamydomonas reinhardtii v5.5 assembly) and the exon/intron structure of known gene models (Augustus 11). Relevant alignment parameters included: multimapping score range=0.66, minimum alignment length=75%. +!Sample_data_processing = Alignment files were used to generate gene-level count summaries with HTSeq (unique hits and “intersection-strict” mode for version v0.6.1p2). +!Sample_data_processing = Genome_build: version 5.5 assembly of the Chlamydomonas genome +!Sample_data_processing = Supplementary_files_format_and_content: Per-library expression estimates in units of FPKMs. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN04448191 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1553144 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE77388 +!Sample_data_row_count = 0 +^SAMPLE = GSM2051200 +!Sample_title = JLDDhoBV4 Biological Replicate #1 +!Sample_geo_accession = GSM2051200 +!Sample_status = Public on Jan 24 2019 +!Sample_submission_date = Jan 29 2016 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas reinhardtii hmox1 mutant +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: hmox1 +!Sample_characteristics_ch1 = treatment: 0.1 mM +!Sample_characteristics_ch1 = light: 4h white light +!Sample_treatment_protocol_ch1 = Cells (4A+, hmox1, ho1C1 or ho1C2) were innoculated in TAP medium (containing 0.5% v/v methanol with or without 0.1 mM BV IXα) at 5×104 cells/ml and grown in the dark at 22 C until the cell density reached ~2×106 cells/ml and then illuminated with white light (150 µmol photons m-2 s-1) for 30 minutes. Cells were harvested before and after light treatment and total RNA was extracted with Trizol and Qiagen RNeasy mini kit. +!Sample_growth_protocol_ch1 = All strains were maintained on TAP (Tris-Acetate-Phosphate) plates with modified recipe of trace metal elements {Kropat, 2011} at room temperature (22 C) under continuous illumination (30 μmol photons m−2 s−1). Liquid cultures were grown on a gyratory shaker (~100 rpm) heterotrophically on TAP medium in darkness. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was prepared as described previously {Castruita, 2011} and RNA quality was assessed by an Agilent 2100 Bioanalyzer at the UC Davis Genome Center. RNA-Seq libraries were sequenced as single-end 100mers using the HiSeq platform from Illumina. +!Sample_description = Illumina's RNA-Seq whole transcriptome analysis +!Sample_data_processing = Illumina Casava1.8 software used for basecalling. +!Sample_data_processing = The STAR aligner (v2.3.0) was used to generate the genome index and perform alignments in single-end mode. Reads were aligned to a genome index that included both the genome sequence (Chlamydomonas reinhardtii v5.5 assembly) and the exon/intron structure of known gene models (Augustus 11). Relevant alignment parameters included: multimapping score range=0.66, minimum alignment length=75%. +!Sample_data_processing = Alignment files were used to generate gene-level count summaries with HTSeq (unique hits and “intersection-strict” mode for version v0.6.1p2). +!Sample_data_processing = Genome_build: version 5.5 assembly of the Chlamydomonas genome +!Sample_data_processing = Supplementary_files_format_and_content: Per-library expression estimates in units of FPKMs. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN04448192 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1553145 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE77388 +!Sample_data_row_count = 0 +^SAMPLE = GSM2051201 +!Sample_title = JLDDhoBV4 Biological Replicate #2 +!Sample_geo_accession = GSM2051201 +!Sample_status = Public on Jan 24 2019 +!Sample_submission_date = Jan 29 2016 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas reinhardtii hmox1 mutant +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: hmox1 +!Sample_characteristics_ch1 = treatment: 0.1 mM +!Sample_characteristics_ch1 = light: 4h white light +!Sample_treatment_protocol_ch1 = Cells (4A+, hmox1, ho1C1 or ho1C2) were innoculated in TAP medium (containing 0.5% v/v methanol with or without 0.1 mM BV IXα) at 5×104 cells/ml and grown in the dark at 22 C until the cell density reached ~2×106 cells/ml and then illuminated with white light (150 µmol photons m-2 s-1) for 30 minutes. Cells were harvested before and after light treatment and total RNA was extracted with Trizol and Qiagen RNeasy mini kit. +!Sample_growth_protocol_ch1 = All strains were maintained on TAP (Tris-Acetate-Phosphate) plates with modified recipe of trace metal elements {Kropat, 2011} at room temperature (22 C) under continuous illumination (30 μmol photons m−2 s−1). Liquid cultures were grown on a gyratory shaker (~100 rpm) heterotrophically on TAP medium in darkness. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was prepared as described previously {Castruita, 2011} and RNA quality was assessed by an Agilent 2100 Bioanalyzer at the UC Davis Genome Center. RNA-Seq libraries were sequenced as single-end 100mers using the HiSeq platform from Illumina. +!Sample_description = Illumina's RNA-Seq whole transcriptome analysis +!Sample_data_processing = Illumina Casava1.8 software used for basecalling. +!Sample_data_processing = The STAR aligner (v2.3.0) was used to generate the genome index and perform alignments in single-end mode. Reads were aligned to a genome index that included both the genome sequence (Chlamydomonas reinhardtii v5.5 assembly) and the exon/intron structure of known gene models (Augustus 11). Relevant alignment parameters included: multimapping score range=0.66, minimum alignment length=75%. +!Sample_data_processing = Alignment files were used to generate gene-level count summaries with HTSeq (unique hits and “intersection-strict” mode for version v0.6.1p2). +!Sample_data_processing = Genome_build: version 5.5 assembly of the Chlamydomonas genome +!Sample_data_processing = Supplementary_files_format_and_content: Per-library expression estimates in units of FPKMs. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN04448193 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1553146 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE77388 +!Sample_data_row_count = 0 +^SAMPLE = GSM2051202 +!Sample_title = JLDDC1NT0 Biological Replicate #1 +!Sample_geo_accession = GSM2051202 +!Sample_status = Public on Jan 24 2019 +!Sample_submission_date = Jan 29 2016 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas reinhardtii hmox1 complemented strain +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: ho1C1 +!Sample_characteristics_ch1 = treatment: 0 mM +!Sample_characteristics_ch1 = light: dark +!Sample_treatment_protocol_ch1 = Cells (4A+, hmox1, ho1C1 or ho1C2) were innoculated in TAP medium (containing 0.5% v/v methanol with or without 0.1 mM BV IXα) at 5×104 cells/ml and grown in the dark at 22 C until the cell density reached ~2×106 cells/ml and then illuminated with white light (150 µmol photons m-2 s-1) for 30 minutes. Cells were harvested before and after light treatment and total RNA was extracted with Trizol and Qiagen RNeasy mini kit. +!Sample_growth_protocol_ch1 = All strains were maintained on TAP (Tris-Acetate-Phosphate) plates with modified recipe of trace metal elements {Kropat, 2011} at room temperature (22 C) under continuous illumination (30 μmol photons m−2 s−1). Liquid cultures were grown on a gyratory shaker (~100 rpm) heterotrophically on TAP medium in darkness. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was prepared as described previously {Castruita, 2011} and RNA quality was assessed by an Agilent 2100 Bioanalyzer at the UC Davis Genome Center. RNA-Seq libraries were sequenced as single-end 100mers using the HiSeq platform from Illumina. +!Sample_description = Illumina's RNA-Seq whole transcriptome analysis +!Sample_data_processing = Illumina Casava1.8 software used for basecalling. +!Sample_data_processing = The STAR aligner (v2.3.0) was used to generate the genome index and perform alignments in single-end mode. Reads were aligned to a genome index that included both the genome sequence (Chlamydomonas reinhardtii v5.5 assembly) and the exon/intron structure of known gene models (Augustus 11). Relevant alignment parameters included: multimapping score range=0.66, minimum alignment length=75%. +!Sample_data_processing = Alignment files were used to generate gene-level count summaries with HTSeq (unique hits and “intersection-strict” mode for version v0.6.1p2). +!Sample_data_processing = Genome_build: version 5.5 assembly of the Chlamydomonas genome +!Sample_data_processing = Supplementary_files_format_and_content: Per-library expression estimates in units of FPKMs. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN04448194 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1553147 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE77388 +!Sample_data_row_count = 0 +^SAMPLE = GSM2051203 +!Sample_title = JLDDC1NT0 Biological Replicate #2 +!Sample_geo_accession = GSM2051203 +!Sample_status = Public on Jan 24 2019 +!Sample_submission_date = Jan 29 2016 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas reinhardtii hmox1 complemented strain +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: ho1C1 +!Sample_characteristics_ch1 = treatment: 0 mM +!Sample_characteristics_ch1 = light: dark +!Sample_treatment_protocol_ch1 = Cells (4A+, hmox1, ho1C1 or ho1C2) were innoculated in TAP medium (containing 0.5% v/v methanol with or without 0.1 mM BV IXα) at 5×104 cells/ml and grown in the dark at 22 C until the cell density reached ~2×106 cells/ml and then illuminated with white light (150 µmol photons m-2 s-1) for 30 minutes. Cells were harvested before and after light treatment and total RNA was extracted with Trizol and Qiagen RNeasy mini kit. +!Sample_growth_protocol_ch1 = All strains were maintained on TAP (Tris-Acetate-Phosphate) plates with modified recipe of trace metal elements {Kropat, 2011} at room temperature (22 C) under continuous illumination (30 μmol photons m−2 s−1). Liquid cultures were grown on a gyratory shaker (~100 rpm) heterotrophically on TAP medium in darkness. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was prepared as described previously {Castruita, 2011} and RNA quality was assessed by an Agilent 2100 Bioanalyzer at the UC Davis Genome Center. RNA-Seq libraries were sequenced as single-end 100mers using the HiSeq platform from Illumina. +!Sample_description = Illumina's RNA-Seq whole transcriptome analysis +!Sample_data_processing = Illumina Casava1.8 software used for basecalling. +!Sample_data_processing = The STAR aligner (v2.3.0) was used to generate the genome index and perform alignments in single-end mode. Reads were aligned to a genome index that included both the genome sequence (Chlamydomonas reinhardtii v5.5 assembly) and the exon/intron structure of known gene models (Augustus 11). Relevant alignment parameters included: multimapping score range=0.66, minimum alignment length=75%. +!Sample_data_processing = Alignment files were used to generate gene-level count summaries with HTSeq (unique hits and “intersection-strict” mode for version v0.6.1p2). +!Sample_data_processing = Genome_build: version 5.5 assembly of the Chlamydomonas genome +!Sample_data_processing = Supplementary_files_format_and_content: Per-library expression estimates in units of FPKMs. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN04448195 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1553148 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE77388 +!Sample_data_row_count = 0 +^SAMPLE = GSM2051204 +!Sample_title = JLDDC1NT05 Biological Replicate #1 +!Sample_geo_accession = GSM2051204 +!Sample_status = Public on Jan 24 2019 +!Sample_submission_date = Jan 29 2016 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas reinhardtii hmox1 complemented strain +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: ho1C1 +!Sample_characteristics_ch1 = treatment: 0 mM +!Sample_characteristics_ch1 = light: 0.5h white light +!Sample_treatment_protocol_ch1 = Cells (4A+, hmox1, ho1C1 or ho1C2) were innoculated in TAP medium (containing 0.5% v/v methanol with or without 0.1 mM BV IXα) at 5×104 cells/ml and grown in the dark at 22 C until the cell density reached ~2×106 cells/ml and then illuminated with white light (150 µmol photons m-2 s-1) for 30 minutes. Cells were harvested before and after light treatment and total RNA was extracted with Trizol and Qiagen RNeasy mini kit. +!Sample_growth_protocol_ch1 = All strains were maintained on TAP (Tris-Acetate-Phosphate) plates with modified recipe of trace metal elements {Kropat, 2011} at room temperature (22 C) under continuous illumination (30 μmol photons m−2 s−1). Liquid cultures were grown on a gyratory shaker (~100 rpm) heterotrophically on TAP medium in darkness. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was prepared as described previously {Castruita, 2011} and RNA quality was assessed by an Agilent 2100 Bioanalyzer at the UC Davis Genome Center. RNA-Seq libraries were sequenced as single-end 100mers using the HiSeq platform from Illumina. +!Sample_description = Illumina's RNA-Seq whole transcriptome analysis +!Sample_data_processing = Illumina Casava1.8 software used for basecalling. +!Sample_data_processing = The STAR aligner (v2.3.0) was used to generate the genome index and perform alignments in single-end mode. Reads were aligned to a genome index that included both the genome sequence (Chlamydomonas reinhardtii v5.5 assembly) and the exon/intron structure of known gene models (Augustus 11). Relevant alignment parameters included: multimapping score range=0.66, minimum alignment length=75%. +!Sample_data_processing = Alignment files were used to generate gene-level count summaries with HTSeq (unique hits and “intersection-strict” mode for version v0.6.1p2). +!Sample_data_processing = Genome_build: version 5.5 assembly of the Chlamydomonas genome +!Sample_data_processing = Supplementary_files_format_and_content: Per-library expression estimates in units of FPKMs. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN04448196 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1553149 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE77388 +!Sample_data_row_count = 0 +^SAMPLE = GSM2051205 +!Sample_title = JLDDC1NT05 Biological Replicate #2 +!Sample_geo_accession = GSM2051205 +!Sample_status = Public on Jan 24 2019 +!Sample_submission_date = Jan 29 2016 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas reinhardtii hmox1 complemented strain +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: ho1C1 +!Sample_characteristics_ch1 = treatment: 0 mM +!Sample_characteristics_ch1 = light: 0.5h white light +!Sample_treatment_protocol_ch1 = Cells (4A+, hmox1, ho1C1 or ho1C2) were innoculated in TAP medium (containing 0.5% v/v methanol with or without 0.1 mM BV IXα) at 5×104 cells/ml and grown in the dark at 22 C until the cell density reached ~2×106 cells/ml and then illuminated with white light (150 µmol photons m-2 s-1) for 30 minutes. Cells were harvested before and after light treatment and total RNA was extracted with Trizol and Qiagen RNeasy mini kit. +!Sample_growth_protocol_ch1 = All strains were maintained on TAP (Tris-Acetate-Phosphate) plates with modified recipe of trace metal elements {Kropat, 2011} at room temperature (22 C) under continuous illumination (30 μmol photons m−2 s−1). Liquid cultures were grown on a gyratory shaker (~100 rpm) heterotrophically on TAP medium in darkness. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was prepared as described previously {Castruita, 2011} and RNA quality was assessed by an Agilent 2100 Bioanalyzer at the UC Davis Genome Center. RNA-Seq libraries were sequenced as single-end 100mers using the HiSeq platform from Illumina. +!Sample_description = Illumina's RNA-Seq whole transcriptome analysis +!Sample_data_processing = Illumina Casava1.8 software used for basecalling. +!Sample_data_processing = The STAR aligner (v2.3.0) was used to generate the genome index and perform alignments in single-end mode. Reads were aligned to a genome index that included both the genome sequence (Chlamydomonas reinhardtii v5.5 assembly) and the exon/intron structure of known gene models (Augustus 11). Relevant alignment parameters included: multimapping score range=0.66, minimum alignment length=75%. +!Sample_data_processing = Alignment files were used to generate gene-level count summaries with HTSeq (unique hits and “intersection-strict” mode for version v0.6.1p2). +!Sample_data_processing = Genome_build: version 5.5 assembly of the Chlamydomonas genome +!Sample_data_processing = Supplementary_files_format_and_content: Per-library expression estimates in units of FPKMs. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN04448197 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1553150 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE77388 +!Sample_data_row_count = 0 +^SAMPLE = GSM2051206 +!Sample_title = JLDDC1NT4 Biological Replicate #1 +!Sample_geo_accession = GSM2051206 +!Sample_status = Public on Jan 24 2019 +!Sample_submission_date = Jan 29 2016 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas reinhardtii hmox1 complemented strain +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: ho1C1 +!Sample_characteristics_ch1 = treatment: 0 mM +!Sample_characteristics_ch1 = light: 4h white light +!Sample_treatment_protocol_ch1 = Cells (4A+, hmox1, ho1C1 or ho1C2) were innoculated in TAP medium (containing 0.5% v/v methanol with or without 0.1 mM BV IXα) at 5×104 cells/ml and grown in the dark at 22 C until the cell density reached ~2×106 cells/ml and then illuminated with white light (150 µmol photons m-2 s-1) for 30 minutes. Cells were harvested before and after light treatment and total RNA was extracted with Trizol and Qiagen RNeasy mini kit. +!Sample_growth_protocol_ch1 = All strains were maintained on TAP (Tris-Acetate-Phosphate) plates with modified recipe of trace metal elements {Kropat, 2011} at room temperature (22 C) under continuous illumination (30 μmol photons m−2 s−1). Liquid cultures were grown on a gyratory shaker (~100 rpm) heterotrophically on TAP medium in darkness. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was prepared as described previously {Castruita, 2011} and RNA quality was assessed by an Agilent 2100 Bioanalyzer at the UC Davis Genome Center. RNA-Seq libraries were sequenced as single-end 100mers using the HiSeq platform from Illumina. +!Sample_description = Illumina's RNA-Seq whole transcriptome analysis +!Sample_data_processing = Illumina Casava1.8 software used for basecalling. +!Sample_data_processing = The STAR aligner (v2.3.0) was used to generate the genome index and perform alignments in single-end mode. Reads were aligned to a genome index that included both the genome sequence (Chlamydomonas reinhardtii v5.5 assembly) and the exon/intron structure of known gene models (Augustus 11). Relevant alignment parameters included: multimapping score range=0.66, minimum alignment length=75%. +!Sample_data_processing = Alignment files were used to generate gene-level count summaries with HTSeq (unique hits and “intersection-strict” mode for version v0.6.1p2). +!Sample_data_processing = Genome_build: version 5.5 assembly of the Chlamydomonas genome +!Sample_data_processing = Supplementary_files_format_and_content: Per-library expression estimates in units of FPKMs. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN04448198 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1553151 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE77388 +!Sample_data_row_count = 0 +^SAMPLE = GSM2051207 +!Sample_title = JLDDC1NT4 Biological Replicate #2 +!Sample_geo_accession = GSM2051207 +!Sample_status = Public on Jan 24 2019 +!Sample_submission_date = Jan 29 2016 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas reinhardtii hmox1 complemented strain +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: ho1C1 +!Sample_characteristics_ch1 = treatment: 0 mM +!Sample_characteristics_ch1 = light: 4h white light +!Sample_treatment_protocol_ch1 = Cells (4A+, hmox1, ho1C1 or ho1C2) were innoculated in TAP medium (containing 0.5% v/v methanol with or without 0.1 mM BV IXα) at 5×104 cells/ml and grown in the dark at 22 C until the cell density reached ~2×106 cells/ml and then illuminated with white light (150 µmol photons m-2 s-1) for 30 minutes. Cells were harvested before and after light treatment and total RNA was extracted with Trizol and Qiagen RNeasy mini kit. +!Sample_growth_protocol_ch1 = All strains were maintained on TAP (Tris-Acetate-Phosphate) plates with modified recipe of trace metal elements {Kropat, 2011} at room temperature (22 C) under continuous illumination (30 μmol photons m−2 s−1). Liquid cultures were grown on a gyratory shaker (~100 rpm) heterotrophically on TAP medium in darkness. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was prepared as described previously {Castruita, 2011} and RNA quality was assessed by an Agilent 2100 Bioanalyzer at the UC Davis Genome Center. RNA-Seq libraries were sequenced as single-end 100mers using the HiSeq platform from Illumina. +!Sample_description = Illumina's RNA-Seq whole transcriptome analysis +!Sample_data_processing = Illumina Casava1.8 software used for basecalling. +!Sample_data_processing = The STAR aligner (v2.3.0) was used to generate the genome index and perform alignments in single-end mode. Reads were aligned to a genome index that included both the genome sequence (Chlamydomonas reinhardtii v5.5 assembly) and the exon/intron structure of known gene models (Augustus 11). Relevant alignment parameters included: multimapping score range=0.66, minimum alignment length=75%. +!Sample_data_processing = Alignment files were used to generate gene-level count summaries with HTSeq (unique hits and “intersection-strict” mode for version v0.6.1p2). +!Sample_data_processing = Genome_build: version 5.5 assembly of the Chlamydomonas genome +!Sample_data_processing = Supplementary_files_format_and_content: Per-library expression estimates in units of FPKMs. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN04448199 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1553152 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE77388 +!Sample_data_row_count = 0 +^SAMPLE = GSM2051208 +!Sample_title = JLDDC2NT0 Biological Replicate #1 +!Sample_geo_accession = GSM2051208 +!Sample_status = Public on Jan 24 2019 +!Sample_submission_date = Jan 29 2016 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas reinhardtii hmox1 complemented strain +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: ho1C2 +!Sample_characteristics_ch1 = treatment: 0 mM +!Sample_characteristics_ch1 = light: dark +!Sample_treatment_protocol_ch1 = Cells (4A+, hmox1, ho1C1 or ho1C2) were innoculated in TAP medium (containing 0.5% v/v methanol with or without 0.1 mM BV IXα) at 5×104 cells/ml and grown in the dark at 22 C until the cell density reached ~2×106 cells/ml and then illuminated with white light (150 µmol photons m-2 s-1) for 30 minutes. Cells were harvested before and after light treatment and total RNA was extracted with Trizol and Qiagen RNeasy mini kit. +!Sample_growth_protocol_ch1 = All strains were maintained on TAP (Tris-Acetate-Phosphate) plates with modified recipe of trace metal elements {Kropat, 2011} at room temperature (22 C) under continuous illumination (30 μmol photons m−2 s−1). Liquid cultures were grown on a gyratory shaker (~100 rpm) heterotrophically on TAP medium in darkness. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was prepared as described previously {Castruita, 2011} and RNA quality was assessed by an Agilent 2100 Bioanalyzer at the UC Davis Genome Center. RNA-Seq libraries were sequenced as single-end 100mers using the HiSeq platform from Illumina. +!Sample_description = Illumina's RNA-Seq whole transcriptome analysis +!Sample_data_processing = Illumina Casava1.8 software used for basecalling. +!Sample_data_processing = The STAR aligner (v2.3.0) was used to generate the genome index and perform alignments in single-end mode. Reads were aligned to a genome index that included both the genome sequence (Chlamydomonas reinhardtii v5.5 assembly) and the exon/intron structure of known gene models (Augustus 11). Relevant alignment parameters included: multimapping score range=0.66, minimum alignment length=75%. +!Sample_data_processing = Alignment files were used to generate gene-level count summaries with HTSeq (unique hits and “intersection-strict” mode for version v0.6.1p2). +!Sample_data_processing = Genome_build: version 5.5 assembly of the Chlamydomonas genome +!Sample_data_processing = Supplementary_files_format_and_content: Per-library expression estimates in units of FPKMs. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN04448200 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1553153 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE77388 +!Sample_data_row_count = 0 +^SAMPLE = GSM2051209 +!Sample_title = JLDDC2NT0 Biological Replicate #2 +!Sample_geo_accession = GSM2051209 +!Sample_status = Public on Jan 24 2019 +!Sample_submission_date = Jan 29 2016 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas reinhardtii hmox1 complemented strain +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: ho1C2 +!Sample_characteristics_ch1 = treatment: 0 mM +!Sample_characteristics_ch1 = light: dark +!Sample_treatment_protocol_ch1 = Cells (4A+, hmox1, ho1C1 or ho1C2) were innoculated in TAP medium (containing 0.5% v/v methanol with or without 0.1 mM BV IXα) at 5×104 cells/ml and grown in the dark at 22 C until the cell density reached ~2×106 cells/ml and then illuminated with white light (150 µmol photons m-2 s-1) for 30 minutes. Cells were harvested before and after light treatment and total RNA was extracted with Trizol and Qiagen RNeasy mini kit. +!Sample_growth_protocol_ch1 = All strains were maintained on TAP (Tris-Acetate-Phosphate) plates with modified recipe of trace metal elements {Kropat, 2011} at room temperature (22 C) under continuous illumination (30 μmol photons m−2 s−1). Liquid cultures were grown on a gyratory shaker (~100 rpm) heterotrophically on TAP medium in darkness. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was prepared as described previously {Castruita, 2011} and RNA quality was assessed by an Agilent 2100 Bioanalyzer at the UC Davis Genome Center. RNA-Seq libraries were sequenced as single-end 100mers using the HiSeq platform from Illumina. +!Sample_description = Illumina's RNA-Seq whole transcriptome analysis +!Sample_data_processing = Illumina Casava1.8 software used for basecalling. +!Sample_data_processing = The STAR aligner (v2.3.0) was used to generate the genome index and perform alignments in single-end mode. Reads were aligned to a genome index that included both the genome sequence (Chlamydomonas reinhardtii v5.5 assembly) and the exon/intron structure of known gene models (Augustus 11). Relevant alignment parameters included: multimapping score range=0.66, minimum alignment length=75%. +!Sample_data_processing = Alignment files were used to generate gene-level count summaries with HTSeq (unique hits and “intersection-strict” mode for version v0.6.1p2). +!Sample_data_processing = Genome_build: version 5.5 assembly of the Chlamydomonas genome +!Sample_data_processing = Supplementary_files_format_and_content: Per-library expression estimates in units of FPKMs. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN04448201 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1553154 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE77388 +!Sample_data_row_count = 0 +^SAMPLE = GSM2051210 +!Sample_title = JLDDC2NT05 Biological Replicate #1 +!Sample_geo_accession = GSM2051210 +!Sample_status = Public on Jan 24 2019 +!Sample_submission_date = Jan 29 2016 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas reinhardtii hmox1 complemented strain +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: ho1C2 +!Sample_characteristics_ch1 = treatment: 0 mM +!Sample_characteristics_ch1 = light: 0.5h white light +!Sample_treatment_protocol_ch1 = Cells (4A+, hmox1, ho1C1 or ho1C2) were innoculated in TAP medium (containing 0.5% v/v methanol with or without 0.1 mM BV IXα) at 5×104 cells/ml and grown in the dark at 22 C until the cell density reached ~2×106 cells/ml and then illuminated with white light (150 µmol photons m-2 s-1) for 30 minutes. Cells were harvested before and after light treatment and total RNA was extracted with Trizol and Qiagen RNeasy mini kit. +!Sample_growth_protocol_ch1 = All strains were maintained on TAP (Tris-Acetate-Phosphate) plates with modified recipe of trace metal elements {Kropat, 2011} at room temperature (22 C) under continuous illumination (30 μmol photons m−2 s−1). Liquid cultures were grown on a gyratory shaker (~100 rpm) heterotrophically on TAP medium in darkness. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was prepared as described previously {Castruita, 2011} and RNA quality was assessed by an Agilent 2100 Bioanalyzer at the UC Davis Genome Center. RNA-Seq libraries were sequenced as single-end 100mers using the HiSeq platform from Illumina. +!Sample_description = Illumina's RNA-Seq whole transcriptome analysis +!Sample_data_processing = Illumina Casava1.8 software used for basecalling. +!Sample_data_processing = The STAR aligner (v2.3.0) was used to generate the genome index and perform alignments in single-end mode. Reads were aligned to a genome index that included both the genome sequence (Chlamydomonas reinhardtii v5.5 assembly) and the exon/intron structure of known gene models (Augustus 11). Relevant alignment parameters included: multimapping score range=0.66, minimum alignment length=75%. +!Sample_data_processing = Alignment files were used to generate gene-level count summaries with HTSeq (unique hits and “intersection-strict” mode for version v0.6.1p2). +!Sample_data_processing = Genome_build: version 5.5 assembly of the Chlamydomonas genome +!Sample_data_processing = Supplementary_files_format_and_content: Per-library expression estimates in units of FPKMs. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN04448202 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1553155 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE77388 +!Sample_data_row_count = 0 +^SAMPLE = GSM2051211 +!Sample_title = JLDDC2NT05 Biological Replicate #2 +!Sample_geo_accession = GSM2051211 +!Sample_status = Public on Jan 24 2019 +!Sample_submission_date = Jan 29 2016 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas reinhardtii hmox1 complemented strain +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: ho1C2 +!Sample_characteristics_ch1 = treatment: 0 mM +!Sample_characteristics_ch1 = light: 0.5h white light +!Sample_treatment_protocol_ch1 = Cells (4A+, hmox1, ho1C1 or ho1C2) were innoculated in TAP medium (containing 0.5% v/v methanol with or without 0.1 mM BV IXα) at 5×104 cells/ml and grown in the dark at 22 C until the cell density reached ~2×106 cells/ml and then illuminated with white light (150 µmol photons m-2 s-1) for 30 minutes. Cells were harvested before and after light treatment and total RNA was extracted with Trizol and Qiagen RNeasy mini kit. +!Sample_growth_protocol_ch1 = All strains were maintained on TAP (Tris-Acetate-Phosphate) plates with modified recipe of trace metal elements {Kropat, 2011} at room temperature (22 C) under continuous illumination (30 μmol photons m−2 s−1). Liquid cultures were grown on a gyratory shaker (~100 rpm) heterotrophically on TAP medium in darkness. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was prepared as described previously {Castruita, 2011} and RNA quality was assessed by an Agilent 2100 Bioanalyzer at the UC Davis Genome Center. RNA-Seq libraries were sequenced as single-end 100mers using the HiSeq platform from Illumina. +!Sample_description = Illumina's RNA-Seq whole transcriptome analysis +!Sample_data_processing = Illumina Casava1.8 software used for basecalling. +!Sample_data_processing = The STAR aligner (v2.3.0) was used to generate the genome index and perform alignments in single-end mode. Reads were aligned to a genome index that included both the genome sequence (Chlamydomonas reinhardtii v5.5 assembly) and the exon/intron structure of known gene models (Augustus 11). Relevant alignment parameters included: multimapping score range=0.66, minimum alignment length=75%. +!Sample_data_processing = Alignment files were used to generate gene-level count summaries with HTSeq (unique hits and “intersection-strict” mode for version v0.6.1p2). +!Sample_data_processing = Genome_build: version 5.5 assembly of the Chlamydomonas genome +!Sample_data_processing = Supplementary_files_format_and_content: Per-library expression estimates in units of FPKMs. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN04448203 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1553156 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE77388 +!Sample_data_row_count = 0 +^SAMPLE = GSM2051212 +!Sample_title = JLDDC2NT4 Biological Replicate #1 +!Sample_geo_accession = GSM2051212 +!Sample_status = Public on Jan 24 2019 +!Sample_submission_date = Jan 29 2016 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas reinhardtii hmox1 complemented strain +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: ho1C2 +!Sample_characteristics_ch1 = treatment: 0 mM +!Sample_characteristics_ch1 = light: 4h white light +!Sample_treatment_protocol_ch1 = Cells (4A+, hmox1, ho1C1 or ho1C2) were innoculated in TAP medium (containing 0.5% v/v methanol with or without 0.1 mM BV IXα) at 5×104 cells/ml and grown in the dark at 22 C until the cell density reached ~2×106 cells/ml and then illuminated with white light (150 µmol photons m-2 s-1) for 30 minutes. Cells were harvested before and after light treatment and total RNA was extracted with Trizol and Qiagen RNeasy mini kit. +!Sample_growth_protocol_ch1 = All strains were maintained on TAP (Tris-Acetate-Phosphate) plates with modified recipe of trace metal elements {Kropat, 2011} at room temperature (22 C) under continuous illumination (30 μmol photons m−2 s−1). Liquid cultures were grown on a gyratory shaker (~100 rpm) heterotrophically on TAP medium in darkness. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was prepared as described previously {Castruita, 2011} and RNA quality was assessed by an Agilent 2100 Bioanalyzer at the UC Davis Genome Center. RNA-Seq libraries were sequenced as single-end 100mers using the HiSeq platform from Illumina. +!Sample_description = Illumina's RNA-Seq whole transcriptome analysis +!Sample_data_processing = Illumina Casava1.8 software used for basecalling. +!Sample_data_processing = The STAR aligner (v2.3.0) was used to generate the genome index and perform alignments in single-end mode. Reads were aligned to a genome index that included both the genome sequence (Chlamydomonas reinhardtii v5.5 assembly) and the exon/intron structure of known gene models (Augustus 11). Relevant alignment parameters included: multimapping score range=0.66, minimum alignment length=75%. +!Sample_data_processing = Alignment files were used to generate gene-level count summaries with HTSeq (unique hits and “intersection-strict” mode for version v0.6.1p2). +!Sample_data_processing = Genome_build: version 5.5 assembly of the Chlamydomonas genome +!Sample_data_processing = Supplementary_files_format_and_content: Per-library expression estimates in units of FPKMs. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN04448204 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1553157 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE77388 +!Sample_data_row_count = 0 +^SAMPLE = GSM2051213 +!Sample_title = JLDDC2NT4 Biological Replicate #2 +!Sample_geo_accession = GSM2051213 +!Sample_status = Public on Jan 24 2019 +!Sample_submission_date = Jan 29 2016 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Chlamydomonas reinhardtii hmox1 complemented strain +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: ho1C2 +!Sample_characteristics_ch1 = treatment: 0 mM +!Sample_characteristics_ch1 = light: 4h white light +!Sample_treatment_protocol_ch1 = Cells (4A+, hmox1, ho1C1 or ho1C2) were innoculated in TAP medium (containing 0.5% v/v methanol with or without 0.1 mM BV IXα) at 5×104 cells/ml and grown in the dark at 22 C until the cell density reached ~2×106 cells/ml and then illuminated with white light (150 µmol photons m-2 s-1) for 30 minutes. Cells were harvested before and after light treatment and total RNA was extracted with Trizol and Qiagen RNeasy mini kit. +!Sample_growth_protocol_ch1 = All strains were maintained on TAP (Tris-Acetate-Phosphate) plates with modified recipe of trace metal elements {Kropat, 2011} at room temperature (22 C) under continuous illumination (30 μmol photons m−2 s−1). Liquid cultures were grown on a gyratory shaker (~100 rpm) heterotrophically on TAP medium in darkness. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was prepared as described previously {Castruita, 2011} and RNA quality was assessed by an Agilent 2100 Bioanalyzer at the UC Davis Genome Center. RNA-Seq libraries were sequenced as single-end 100mers using the HiSeq platform from Illumina. +!Sample_description = Illumina's RNA-Seq whole transcriptome analysis +!Sample_data_processing = Illumina Casava1.8 software used for basecalling. +!Sample_data_processing = The STAR aligner (v2.3.0) was used to generate the genome index and perform alignments in single-end mode. Reads were aligned to a genome index that included both the genome sequence (Chlamydomonas reinhardtii v5.5 assembly) and the exon/intron structure of known gene models (Augustus 11). Relevant alignment parameters included: multimapping score range=0.66, minimum alignment length=75%. +!Sample_data_processing = Alignment files were used to generate gene-level count summaries with HTSeq (unique hits and “intersection-strict” mode for version v0.6.1p2). +!Sample_data_processing = Genome_build: version 5.5 assembly of the Chlamydomonas genome +!Sample_data_processing = Supplementary_files_format_and_content: Per-library expression estimates in units of FPKMs. +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sabeeha,,Merchant +!Sample_contact_email = merchant@chem.ucla.edu +!Sample_contact_phone = 310-825-8300 +!Sample_contact_department = Department of Chemistry and Biochemistry +!Sample_contact_institute = University of California Los Angeles +!Sample_contact_address = 607 Charles E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095-1569 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN04448205 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1553158 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE77388 +!Sample_data_row_count = 0 +^SAMPLE = GSM2719230 +!Sample_title = diurnal growth - dark +!Sample_geo_accession = GSM2719230 +!Sample_status = Public on Nov 27 2017 +!Sample_submission_date = Jul 27 2017 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = liquid culture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: CC-4351 +!Sample_characteristics_ch1 = media: high salt medium +!Sample_characteristics_ch1 = light regime: 12h light / 12h dark +!Sample_characteristics_ch1 = library protocol: RiboZero +!Sample_growth_protocol_ch1 = Diurnally grown culture sampled at the end of the dark phase. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was purified from pelleted cells by freezing in SDS/proteinase K digestion buffer followed extraction with Trizol reagent. +!Sample_extract_protocol_ch1 = ~2 ug total RNA was used as starting material for either rRNA-depletion by RiboZero Plant Leaf kit or for enrichment of poly-A transcripts by binding oligo-T beads (indicated by "library protocol" above). The resulting RNA was then used to generate strand-specific Illumina libraries. +!Sample_description = processed data file: fpkms.diurnal.tsv +!Sample_data_processing = Basecalling performed using Illumina RTA software. +!Sample_data_processing = Conversion of qseq to fastq format and demultiplexing by in-house scripts +!Sample_data_processing = Removal of contaminating rRNA reads by alignment to rRNA+snoRNA.fasta with RNA-STAR (STAR_2.4.0j). Unmapped reads selected for further analysis with "--outReadsUnmapped Fastx" option of STAR. +!Sample_data_processing = Alignment to C.reinhardtii nuclear genome (Phytozome v5.5) plus chloroplast genome (CPv4) plus mitochondrial genome (MTv4) by RNA-STAR (STAR_2.4.0j) with default parameters except --alignIntronMax 5000 +!Sample_data_processing = SAM alignments sorted and converted to BAM format by samtools (v1.3). +!Sample_data_processing = Counts per gene and FPKMs calculated by cuffdiff (v2.0.2) with "--multi-read-correct --max-bundle-frags 1000000000 --library-type fr-firststrand" +!Sample_data_processing = Genome_build: Cre.nuc.v5.5.cp.v4.4.mt.v4.4 +!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files (.tsv) containing transcript abundance determinations calculated as FPKMs +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sean,D.,Gallaher +!Sample_contact_laboratory = Sabeeha Merchant +!Sample_contact_department = Chem & BioChem +!Sample_contact_institute = UCLA +!Sample_contact_address = 607 Charle E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN07418717 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3041721 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE101944 +!Sample_data_row_count = 0 +^SAMPLE = GSM2719231 +!Sample_title = diurnal growth - light +!Sample_geo_accession = GSM2719231 +!Sample_status = Public on Nov 27 2017 +!Sample_submission_date = Jul 27 2017 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = liquid culture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: CC-4351 +!Sample_characteristics_ch1 = media: high salt medium +!Sample_characteristics_ch1 = light regime: 12h light / 12h dark +!Sample_characteristics_ch1 = library protocol: RiboZero +!Sample_growth_protocol_ch1 = Diurnally grown culture sampled 1 h into the light phase. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was purified from pelleted cells by freezing in SDS/proteinase K digestion buffer followed extraction with Trizol reagent. +!Sample_extract_protocol_ch1 = ~2 ug total RNA was used as starting material for either rRNA-depletion by RiboZero Plant Leaf kit or for enrichment of poly-A transcripts by binding oligo-T beads (indicated by "library protocol" above). The resulting RNA was then used to generate strand-specific Illumina libraries. +!Sample_description = processed data file: fpkms.diurnal.tsv +!Sample_data_processing = Basecalling performed using Illumina RTA software. +!Sample_data_processing = Conversion of qseq to fastq format and demultiplexing by in-house scripts +!Sample_data_processing = Removal of contaminating rRNA reads by alignment to rRNA+snoRNA.fasta with RNA-STAR (STAR_2.4.0j). Unmapped reads selected for further analysis with "--outReadsUnmapped Fastx" option of STAR. +!Sample_data_processing = Alignment to C.reinhardtii nuclear genome (Phytozome v5.5) plus chloroplast genome (CPv4) plus mitochondrial genome (MTv4) by RNA-STAR (STAR_2.4.0j) with default parameters except --alignIntronMax 5000 +!Sample_data_processing = SAM alignments sorted and converted to BAM format by samtools (v1.3). +!Sample_data_processing = Counts per gene and FPKMs calculated by cuffdiff (v2.0.2) with "--multi-read-correct --max-bundle-frags 1000000000 --library-type fr-firststrand" +!Sample_data_processing = Genome_build: Cre.nuc.v5.5.cp.v4.4.mt.v4.4 +!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files (.tsv) containing transcript abundance determinations calculated as FPKMs +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sean,D.,Gallaher +!Sample_contact_laboratory = Sabeeha Merchant +!Sample_contact_department = Chem & BioChem +!Sample_contact_institute = UCLA +!Sample_contact_address = 607 Charle E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN07418718 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3041722 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE101944 +!Sample_data_row_count = 0 +^SAMPLE = GSM2719232 +!Sample_title = media +Fe - RiboZero +!Sample_geo_accession = GSM2719232 +!Sample_status = Public on Nov 27 2017 +!Sample_submission_date = Jul 27 2017 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = liquid culture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: CC-4532 +!Sample_characteristics_ch1 = media: tris acetate phosphate medium +Fe +!Sample_characteristics_ch1 = light regime: continuous light +!Sample_characteristics_ch1 = library protocol: RiboZero +!Sample_growth_protocol_ch1 = Growth in media with Fe, RiboZero library. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was purified from pelleted cells by freezing in SDS/proteinase K digestion buffer followed extraction with Trizol reagent. +!Sample_extract_protocol_ch1 = ~2 ug total RNA was used as starting material for either rRNA-depletion by RiboZero Plant Leaf kit or for enrichment of poly-A transcripts by binding oligo-T beads (indicated by "library protocol" above). The resulting RNA was then used to generate strand-specific Illumina libraries. +!Sample_description = processed data file: fpkms.iron_PAvsRZ.tsv +!Sample_data_processing = Basecalling performed using Illumina RTA software. +!Sample_data_processing = Conversion of qseq to fastq format and demultiplexing by in-house scripts +!Sample_data_processing = Removal of contaminating rRNA reads by alignment to rRNA+snoRNA.fasta with RNA-STAR (STAR_2.4.0j). Unmapped reads selected for further analysis with "--outReadsUnmapped Fastx" option of STAR. +!Sample_data_processing = Alignment to C.reinhardtii nuclear genome (Phytozome v5.5) plus chloroplast genome (CPv4) plus mitochondrial genome (MTv4) by RNA-STAR (STAR_2.4.0j) with default parameters except --alignIntronMax 5000 +!Sample_data_processing = SAM alignments sorted and converted to BAM format by samtools (v1.3). +!Sample_data_processing = Counts per gene and FPKMs calculated by cuffdiff (v2.0.2) with "--multi-read-correct --max-bundle-frags 1000000000 --library-type fr-firststrand" +!Sample_data_processing = Genome_build: Cre.nuc.v5.5.cp.v4.4.mt.v4.4 +!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files (.tsv) containing transcript abundance determinations calculated as FPKMs +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sean,D.,Gallaher +!Sample_contact_laboratory = Sabeeha Merchant +!Sample_contact_department = Chem & BioChem +!Sample_contact_institute = UCLA +!Sample_contact_address = 607 Charle E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN07418720 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3041723 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE101944 +!Sample_data_row_count = 0 +^SAMPLE = GSM2719233 +!Sample_title = media -Fe - RiboZero +!Sample_geo_accession = GSM2719233 +!Sample_status = Public on Nov 27 2017 +!Sample_submission_date = Jul 27 2017 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = liquid culture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: CC-4532 +!Sample_characteristics_ch1 = media: tris acetate phosphate medium -Fe +!Sample_characteristics_ch1 = light regime: continuous light +!Sample_characteristics_ch1 = library protocol: RiboZero +!Sample_growth_protocol_ch1 = 4 h after transfer to medium without Fe, RiboZero library. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was purified from pelleted cells by freezing in SDS/proteinase K digestion buffer followed extraction with Trizol reagent. +!Sample_extract_protocol_ch1 = ~2 ug total RNA was used as starting material for either rRNA-depletion by RiboZero Plant Leaf kit or for enrichment of poly-A transcripts by binding oligo-T beads (indicated by "library protocol" above). The resulting RNA was then used to generate strand-specific Illumina libraries. +!Sample_description = processed data file: fpkms.iron_PAvsRZ.tsv +!Sample_data_processing = Basecalling performed using Illumina RTA software. +!Sample_data_processing = Conversion of qseq to fastq format and demultiplexing by in-house scripts +!Sample_data_processing = Removal of contaminating rRNA reads by alignment to rRNA+snoRNA.fasta with RNA-STAR (STAR_2.4.0j). Unmapped reads selected for further analysis with "--outReadsUnmapped Fastx" option of STAR. +!Sample_data_processing = Alignment to C.reinhardtii nuclear genome (Phytozome v5.5) plus chloroplast genome (CPv4) plus mitochondrial genome (MTv4) by RNA-STAR (STAR_2.4.0j) with default parameters except --alignIntronMax 5000 +!Sample_data_processing = SAM alignments sorted and converted to BAM format by samtools (v1.3). +!Sample_data_processing = Counts per gene and FPKMs calculated by cuffdiff (v2.0.2) with "--multi-read-correct --max-bundle-frags 1000000000 --library-type fr-firststrand" +!Sample_data_processing = Genome_build: Cre.nuc.v5.5.cp.v4.4.mt.v4.4 +!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files (.tsv) containing transcript abundance determinations calculated as FPKMs +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sean,D.,Gallaher +!Sample_contact_laboratory = Sabeeha Merchant +!Sample_contact_department = Chem & BioChem +!Sample_contact_institute = UCLA +!Sample_contact_address = 607 Charle E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN07418719 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3041724 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE101944 +!Sample_data_row_count = 0 +^SAMPLE = GSM2719234 +!Sample_title = media +Fe - poly-A +!Sample_geo_accession = GSM2719234 +!Sample_status = Public on Nov 27 2017 +!Sample_submission_date = Jul 27 2017 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = liquid culture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: CC-4532 +!Sample_characteristics_ch1 = media: tris acetate phosphate medium +Fe +!Sample_characteristics_ch1 = light regime: continuous light +!Sample_characteristics_ch1 = library protocol: poly-A +!Sample_growth_protocol_ch1 = Growth in media with Fe, poly-A enriched library. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was purified from pelleted cells by freezing in SDS/proteinase K digestion buffer followed extraction with Trizol reagent. +!Sample_extract_protocol_ch1 = ~2 ug total RNA was used as starting material for either rRNA-depletion by RiboZero Plant Leaf kit or for enrichment of poly-A transcripts by binding oligo-T beads (indicated by "library protocol" above). The resulting RNA was then used to generate strand-specific Illumina libraries. +!Sample_description = processed data file: fpkms.iron_PAvsRZ.tsv +!Sample_data_processing = Basecalling performed using Illumina RTA software. +!Sample_data_processing = Conversion of qseq to fastq format and demultiplexing by in-house scripts +!Sample_data_processing = Removal of contaminating rRNA reads by alignment to rRNA+snoRNA.fasta with RNA-STAR (STAR_2.4.0j). Unmapped reads selected for further analysis with "--outReadsUnmapped Fastx" option of STAR. +!Sample_data_processing = Alignment to C.reinhardtii nuclear genome (Phytozome v5.5) plus chloroplast genome (CPv4) plus mitochondrial genome (MTv4) by RNA-STAR (STAR_2.4.0j) with default parameters except --alignIntronMax 5000 +!Sample_data_processing = SAM alignments sorted and converted to BAM format by samtools (v1.3). +!Sample_data_processing = Counts per gene and FPKMs calculated by cuffdiff (v2.0.2) with "--multi-read-correct --max-bundle-frags 1000000000 --library-type fr-firststrand" +!Sample_data_processing = Genome_build: Cre.nuc.v5.5.cp.v4.4.mt.v4.4 +!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files (.tsv) containing transcript abundance determinations calculated as FPKMs +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sean,D.,Gallaher +!Sample_contact_laboratory = Sabeeha Merchant +!Sample_contact_department = Chem & BioChem +!Sample_contact_institute = UCLA +!Sample_contact_address = 607 Charle E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN07418723 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3041725 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE101944 +!Sample_data_row_count = 0 +^SAMPLE = GSM2719235 +!Sample_title = media -Fe - poly-A +!Sample_geo_accession = GSM2719235 +!Sample_status = Public on Nov 27 2017 +!Sample_submission_date = Jul 27 2017 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = liquid culture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: CC-4532 +!Sample_characteristics_ch1 = media: tris acetate phosphate medium -Fe +!Sample_characteristics_ch1 = light regime: continuous light +!Sample_characteristics_ch1 = library protocol: poly-A +!Sample_growth_protocol_ch1 = 4 h after transfer to medium without Fe, poly-A enriched library. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was purified from pelleted cells by freezing in SDS/proteinase K digestion buffer followed extraction with Trizol reagent. +!Sample_extract_protocol_ch1 = ~2 ug total RNA was used as starting material for either rRNA-depletion by RiboZero Plant Leaf kit or for enrichment of poly-A transcripts by binding oligo-T beads (indicated by "library protocol" above). The resulting RNA was then used to generate strand-specific Illumina libraries. +!Sample_description = processed data file: fpkms.iron_PAvsRZ.tsv +!Sample_data_processing = Basecalling performed using Illumina RTA software. +!Sample_data_processing = Conversion of qseq to fastq format and demultiplexing by in-house scripts +!Sample_data_processing = Removal of contaminating rRNA reads by alignment to rRNA+snoRNA.fasta with RNA-STAR (STAR_2.4.0j). Unmapped reads selected for further analysis with "--outReadsUnmapped Fastx" option of STAR. +!Sample_data_processing = Alignment to C.reinhardtii nuclear genome (Phytozome v5.5) plus chloroplast genome (CPv4) plus mitochondrial genome (MTv4) by RNA-STAR (STAR_2.4.0j) with default parameters except --alignIntronMax 5000 +!Sample_data_processing = SAM alignments sorted and converted to BAM format by samtools (v1.3). +!Sample_data_processing = Counts per gene and FPKMs calculated by cuffdiff (v2.0.2) with "--multi-read-correct --max-bundle-frags 1000000000 --library-type fr-firststrand" +!Sample_data_processing = Genome_build: Cre.nuc.v5.5.cp.v4.4.mt.v4.4 +!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files (.tsv) containing transcript abundance determinations calculated as FPKMs +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sean,D.,Gallaher +!Sample_contact_laboratory = Sabeeha Merchant +!Sample_contact_department = Chem & BioChem +!Sample_contact_institute = UCLA +!Sample_contact_address = 607 Charle E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN07418721 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3041726 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE101944 +!Sample_data_row_count = 0 +^SAMPLE = GSM2719236 +!Sample_title = media +Cu +!Sample_geo_accession = GSM2719236 +!Sample_status = Public on Nov 27 2017 +!Sample_submission_date = Jul 27 2017 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = liquid culture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: CC-124 x CC-4425 +!Sample_characteristics_ch1 = media: tris acetate phosphate medium +Cu +!Sample_characteristics_ch1 = light regime: continuous light +!Sample_characteristics_ch1 = library protocol: RiboZero +!Sample_growth_protocol_ch1 = Growth in media with Cu. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was purified from pelleted cells by freezing in SDS/proteinase K digestion buffer followed extraction with Trizol reagent. +!Sample_extract_protocol_ch1 = ~2 ug total RNA was used as starting material for either rRNA-depletion by RiboZero Plant Leaf kit or for enrichment of poly-A transcripts by binding oligo-T beads (indicated by "library protocol" above). The resulting RNA was then used to generate strand-specific Illumina libraries. +!Sample_description = processed data file: fpkms.copper.tsv +!Sample_data_processing = Basecalling performed using Illumina RTA software. +!Sample_data_processing = Conversion of qseq to fastq format and demultiplexing by in-house scripts +!Sample_data_processing = Removal of contaminating rRNA reads by alignment to rRNA+snoRNA.fasta with RNA-STAR (STAR_2.4.0j). Unmapped reads selected for further analysis with "--outReadsUnmapped Fastx" option of STAR. +!Sample_data_processing = Alignment to C.reinhardtii nuclear genome (Phytozome v5.5) plus chloroplast genome (CPv4) plus mitochondrial genome (MTv4) by RNA-STAR (STAR_2.4.0j) with default parameters except --alignIntronMax 5000 +!Sample_data_processing = SAM alignments sorted and converted to BAM format by samtools (v1.3). +!Sample_data_processing = Counts per gene and FPKMs calculated by cuffdiff (v2.0.2) with "--multi-read-correct --max-bundle-frags 1000000000 --library-type fr-firststrand" +!Sample_data_processing = Genome_build: Cre.nuc.v5.5.cp.v4.4.mt.v4.4 +!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files (.tsv) containing transcript abundance determinations calculated as FPKMs +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sean,D.,Gallaher +!Sample_contact_laboratory = Sabeeha Merchant +!Sample_contact_department = Chem & BioChem +!Sample_contact_institute = UCLA +!Sample_contact_address = 607 Charle E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN07418722 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3041727 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE101944 +!Sample_data_row_count = 0 +^SAMPLE = GSM2719237 +!Sample_title = media -Cu +!Sample_geo_accession = GSM2719237 +!Sample_status = Public on Nov 27 2017 +!Sample_submission_date = Jul 27 2017 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = liquid culture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: CC-124 x CC-4425 +!Sample_characteristics_ch1 = media: tris acetate phosphate medium -Cu +!Sample_characteristics_ch1 = light regime: continuous light +!Sample_characteristics_ch1 = library protocol: RiboZero +!Sample_growth_protocol_ch1 = Growth in media without Cu. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was purified from pelleted cells by freezing in SDS/proteinase K digestion buffer followed extraction with Trizol reagent. +!Sample_extract_protocol_ch1 = ~2 ug total RNA was used as starting material for either rRNA-depletion by RiboZero Plant Leaf kit or for enrichment of poly-A transcripts by binding oligo-T beads (indicated by "library protocol" above). The resulting RNA was then used to generate strand-specific Illumina libraries. +!Sample_description = processed data file: fpkms.copper.tsv +!Sample_data_processing = Basecalling performed using Illumina RTA software. +!Sample_data_processing = Conversion of qseq to fastq format and demultiplexing by in-house scripts +!Sample_data_processing = Removal of contaminating rRNA reads by alignment to rRNA+snoRNA.fasta with RNA-STAR (STAR_2.4.0j). Unmapped reads selected for further analysis with "--outReadsUnmapped Fastx" option of STAR. +!Sample_data_processing = Alignment to C.reinhardtii nuclear genome (Phytozome v5.5) plus chloroplast genome (CPv4) plus mitochondrial genome (MTv4) by RNA-STAR (STAR_2.4.0j) with default parameters except --alignIntronMax 5000 +!Sample_data_processing = SAM alignments sorted and converted to BAM format by samtools (v1.3). +!Sample_data_processing = Counts per gene and FPKMs calculated by cuffdiff (v2.0.2) with "--multi-read-correct --max-bundle-frags 1000000000 --library-type fr-firststrand" +!Sample_data_processing = Genome_build: Cre.nuc.v5.5.cp.v4.4.mt.v4.4 +!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files (.tsv) containing transcript abundance determinations calculated as FPKMs +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sean,D.,Gallaher +!Sample_contact_laboratory = Sabeeha Merchant +!Sample_contact_department = Chem & BioChem +!Sample_contact_institute = UCLA +!Sample_contact_address = 607 Charle E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN07418739 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3041728 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE101944 +!Sample_data_row_count = 0 +^SAMPLE = GSM2719238 +!Sample_title = mt+ vegetative +!Sample_geo_accession = GSM2719238 +!Sample_status = Public on Nov 27 2017 +!Sample_submission_date = Jul 27 2017 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = liquid culture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: CC-620 +!Sample_characteristics_ch1 = media: high salt medium +!Sample_characteristics_ch1 = light regime: continuous light +!Sample_characteristics_ch1 = library protocol: RiboZero +!Sample_growth_protocol_ch1 = Vegetatively growing culture of mt+ strain. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was purified from pelleted cells by freezing in SDS/proteinase K digestion buffer followed extraction with Trizol reagent. +!Sample_extract_protocol_ch1 = ~2 ug total RNA was used as starting material for either rRNA-depletion by RiboZero Plant Leaf kit or for enrichment of poly-A transcripts by binding oligo-T beads (indicated by "library protocol" above). The resulting RNA was then used to generate strand-specific Illumina libraries. +!Sample_description = processed data file: fpkms.sexual.tsv +!Sample_data_processing = Basecalling performed using Illumina RTA software. +!Sample_data_processing = Conversion of qseq to fastq format and demultiplexing by in-house scripts +!Sample_data_processing = Removal of contaminating rRNA reads by alignment to rRNA+snoRNA.fasta with RNA-STAR (STAR_2.4.0j). Unmapped reads selected for further analysis with "--outReadsUnmapped Fastx" option of STAR. +!Sample_data_processing = Alignment to C.reinhardtii nuclear genome (Phytozome v5.5) plus chloroplast genome (CPv4) plus mitochondrial genome (MTv4) by RNA-STAR (STAR_2.4.0j) with default parameters except --alignIntronMax 5000 +!Sample_data_processing = SAM alignments sorted and converted to BAM format by samtools (v1.3). +!Sample_data_processing = Counts per gene and FPKMs calculated by cuffdiff (v2.0.2) with "--multi-read-correct --max-bundle-frags 1000000000 --library-type fr-firststrand" +!Sample_data_processing = Genome_build: Cre.nuc.v5.5.cp.v4.4.mt.v4.4 +!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files (.tsv) containing transcript abundance determinations calculated as FPKMs +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sean,D.,Gallaher +!Sample_contact_laboratory = Sabeeha Merchant +!Sample_contact_department = Chem & BioChem +!Sample_contact_institute = UCLA +!Sample_contact_address = 607 Charle E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN07418738 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3041729 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE101944 +!Sample_data_row_count = 0 +^SAMPLE = GSM2719239 +!Sample_title = mt- vegetative +!Sample_geo_accession = GSM2719239 +!Sample_status = Public on Nov 27 2017 +!Sample_submission_date = Jul 27 2017 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = liquid culture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: CJU10 +!Sample_characteristics_ch1 = media: high salt medium +!Sample_characteristics_ch1 = light regime: continuous light +!Sample_characteristics_ch1 = library protocol: RiboZero +!Sample_growth_protocol_ch1 = Vegetatively growing culture of mt- strain. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was purified from pelleted cells by freezing in SDS/proteinase K digestion buffer followed extraction with Trizol reagent. +!Sample_extract_protocol_ch1 = ~2 ug total RNA was used as starting material for either rRNA-depletion by RiboZero Plant Leaf kit or for enrichment of poly-A transcripts by binding oligo-T beads (indicated by "library protocol" above). The resulting RNA was then used to generate strand-specific Illumina libraries. +!Sample_description = processed data file: fpkms.sexual.tsv +!Sample_data_processing = Basecalling performed using Illumina RTA software. +!Sample_data_processing = Conversion of qseq to fastq format and demultiplexing by in-house scripts +!Sample_data_processing = Removal of contaminating rRNA reads by alignment to rRNA+snoRNA.fasta with RNA-STAR (STAR_2.4.0j). Unmapped reads selected for further analysis with "--outReadsUnmapped Fastx" option of STAR. +!Sample_data_processing = Alignment to C.reinhardtii nuclear genome (Phytozome v5.5) plus chloroplast genome (CPv4) plus mitochondrial genome (MTv4) by RNA-STAR (STAR_2.4.0j) with default parameters except --alignIntronMax 5000 +!Sample_data_processing = SAM alignments sorted and converted to BAM format by samtools (v1.3). +!Sample_data_processing = Counts per gene and FPKMs calculated by cuffdiff (v2.0.2) with "--multi-read-correct --max-bundle-frags 1000000000 --library-type fr-firststrand" +!Sample_data_processing = Genome_build: Cre.nuc.v5.5.cp.v4.4.mt.v4.4 +!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files (.tsv) containing transcript abundance determinations calculated as FPKMs +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sean,D.,Gallaher +!Sample_contact_laboratory = Sabeeha Merchant +!Sample_contact_department = Chem & BioChem +!Sample_contact_institute = UCLA +!Sample_contact_address = 607 Charle E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN07418725 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3041730 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE101944 +!Sample_data_row_count = 0 +^SAMPLE = GSM2719240 +!Sample_title = mt+ gamete +!Sample_geo_accession = GSM2719240 +!Sample_status = Public on Nov 27 2017 +!Sample_submission_date = Jul 27 2017 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = liquid culture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: CC-620 +!Sample_characteristics_ch1 = media: high salt medium -N +!Sample_characteristics_ch1 = light regime: continuous light +!Sample_characteristics_ch1 = library protocol: RiboZero +!Sample_growth_protocol_ch1 = Gametes of mt+ strain. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was purified from pelleted cells by freezing in SDS/proteinase K digestion buffer followed extraction with Trizol reagent. +!Sample_extract_protocol_ch1 = ~2 ug total RNA was used as starting material for either rRNA-depletion by RiboZero Plant Leaf kit or for enrichment of poly-A transcripts by binding oligo-T beads (indicated by "library protocol" above). The resulting RNA was then used to generate strand-specific Illumina libraries. +!Sample_description = processed data file: fpkms.sexual.tsv +!Sample_data_processing = Basecalling performed using Illumina RTA software. +!Sample_data_processing = Conversion of qseq to fastq format and demultiplexing by in-house scripts +!Sample_data_processing = Removal of contaminating rRNA reads by alignment to rRNA+snoRNA.fasta with RNA-STAR (STAR_2.4.0j). Unmapped reads selected for further analysis with "--outReadsUnmapped Fastx" option of STAR. +!Sample_data_processing = Alignment to C.reinhardtii nuclear genome (Phytozome v5.5) plus chloroplast genome (CPv4) plus mitochondrial genome (MTv4) by RNA-STAR (STAR_2.4.0j) with default parameters except --alignIntronMax 5000 +!Sample_data_processing = SAM alignments sorted and converted to BAM format by samtools (v1.3). +!Sample_data_processing = Counts per gene and FPKMs calculated by cuffdiff (v2.0.2) with "--multi-read-correct --max-bundle-frags 1000000000 --library-type fr-firststrand" +!Sample_data_processing = Genome_build: Cre.nuc.v5.5.cp.v4.4.mt.v4.4 +!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files (.tsv) containing transcript abundance determinations calculated as FPKMs +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sean,D.,Gallaher +!Sample_contact_laboratory = Sabeeha Merchant +!Sample_contact_department = Chem & BioChem +!Sample_contact_institute = UCLA +!Sample_contact_address = 607 Charle E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN07418714 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3041731 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE101944 +!Sample_data_row_count = 0 +^SAMPLE = GSM2719241 +!Sample_title = mt- gamete +!Sample_geo_accession = GSM2719241 +!Sample_status = Public on Nov 27 2017 +!Sample_submission_date = Jul 27 2017 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = liquid culture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: CJU10 +!Sample_characteristics_ch1 = media: high salt medium -N +!Sample_characteristics_ch1 = light regime: continuous light +!Sample_characteristics_ch1 = library protocol: RiboZero +!Sample_growth_protocol_ch1 = Gametes of mt- strain. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was purified from pelleted cells by freezing in SDS/proteinase K digestion buffer followed extraction with Trizol reagent. +!Sample_extract_protocol_ch1 = ~2 ug total RNA was used as starting material for either rRNA-depletion by RiboZero Plant Leaf kit or for enrichment of poly-A transcripts by binding oligo-T beads (indicated by "library protocol" above). The resulting RNA was then used to generate strand-specific Illumina libraries. +!Sample_description = processed data file: fpkms.sexual.tsv +!Sample_data_processing = Basecalling performed using Illumina RTA software. +!Sample_data_processing = Conversion of qseq to fastq format and demultiplexing by in-house scripts +!Sample_data_processing = Removal of contaminating rRNA reads by alignment to rRNA+snoRNA.fasta with RNA-STAR (STAR_2.4.0j). Unmapped reads selected for further analysis with "--outReadsUnmapped Fastx" option of STAR. +!Sample_data_processing = Alignment to C.reinhardtii nuclear genome (Phytozome v5.5) plus chloroplast genome (CPv4) plus mitochondrial genome (MTv4) by RNA-STAR (STAR_2.4.0j) with default parameters except --alignIntronMax 5000 +!Sample_data_processing = SAM alignments sorted and converted to BAM format by samtools (v1.3). +!Sample_data_processing = Counts per gene and FPKMs calculated by cuffdiff (v2.0.2) with "--multi-read-correct --max-bundle-frags 1000000000 --library-type fr-firststrand" +!Sample_data_processing = Genome_build: Cre.nuc.v5.5.cp.v4.4.mt.v4.4 +!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files (.tsv) containing transcript abundance determinations calculated as FPKMs +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sean,D.,Gallaher +!Sample_contact_laboratory = Sabeeha Merchant +!Sample_contact_department = Chem & BioChem +!Sample_contact_institute = UCLA +!Sample_contact_address = 607 Charle E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN07418724 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3041732 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE101944 +!Sample_data_row_count = 0 +^SAMPLE = GSM2719242 +!Sample_title = zygote +!Sample_geo_accession = GSM2719242 +!Sample_status = Public on Nov 27 2017 +!Sample_submission_date = Jul 27 2017 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = liquid culture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: CC-620 x CJU10 +!Sample_characteristics_ch1 = media: high salt medium -N +!Sample_characteristics_ch1 = light regime: continuous dark +!Sample_characteristics_ch1 = library protocol: RiboZero +!Sample_growth_protocol_ch1 = Zygotes 1 d after cross of mt+ and mt- gametes. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was purified from pelleted cells by freezing in SDS/proteinase K digestion buffer followed extraction with Trizol reagent. +!Sample_extract_protocol_ch1 = ~2 ug total RNA was used as starting material for either rRNA-depletion by RiboZero Plant Leaf kit or for enrichment of poly-A transcripts by binding oligo-T beads (indicated by "library protocol" above). The resulting RNA was then used to generate strand-specific Illumina libraries. +!Sample_description = processed data file: fpkms.sexual.tsv +!Sample_data_processing = Basecalling performed using Illumina RTA software. +!Sample_data_processing = Conversion of qseq to fastq format and demultiplexing by in-house scripts +!Sample_data_processing = Removal of contaminating rRNA reads by alignment to rRNA+snoRNA.fasta with RNA-STAR (STAR_2.4.0j). Unmapped reads selected for further analysis with "--outReadsUnmapped Fastx" option of STAR. +!Sample_data_processing = Alignment to C.reinhardtii nuclear genome (Phytozome v5.5) plus chloroplast genome (CPv4) plus mitochondrial genome (MTv4) by RNA-STAR (STAR_2.4.0j) with default parameters except --alignIntronMax 5000 +!Sample_data_processing = SAM alignments sorted and converted to BAM format by samtools (v1.3). +!Sample_data_processing = Counts per gene and FPKMs calculated by cuffdiff (v2.0.2) with "--multi-read-correct --max-bundle-frags 1000000000 --library-type fr-firststrand" +!Sample_data_processing = Genome_build: Cre.nuc.v5.5.cp.v4.4.mt.v4.4 +!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files (.tsv) containing transcript abundance determinations calculated as FPKMs +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sean,D.,Gallaher +!Sample_contact_laboratory = Sabeeha Merchant +!Sample_contact_department = Chem & BioChem +!Sample_contact_institute = UCLA +!Sample_contact_address = 607 Charle E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN07418715 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3041733 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE101944 +!Sample_data_row_count = 0 +^SAMPLE = GSM2719243 +!Sample_title = post-germination +!Sample_geo_accession = GSM2719243 +!Sample_status = Public on Nov 27 2017 +!Sample_submission_date = Jul 27 2017 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = liquid culture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: CC-620 x CJU10 +!Sample_characteristics_ch1 = media: tris acetate phosphate medium +!Sample_characteristics_ch1 = light regime: continuous light +!Sample_characteristics_ch1 = library protocol: RiboZero +!Sample_growth_protocol_ch1 = Vegetatively growing cells following germination. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was purified from pelleted cells by freezing in SDS/proteinase K digestion buffer followed extraction with Trizol reagent. +!Sample_extract_protocol_ch1 = ~2 ug total RNA was used as starting material for either rRNA-depletion by RiboZero Plant Leaf kit or for enrichment of poly-A transcripts by binding oligo-T beads (indicated by "library protocol" above). The resulting RNA was then used to generate strand-specific Illumina libraries. +!Sample_description = processed data file: fpkms.sexual.tsv +!Sample_data_processing = Basecalling performed using Illumina RTA software. +!Sample_data_processing = Conversion of qseq to fastq format and demultiplexing by in-house scripts +!Sample_data_processing = Removal of contaminating rRNA reads by alignment to rRNA+snoRNA.fasta with RNA-STAR (STAR_2.4.0j). Unmapped reads selected for further analysis with "--outReadsUnmapped Fastx" option of STAR. +!Sample_data_processing = Alignment to C.reinhardtii nuclear genome (Phytozome v5.5) plus chloroplast genome (CPv4) plus mitochondrial genome (MTv4) by RNA-STAR (STAR_2.4.0j) with default parameters except --alignIntronMax 5000 +!Sample_data_processing = SAM alignments sorted and converted to BAM format by samtools (v1.3). +!Sample_data_processing = Counts per gene and FPKMs calculated by cuffdiff (v2.0.2) with "--multi-read-correct --max-bundle-frags 1000000000 --library-type fr-firststrand" +!Sample_data_processing = Genome_build: Cre.nuc.v5.5.cp.v4.4.mt.v4.4 +!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files (.tsv) containing transcript abundance determinations calculated as FPKMs +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sean,D.,Gallaher +!Sample_contact_laboratory = Sabeeha Merchant +!Sample_contact_department = Chem & BioChem +!Sample_contact_institute = UCLA +!Sample_contact_address = 607 Charle E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN07418716 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3041734 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE101944 +!Sample_data_row_count = 0 +^SAMPLE = GSM3069464 +!Sample_title = dark -11 h +!Sample_geo_accession = GSM3069464 +!Sample_status = Public on Jan 03 2019 +!Sample_submission_date = Mar 27 2018 +!Sample_last_update_date = Jan 03 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = liquid culture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: CC-5390 +!Sample_characteristics_ch1 = time point: -11 h +!Sample_characteristics_ch1 = light: dark +!Sample_characteristics_ch1 = temperature: 18 C +!Sample_characteristics_ch1 = carbon dioxide: air bubbling +!Sample_treatment_protocol_ch1 = Samples collected over multiple time points over the course 1 day. +!Sample_growth_protocol_ch1 = Cultures were grown in a photobioreactor on a 12 h light / 12 h dark cycle in HSM media with air bubbling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was purified by extraction with Trizol reagent. +!Sample_extract_protocol_ch1 = ~2 ug total RNA was used as starting material for rRNA-depletion by RiboZero Plant Leaf kit. The resulting RNA was then used to generate strand-specific Illumina libraries. +!Sample_description = Diurnally grown culture sampled 11 h before the light phase. +!Sample_data_processing = Basecalling performed using Illumina RTA software. +!Sample_data_processing = Conversion of qseq to fastq format and demultiplexing by in-house scripts +!Sample_data_processing = Removal of contaminating rRNA reads by alignment to rRNA+snoRNA.fasta with RNA-STAR (STAR_2.4.0j). Unmapped reads selected for further analysis with "--outReadsUnmapped Fastx" option of STAR. +!Sample_data_processing = Alignment to C.reinhardtii nuclear genome (Phytozome v5.5) plus chloroplast genome (CPv4) plus mitochondrial genome (MTv4) by RNA-STAR (STAR_2.4.0j) with default parameters except --alignIntronMax 5000 +!Sample_data_processing = SAM alignments sorted and converted to BAM format by samtools (v1.3). +!Sample_data_processing = Counts per gene and FPKMs calculated by cuffdiff (v2.0.2) with "--multi-read-correct --max-bundle-frags 1000000000 --library-type fr-firststrand" +!Sample_data_processing = Genome_build: Cre.nuc.v5.5.cp.v4.4.mt.v4.4 +!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files (.tsv) containing transcript abundance determinations calculated as FPKMs +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sean,D.,Gallaher +!Sample_contact_laboratory = Sabeeha Merchant +!Sample_contact_department = Chem & BioChem +!Sample_contact_institute = UCLA +!Sample_contact_address = 607 Charle E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08801672 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3853407 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE112394 +!Sample_data_row_count = 0 +^SAMPLE = GSM3069465 +!Sample_title = dark -9 h +!Sample_geo_accession = GSM3069465 +!Sample_status = Public on Jan 03 2019 +!Sample_submission_date = Mar 27 2018 +!Sample_last_update_date = Jan 03 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = liquid culture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: CC-5390 +!Sample_characteristics_ch1 = time point: -9 h +!Sample_characteristics_ch1 = light: dark +!Sample_characteristics_ch1 = temperature: 18 C +!Sample_characteristics_ch1 = carbon dioxide: air bubbling +!Sample_treatment_protocol_ch1 = Samples collected over multiple time points over the course 1 day. +!Sample_growth_protocol_ch1 = Cultures were grown in a photobioreactor on a 12 h light / 12 h dark cycle in HSM media with air bubbling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was purified by extraction with Trizol reagent. +!Sample_extract_protocol_ch1 = ~2 ug total RNA was used as starting material for rRNA-depletion by RiboZero Plant Leaf kit. The resulting RNA was then used to generate strand-specific Illumina libraries. +!Sample_description = Diurnally grown culture sampled 9 h before the light phase. +!Sample_data_processing = Basecalling performed using Illumina RTA software. +!Sample_data_processing = Conversion of qseq to fastq format and demultiplexing by in-house scripts +!Sample_data_processing = Removal of contaminating rRNA reads by alignment to rRNA+snoRNA.fasta with RNA-STAR (STAR_2.4.0j). Unmapped reads selected for further analysis with "--outReadsUnmapped Fastx" option of STAR. +!Sample_data_processing = Alignment to C.reinhardtii nuclear genome (Phytozome v5.5) plus chloroplast genome (CPv4) plus mitochondrial genome (MTv4) by RNA-STAR (STAR_2.4.0j) with default parameters except --alignIntronMax 5000 +!Sample_data_processing = SAM alignments sorted and converted to BAM format by samtools (v1.3). +!Sample_data_processing = Counts per gene and FPKMs calculated by cuffdiff (v2.0.2) with "--multi-read-correct --max-bundle-frags 1000000000 --library-type fr-firststrand" +!Sample_data_processing = Genome_build: Cre.nuc.v5.5.cp.v4.4.mt.v4.4 +!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files (.tsv) containing transcript abundance determinations calculated as FPKMs +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sean,D.,Gallaher +!Sample_contact_laboratory = Sabeeha Merchant +!Sample_contact_department = Chem & BioChem +!Sample_contact_institute = UCLA +!Sample_contact_address = 607 Charle E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08801671 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3853408 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE112394 +!Sample_data_row_count = 0 +^SAMPLE = GSM3069466 +!Sample_title = dark -7 h +!Sample_geo_accession = GSM3069466 +!Sample_status = Public on Jan 03 2019 +!Sample_submission_date = Mar 27 2018 +!Sample_last_update_date = Jan 03 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = liquid culture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: CC-5390 +!Sample_characteristics_ch1 = time point: -7 h +!Sample_characteristics_ch1 = light: dark +!Sample_characteristics_ch1 = temperature: 18 C +!Sample_characteristics_ch1 = carbon dioxide: air bubbling +!Sample_treatment_protocol_ch1 = Samples collected over multiple time points over the course 1 day. +!Sample_growth_protocol_ch1 = Cultures were grown in a photobioreactor on a 12 h light / 12 h dark cycle in HSM media with air bubbling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was purified by extraction with Trizol reagent. +!Sample_extract_protocol_ch1 = ~2 ug total RNA was used as starting material for rRNA-depletion by RiboZero Plant Leaf kit. The resulting RNA was then used to generate strand-specific Illumina libraries. +!Sample_description = Diurnally grown culture sampled 7 h before the light phase. +!Sample_data_processing = Basecalling performed using Illumina RTA software. +!Sample_data_processing = Conversion of qseq to fastq format and demultiplexing by in-house scripts +!Sample_data_processing = Removal of contaminating rRNA reads by alignment to rRNA+snoRNA.fasta with RNA-STAR (STAR_2.4.0j). Unmapped reads selected for further analysis with "--outReadsUnmapped Fastx" option of STAR. +!Sample_data_processing = Alignment to C.reinhardtii nuclear genome (Phytozome v5.5) plus chloroplast genome (CPv4) plus mitochondrial genome (MTv4) by RNA-STAR (STAR_2.4.0j) with default parameters except --alignIntronMax 5000 +!Sample_data_processing = SAM alignments sorted and converted to BAM format by samtools (v1.3). +!Sample_data_processing = Counts per gene and FPKMs calculated by cuffdiff (v2.0.2) with "--multi-read-correct --max-bundle-frags 1000000000 --library-type fr-firststrand" +!Sample_data_processing = Genome_build: Cre.nuc.v5.5.cp.v4.4.mt.v4.4 +!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files (.tsv) containing transcript abundance determinations calculated as FPKMs +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sean,D.,Gallaher +!Sample_contact_laboratory = Sabeeha Merchant +!Sample_contact_department = Chem & BioChem +!Sample_contact_institute = UCLA +!Sample_contact_address = 607 Charle E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08801670 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3853409 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE112394 +!Sample_data_row_count = 0 +^SAMPLE = GSM3069467 +!Sample_title = dark -5 h +!Sample_geo_accession = GSM3069467 +!Sample_status = Public on Jan 03 2019 +!Sample_submission_date = Mar 27 2018 +!Sample_last_update_date = Jan 03 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = liquid culture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: CC-5390 +!Sample_characteristics_ch1 = time point: -5 h +!Sample_characteristics_ch1 = light: dark +!Sample_characteristics_ch1 = temperature: 18 C +!Sample_characteristics_ch1 = carbon dioxide: air bubbling +!Sample_treatment_protocol_ch1 = Samples collected over multiple time points over the course 1 day. +!Sample_growth_protocol_ch1 = Cultures were grown in a photobioreactor on a 12 h light / 12 h dark cycle in HSM media with air bubbling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was purified by extraction with Trizol reagent. +!Sample_extract_protocol_ch1 = ~2 ug total RNA was used as starting material for rRNA-depletion by RiboZero Plant Leaf kit. The resulting RNA was then used to generate strand-specific Illumina libraries. +!Sample_description = Diurnally grown culture sampled 5 h before the light phase. +!Sample_data_processing = Basecalling performed using Illumina RTA software. +!Sample_data_processing = Conversion of qseq to fastq format and demultiplexing by in-house scripts +!Sample_data_processing = Removal of contaminating rRNA reads by alignment to rRNA+snoRNA.fasta with RNA-STAR (STAR_2.4.0j). Unmapped reads selected for further analysis with "--outReadsUnmapped Fastx" option of STAR. +!Sample_data_processing = Alignment to C.reinhardtii nuclear genome (Phytozome v5.5) plus chloroplast genome (CPv4) plus mitochondrial genome (MTv4) by RNA-STAR (STAR_2.4.0j) with default parameters except --alignIntronMax 5000 +!Sample_data_processing = SAM alignments sorted and converted to BAM format by samtools (v1.3). +!Sample_data_processing = Counts per gene and FPKMs calculated by cuffdiff (v2.0.2) with "--multi-read-correct --max-bundle-frags 1000000000 --library-type fr-firststrand" +!Sample_data_processing = Genome_build: Cre.nuc.v5.5.cp.v4.4.mt.v4.4 +!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files (.tsv) containing transcript abundance determinations calculated as FPKMs +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sean,D.,Gallaher +!Sample_contact_laboratory = Sabeeha Merchant +!Sample_contact_department = Chem & BioChem +!Sample_contact_institute = UCLA +!Sample_contact_address = 607 Charle E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08801669 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3853410 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE112394 +!Sample_data_row_count = 0 +^SAMPLE = GSM3069468 +!Sample_title = dark -3 h +!Sample_geo_accession = GSM3069468 +!Sample_status = Public on Jan 03 2019 +!Sample_submission_date = Mar 27 2018 +!Sample_last_update_date = Jan 03 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = liquid culture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: CC-5390 +!Sample_characteristics_ch1 = time point: -3 h +!Sample_characteristics_ch1 = light: dark +!Sample_characteristics_ch1 = temperature: 18 C +!Sample_characteristics_ch1 = carbon dioxide: air bubbling +!Sample_treatment_protocol_ch1 = Samples collected over multiple time points over the course 1 day. +!Sample_growth_protocol_ch1 = Cultures were grown in a photobioreactor on a 12 h light / 12 h dark cycle in HSM media with air bubbling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was purified by extraction with Trizol reagent. +!Sample_extract_protocol_ch1 = ~2 ug total RNA was used as starting material for rRNA-depletion by RiboZero Plant Leaf kit. The resulting RNA was then used to generate strand-specific Illumina libraries. +!Sample_description = Diurnally grown culture sampled 3 h before the light phase. +!Sample_data_processing = Basecalling performed using Illumina RTA software. +!Sample_data_processing = Conversion of qseq to fastq format and demultiplexing by in-house scripts +!Sample_data_processing = Removal of contaminating rRNA reads by alignment to rRNA+snoRNA.fasta with RNA-STAR (STAR_2.4.0j). Unmapped reads selected for further analysis with "--outReadsUnmapped Fastx" option of STAR. +!Sample_data_processing = Alignment to C.reinhardtii nuclear genome (Phytozome v5.5) plus chloroplast genome (CPv4) plus mitochondrial genome (MTv4) by RNA-STAR (STAR_2.4.0j) with default parameters except --alignIntronMax 5000 +!Sample_data_processing = SAM alignments sorted and converted to BAM format by samtools (v1.3). +!Sample_data_processing = Counts per gene and FPKMs calculated by cuffdiff (v2.0.2) with "--multi-read-correct --max-bundle-frags 1000000000 --library-type fr-firststrand" +!Sample_data_processing = Genome_build: Cre.nuc.v5.5.cp.v4.4.mt.v4.4 +!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files (.tsv) containing transcript abundance determinations calculated as FPKMs +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sean,D.,Gallaher +!Sample_contact_laboratory = Sabeeha Merchant +!Sample_contact_department = Chem & BioChem +!Sample_contact_institute = UCLA +!Sample_contact_address = 607 Charle E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08801668 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3853411 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE112394 +!Sample_data_row_count = 0 +^SAMPLE = GSM3069469 +!Sample_title = dark -1 h +!Sample_geo_accession = GSM3069469 +!Sample_status = Public on Jan 03 2019 +!Sample_submission_date = Mar 27 2018 +!Sample_last_update_date = Jan 03 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = liquid culture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: CC-5390 +!Sample_characteristics_ch1 = time point: -1 h +!Sample_characteristics_ch1 = light: dark +!Sample_characteristics_ch1 = temperature: 18 C +!Sample_characteristics_ch1 = carbon dioxide: air bubbling +!Sample_treatment_protocol_ch1 = Samples collected over multiple time points over the course 1 day. +!Sample_growth_protocol_ch1 = Cultures were grown in a photobioreactor on a 12 h light / 12 h dark cycle in HSM media with air bubbling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was purified by extraction with Trizol reagent. +!Sample_extract_protocol_ch1 = ~2 ug total RNA was used as starting material for rRNA-depletion by RiboZero Plant Leaf kit. The resulting RNA was then used to generate strand-specific Illumina libraries. +!Sample_description = Diurnally grown culture sampled 1 h before the light phase. +!Sample_data_processing = Basecalling performed using Illumina RTA software. +!Sample_data_processing = Conversion of qseq to fastq format and demultiplexing by in-house scripts +!Sample_data_processing = Removal of contaminating rRNA reads by alignment to rRNA+snoRNA.fasta with RNA-STAR (STAR_2.4.0j). Unmapped reads selected for further analysis with "--outReadsUnmapped Fastx" option of STAR. +!Sample_data_processing = Alignment to C.reinhardtii nuclear genome (Phytozome v5.5) plus chloroplast genome (CPv4) plus mitochondrial genome (MTv4) by RNA-STAR (STAR_2.4.0j) with default parameters except --alignIntronMax 5000 +!Sample_data_processing = SAM alignments sorted and converted to BAM format by samtools (v1.3). +!Sample_data_processing = Counts per gene and FPKMs calculated by cuffdiff (v2.0.2) with "--multi-read-correct --max-bundle-frags 1000000000 --library-type fr-firststrand" +!Sample_data_processing = Genome_build: Cre.nuc.v5.5.cp.v4.4.mt.v4.4 +!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files (.tsv) containing transcript abundance determinations calculated as FPKMs +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sean,D.,Gallaher +!Sample_contact_laboratory = Sabeeha Merchant +!Sample_contact_department = Chem & BioChem +!Sample_contact_institute = UCLA +!Sample_contact_address = 607 Charle E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08801667 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3853412 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE112394 +!Sample_data_row_count = 0 +^SAMPLE = GSM3069470 +!Sample_title = dark -0.5 h +!Sample_geo_accession = GSM3069470 +!Sample_status = Public on Jan 03 2019 +!Sample_submission_date = Mar 27 2018 +!Sample_last_update_date = Jan 03 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = liquid culture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: CC-5390 +!Sample_characteristics_ch1 = time point: -0.5 h +!Sample_characteristics_ch1 = light: dark +!Sample_characteristics_ch1 = temperature: 18 C +!Sample_characteristics_ch1 = carbon dioxide: air bubbling +!Sample_treatment_protocol_ch1 = Samples collected over multiple time points over the course 1 day. +!Sample_growth_protocol_ch1 = Cultures were grown in a photobioreactor on a 12 h light / 12 h dark cycle in HSM media with air bubbling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was purified by extraction with Trizol reagent. +!Sample_extract_protocol_ch1 = ~2 ug total RNA was used as starting material for rRNA-depletion by RiboZero Plant Leaf kit. The resulting RNA was then used to generate strand-specific Illumina libraries. +!Sample_description = Diurnally grown culture sampled 0.5 h before the light phase. +!Sample_data_processing = Basecalling performed using Illumina RTA software. +!Sample_data_processing = Conversion of qseq to fastq format and demultiplexing by in-house scripts +!Sample_data_processing = Removal of contaminating rRNA reads by alignment to rRNA+snoRNA.fasta with RNA-STAR (STAR_2.4.0j). Unmapped reads selected for further analysis with "--outReadsUnmapped Fastx" option of STAR. +!Sample_data_processing = Alignment to C.reinhardtii nuclear genome (Phytozome v5.5) plus chloroplast genome (CPv4) plus mitochondrial genome (MTv4) by RNA-STAR (STAR_2.4.0j) with default parameters except --alignIntronMax 5000 +!Sample_data_processing = SAM alignments sorted and converted to BAM format by samtools (v1.3). +!Sample_data_processing = Counts per gene and FPKMs calculated by cuffdiff (v2.0.2) with "--multi-read-correct --max-bundle-frags 1000000000 --library-type fr-firststrand" +!Sample_data_processing = Genome_build: Cre.nuc.v5.5.cp.v4.4.mt.v4.4 +!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files (.tsv) containing transcript abundance determinations calculated as FPKMs +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sean,D.,Gallaher +!Sample_contact_laboratory = Sabeeha Merchant +!Sample_contact_department = Chem & BioChem +!Sample_contact_institute = UCLA +!Sample_contact_address = 607 Charle E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08801666 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3853413 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE112394 +!Sample_data_row_count = 0 +^SAMPLE = GSM3069471 +!Sample_title = dark 0 h +!Sample_geo_accession = GSM3069471 +!Sample_status = Public on Jan 03 2019 +!Sample_submission_date = Mar 27 2018 +!Sample_last_update_date = Jan 03 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = liquid culture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: CC-5390 +!Sample_characteristics_ch1 = time point: 0 h +!Sample_characteristics_ch1 = light: dark +!Sample_characteristics_ch1 = temperature: 18 C +!Sample_characteristics_ch1 = carbon dioxide: air bubbling +!Sample_treatment_protocol_ch1 = Samples collected over multiple time points over the course 1 day. +!Sample_growth_protocol_ch1 = Cultures were grown in a photobioreactor on a 12 h light / 12 h dark cycle in HSM media with air bubbling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was purified by extraction with Trizol reagent. +!Sample_extract_protocol_ch1 = ~2 ug total RNA was used as starting material for rRNA-depletion by RiboZero Plant Leaf kit. The resulting RNA was then used to generate strand-specific Illumina libraries. +!Sample_description = Diurnally grown culture sampled right before the dark to light transition. +!Sample_data_processing = Basecalling performed using Illumina RTA software. +!Sample_data_processing = Conversion of qseq to fastq format and demultiplexing by in-house scripts +!Sample_data_processing = Removal of contaminating rRNA reads by alignment to rRNA+snoRNA.fasta with RNA-STAR (STAR_2.4.0j). Unmapped reads selected for further analysis with "--outReadsUnmapped Fastx" option of STAR. +!Sample_data_processing = Alignment to C.reinhardtii nuclear genome (Phytozome v5.5) plus chloroplast genome (CPv4) plus mitochondrial genome (MTv4) by RNA-STAR (STAR_2.4.0j) with default parameters except --alignIntronMax 5000 +!Sample_data_processing = SAM alignments sorted and converted to BAM format by samtools (v1.3). +!Sample_data_processing = Counts per gene and FPKMs calculated by cuffdiff (v2.0.2) with "--multi-read-correct --max-bundle-frags 1000000000 --library-type fr-firststrand" +!Sample_data_processing = Genome_build: Cre.nuc.v5.5.cp.v4.4.mt.v4.4 +!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files (.tsv) containing transcript abundance determinations calculated as FPKMs +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sean,D.,Gallaher +!Sample_contact_laboratory = Sabeeha Merchant +!Sample_contact_department = Chem & BioChem +!Sample_contact_institute = UCLA +!Sample_contact_address = 607 Charle E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08801665 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3853414 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE112394 +!Sample_data_row_count = 0 +^SAMPLE = GSM3069472 +!Sample_title = light 0.5 h +!Sample_geo_accession = GSM3069472 +!Sample_status = Public on Jan 03 2019 +!Sample_submission_date = Mar 27 2018 +!Sample_last_update_date = Jan 03 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = liquid culture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: CC-5390 +!Sample_characteristics_ch1 = time point: 0.5 h +!Sample_characteristics_ch1 = light: light (200 PFD) +!Sample_characteristics_ch1 = temperature: 28 C +!Sample_characteristics_ch1 = carbon dioxide: air bubbling +!Sample_treatment_protocol_ch1 = Samples collected over multiple time points over the course 1 day. +!Sample_growth_protocol_ch1 = Cultures were grown in a photobioreactor on a 12 h light / 12 h dark cycle in HSM media with air bubbling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was purified by extraction with Trizol reagent. +!Sample_extract_protocol_ch1 = ~2 ug total RNA was used as starting material for rRNA-depletion by RiboZero Plant Leaf kit. The resulting RNA was then used to generate strand-specific Illumina libraries. +!Sample_description = Diurnally grown culture sampled 0.5 h into the light phase. +!Sample_data_processing = Basecalling performed using Illumina RTA software. +!Sample_data_processing = Conversion of qseq to fastq format and demultiplexing by in-house scripts +!Sample_data_processing = Removal of contaminating rRNA reads by alignment to rRNA+snoRNA.fasta with RNA-STAR (STAR_2.4.0j). Unmapped reads selected for further analysis with "--outReadsUnmapped Fastx" option of STAR. +!Sample_data_processing = Alignment to C.reinhardtii nuclear genome (Phytozome v5.5) plus chloroplast genome (CPv4) plus mitochondrial genome (MTv4) by RNA-STAR (STAR_2.4.0j) with default parameters except --alignIntronMax 5000 +!Sample_data_processing = SAM alignments sorted and converted to BAM format by samtools (v1.3). +!Sample_data_processing = Counts per gene and FPKMs calculated by cuffdiff (v2.0.2) with "--multi-read-correct --max-bundle-frags 1000000000 --library-type fr-firststrand" +!Sample_data_processing = Genome_build: Cre.nuc.v5.5.cp.v4.4.mt.v4.4 +!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files (.tsv) containing transcript abundance determinations calculated as FPKMs +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sean,D.,Gallaher +!Sample_contact_laboratory = Sabeeha Merchant +!Sample_contact_department = Chem & BioChem +!Sample_contact_institute = UCLA +!Sample_contact_address = 607 Charle E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08801664 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3853415 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE112394 +!Sample_data_row_count = 0 +^SAMPLE = GSM3069473 +!Sample_title = light 1 h +!Sample_geo_accession = GSM3069473 +!Sample_status = Public on Jan 03 2019 +!Sample_submission_date = Mar 27 2018 +!Sample_last_update_date = Jan 03 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = liquid culture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: CC-5390 +!Sample_characteristics_ch1 = time point: 1 h +!Sample_characteristics_ch1 = light: light (200 PFD) +!Sample_characteristics_ch1 = temperature: 28 C +!Sample_characteristics_ch1 = carbon dioxide: air bubbling +!Sample_treatment_protocol_ch1 = Samples collected over multiple time points over the course 1 day. +!Sample_growth_protocol_ch1 = Cultures were grown in a photobioreactor on a 12 h light / 12 h dark cycle in HSM media with air bubbling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was purified by extraction with Trizol reagent. +!Sample_extract_protocol_ch1 = ~2 ug total RNA was used as starting material for rRNA-depletion by RiboZero Plant Leaf kit. The resulting RNA was then used to generate strand-specific Illumina libraries. +!Sample_description = Diurnally grown culture sampled 1 h into the light phase. +!Sample_data_processing = Basecalling performed using Illumina RTA software. +!Sample_data_processing = Conversion of qseq to fastq format and demultiplexing by in-house scripts +!Sample_data_processing = Removal of contaminating rRNA reads by alignment to rRNA+snoRNA.fasta with RNA-STAR (STAR_2.4.0j). Unmapped reads selected for further analysis with "--outReadsUnmapped Fastx" option of STAR. +!Sample_data_processing = Alignment to C.reinhardtii nuclear genome (Phytozome v5.5) plus chloroplast genome (CPv4) plus mitochondrial genome (MTv4) by RNA-STAR (STAR_2.4.0j) with default parameters except --alignIntronMax 5000 +!Sample_data_processing = SAM alignments sorted and converted to BAM format by samtools (v1.3). +!Sample_data_processing = Counts per gene and FPKMs calculated by cuffdiff (v2.0.2) with "--multi-read-correct --max-bundle-frags 1000000000 --library-type fr-firststrand" +!Sample_data_processing = Genome_build: Cre.nuc.v5.5.cp.v4.4.mt.v4.4 +!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files (.tsv) containing transcript abundance determinations calculated as FPKMs +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sean,D.,Gallaher +!Sample_contact_laboratory = Sabeeha Merchant +!Sample_contact_department = Chem & BioChem +!Sample_contact_institute = UCLA +!Sample_contact_address = 607 Charle E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08801663 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3853416 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE112394 +!Sample_data_row_count = 0 +^SAMPLE = GSM3069474 +!Sample_title = light 3 h +!Sample_geo_accession = GSM3069474 +!Sample_status = Public on Jan 03 2019 +!Sample_submission_date = Mar 27 2018 +!Sample_last_update_date = Jan 03 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = liquid culture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: CC-5390 +!Sample_characteristics_ch1 = time point: 3 h +!Sample_characteristics_ch1 = light: light (200 PFD) +!Sample_characteristics_ch1 = temperature: 28 C +!Sample_characteristics_ch1 = carbon dioxide: air bubbling +!Sample_treatment_protocol_ch1 = Samples collected over multiple time points over the course 1 day. +!Sample_growth_protocol_ch1 = Cultures were grown in a photobioreactor on a 12 h light / 12 h dark cycle in HSM media with air bubbling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was purified by extraction with Trizol reagent. +!Sample_extract_protocol_ch1 = ~2 ug total RNA was used as starting material for rRNA-depletion by RiboZero Plant Leaf kit. The resulting RNA was then used to generate strand-specific Illumina libraries. +!Sample_description = Diurnally grown culture sampled 3 h into the light phase. +!Sample_data_processing = Basecalling performed using Illumina RTA software. +!Sample_data_processing = Conversion of qseq to fastq format and demultiplexing by in-house scripts +!Sample_data_processing = Removal of contaminating rRNA reads by alignment to rRNA+snoRNA.fasta with RNA-STAR (STAR_2.4.0j). Unmapped reads selected for further analysis with "--outReadsUnmapped Fastx" option of STAR. +!Sample_data_processing = Alignment to C.reinhardtii nuclear genome (Phytozome v5.5) plus chloroplast genome (CPv4) plus mitochondrial genome (MTv4) by RNA-STAR (STAR_2.4.0j) with default parameters except --alignIntronMax 5000 +!Sample_data_processing = SAM alignments sorted and converted to BAM format by samtools (v1.3). +!Sample_data_processing = Counts per gene and FPKMs calculated by cuffdiff (v2.0.2) with "--multi-read-correct --max-bundle-frags 1000000000 --library-type fr-firststrand" +!Sample_data_processing = Genome_build: Cre.nuc.v5.5.cp.v4.4.mt.v4.4 +!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files (.tsv) containing transcript abundance determinations calculated as FPKMs +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sean,D.,Gallaher +!Sample_contact_laboratory = Sabeeha Merchant +!Sample_contact_department = Chem & BioChem +!Sample_contact_institute = UCLA +!Sample_contact_address = 607 Charle E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08801690 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3853417 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE112394 +!Sample_data_row_count = 0 +^SAMPLE = GSM3069475 +!Sample_title = light 5 h +!Sample_geo_accession = GSM3069475 +!Sample_status = Public on Jan 03 2019 +!Sample_submission_date = Mar 27 2018 +!Sample_last_update_date = Jan 03 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = liquid culture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: CC-5390 +!Sample_characteristics_ch1 = time point: 5 h +!Sample_characteristics_ch1 = light: light (200 PFD) +!Sample_characteristics_ch1 = temperature: 28 C +!Sample_characteristics_ch1 = carbon dioxide: air bubbling +!Sample_treatment_protocol_ch1 = Samples collected over multiple time points over the course 1 day. +!Sample_growth_protocol_ch1 = Cultures were grown in a photobioreactor on a 12 h light / 12 h dark cycle in HSM media with air bubbling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was purified by extraction with Trizol reagent. +!Sample_extract_protocol_ch1 = ~2 ug total RNA was used as starting material for rRNA-depletion by RiboZero Plant Leaf kit. The resulting RNA was then used to generate strand-specific Illumina libraries. +!Sample_description = Diurnally grown culture sampled 5 h into the light phase. +!Sample_data_processing = Basecalling performed using Illumina RTA software. +!Sample_data_processing = Conversion of qseq to fastq format and demultiplexing by in-house scripts +!Sample_data_processing = Removal of contaminating rRNA reads by alignment to rRNA+snoRNA.fasta with RNA-STAR (STAR_2.4.0j). Unmapped reads selected for further analysis with "--outReadsUnmapped Fastx" option of STAR. +!Sample_data_processing = Alignment to C.reinhardtii nuclear genome (Phytozome v5.5) plus chloroplast genome (CPv4) plus mitochondrial genome (MTv4) by RNA-STAR (STAR_2.4.0j) with default parameters except --alignIntronMax 5000 +!Sample_data_processing = SAM alignments sorted and converted to BAM format by samtools (v1.3). +!Sample_data_processing = Counts per gene and FPKMs calculated by cuffdiff (v2.0.2) with "--multi-read-correct --max-bundle-frags 1000000000 --library-type fr-firststrand" +!Sample_data_processing = Genome_build: Cre.nuc.v5.5.cp.v4.4.mt.v4.4 +!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files (.tsv) containing transcript abundance determinations calculated as FPKMs +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sean,D.,Gallaher +!Sample_contact_laboratory = Sabeeha Merchant +!Sample_contact_department = Chem & BioChem +!Sample_contact_institute = UCLA +!Sample_contact_address = 607 Charle E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08801689 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3853418 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE112394 +!Sample_data_row_count = 0 +^SAMPLE = GSM3069476 +!Sample_title = light 7 h +!Sample_geo_accession = GSM3069476 +!Sample_status = Public on Jan 03 2019 +!Sample_submission_date = Mar 27 2018 +!Sample_last_update_date = Jan 03 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = liquid culture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: CC-5390 +!Sample_characteristics_ch1 = time point: 7 h +!Sample_characteristics_ch1 = light: light (200 PFD) +!Sample_characteristics_ch1 = temperature: 28 C +!Sample_characteristics_ch1 = carbon dioxide: air bubbling +!Sample_treatment_protocol_ch1 = Samples collected over multiple time points over the course 1 day. +!Sample_growth_protocol_ch1 = Cultures were grown in a photobioreactor on a 12 h light / 12 h dark cycle in HSM media with air bubbling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was purified by extraction with Trizol reagent. +!Sample_extract_protocol_ch1 = ~2 ug total RNA was used as starting material for rRNA-depletion by RiboZero Plant Leaf kit. The resulting RNA was then used to generate strand-specific Illumina libraries. +!Sample_description = Diurnally grown culture sampled 7 h into the light phase. +!Sample_data_processing = Basecalling performed using Illumina RTA software. +!Sample_data_processing = Conversion of qseq to fastq format and demultiplexing by in-house scripts +!Sample_data_processing = Removal of contaminating rRNA reads by alignment to rRNA+snoRNA.fasta with RNA-STAR (STAR_2.4.0j). Unmapped reads selected for further analysis with "--outReadsUnmapped Fastx" option of STAR. +!Sample_data_processing = Alignment to C.reinhardtii nuclear genome (Phytozome v5.5) plus chloroplast genome (CPv4) plus mitochondrial genome (MTv4) by RNA-STAR (STAR_2.4.0j) with default parameters except --alignIntronMax 5000 +!Sample_data_processing = SAM alignments sorted and converted to BAM format by samtools (v1.3). +!Sample_data_processing = Counts per gene and FPKMs calculated by cuffdiff (v2.0.2) with "--multi-read-correct --max-bundle-frags 1000000000 --library-type fr-firststrand" +!Sample_data_processing = Genome_build: Cre.nuc.v5.5.cp.v4.4.mt.v4.4 +!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files (.tsv) containing transcript abundance determinations calculated as FPKMs +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sean,D.,Gallaher +!Sample_contact_laboratory = Sabeeha Merchant +!Sample_contact_department = Chem & BioChem +!Sample_contact_institute = UCLA +!Sample_contact_address = 607 Charle E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08801694 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3853419 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE112394 +!Sample_data_row_count = 0 +^SAMPLE = GSM3069477 +!Sample_title = light 9 h +!Sample_geo_accession = GSM3069477 +!Sample_status = Public on Jan 03 2019 +!Sample_submission_date = Mar 27 2018 +!Sample_last_update_date = Jan 03 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = liquid culture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: CC-5390 +!Sample_characteristics_ch1 = time point: 9 h +!Sample_characteristics_ch1 = light: light (200 PFD) +!Sample_characteristics_ch1 = temperature: 28 C +!Sample_characteristics_ch1 = carbon dioxide: air bubbling +!Sample_treatment_protocol_ch1 = Samples collected over multiple time points over the course 1 day. +!Sample_growth_protocol_ch1 = Cultures were grown in a photobioreactor on a 12 h light / 12 h dark cycle in HSM media with air bubbling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was purified by extraction with Trizol reagent. +!Sample_extract_protocol_ch1 = ~2 ug total RNA was used as starting material for rRNA-depletion by RiboZero Plant Leaf kit. The resulting RNA was then used to generate strand-specific Illumina libraries. +!Sample_description = Diurnally grown culture sampled 9 h into the light phase. +!Sample_data_processing = Basecalling performed using Illumina RTA software. +!Sample_data_processing = Conversion of qseq to fastq format and demultiplexing by in-house scripts +!Sample_data_processing = Removal of contaminating rRNA reads by alignment to rRNA+snoRNA.fasta with RNA-STAR (STAR_2.4.0j). Unmapped reads selected for further analysis with "--outReadsUnmapped Fastx" option of STAR. +!Sample_data_processing = Alignment to C.reinhardtii nuclear genome (Phytozome v5.5) plus chloroplast genome (CPv4) plus mitochondrial genome (MTv4) by RNA-STAR (STAR_2.4.0j) with default parameters except --alignIntronMax 5000 +!Sample_data_processing = SAM alignments sorted and converted to BAM format by samtools (v1.3). +!Sample_data_processing = Counts per gene and FPKMs calculated by cuffdiff (v2.0.2) with "--multi-read-correct --max-bundle-frags 1000000000 --library-type fr-firststrand" +!Sample_data_processing = Genome_build: Cre.nuc.v5.5.cp.v4.4.mt.v4.4 +!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files (.tsv) containing transcript abundance determinations calculated as FPKMs +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sean,D.,Gallaher +!Sample_contact_laboratory = Sabeeha Merchant +!Sample_contact_department = Chem & BioChem +!Sample_contact_institute = UCLA +!Sample_contact_address = 607 Charle E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08801693 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3853420 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE112394 +!Sample_data_row_count = 0 +^SAMPLE = GSM3069478 +!Sample_title = light 11 h +!Sample_geo_accession = GSM3069478 +!Sample_status = Public on Jan 03 2019 +!Sample_submission_date = Mar 27 2018 +!Sample_last_update_date = Jan 03 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = liquid culture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: CC-5390 +!Sample_characteristics_ch1 = time point: 11 h +!Sample_characteristics_ch1 = light: light (200 PFD) +!Sample_characteristics_ch1 = temperature: 28 C +!Sample_characteristics_ch1 = carbon dioxide: air bubbling +!Sample_treatment_protocol_ch1 = Samples collected over multiple time points over the course 1 day. +!Sample_growth_protocol_ch1 = Cultures were grown in a photobioreactor on a 12 h light / 12 h dark cycle in HSM media with air bubbling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was purified by extraction with Trizol reagent. +!Sample_extract_protocol_ch1 = ~2 ug total RNA was used as starting material for rRNA-depletion by RiboZero Plant Leaf kit. The resulting RNA was then used to generate strand-specific Illumina libraries. +!Sample_description = Diurnally grown culture sampled 11 h into the light phase. +!Sample_data_processing = Basecalling performed using Illumina RTA software. +!Sample_data_processing = Conversion of qseq to fastq format and demultiplexing by in-house scripts +!Sample_data_processing = Removal of contaminating rRNA reads by alignment to rRNA+snoRNA.fasta with RNA-STAR (STAR_2.4.0j). Unmapped reads selected for further analysis with "--outReadsUnmapped Fastx" option of STAR. +!Sample_data_processing = Alignment to C.reinhardtii nuclear genome (Phytozome v5.5) plus chloroplast genome (CPv4) plus mitochondrial genome (MTv4) by RNA-STAR (STAR_2.4.0j) with default parameters except --alignIntronMax 5000 +!Sample_data_processing = SAM alignments sorted and converted to BAM format by samtools (v1.3). +!Sample_data_processing = Counts per gene and FPKMs calculated by cuffdiff (v2.0.2) with "--multi-read-correct --max-bundle-frags 1000000000 --library-type fr-firststrand" +!Sample_data_processing = Genome_build: Cre.nuc.v5.5.cp.v4.4.mt.v4.4 +!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files (.tsv) containing transcript abundance determinations calculated as FPKMs +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sean,D.,Gallaher +!Sample_contact_laboratory = Sabeeha Merchant +!Sample_contact_department = Chem & BioChem +!Sample_contact_institute = UCLA +!Sample_contact_address = 607 Charle E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08801692 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3853421 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE112394 +!Sample_data_row_count = 0 +^SAMPLE = GSM3069479 +!Sample_title = dark 13 h +!Sample_geo_accession = GSM3069479 +!Sample_status = Public on Jan 03 2019 +!Sample_submission_date = Mar 27 2018 +!Sample_last_update_date = Jan 03 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = liquid culture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: CC-5390 +!Sample_characteristics_ch1 = time point: 13 h +!Sample_characteristics_ch1 = light: dark +!Sample_characteristics_ch1 = temperature: 18 C +!Sample_characteristics_ch1 = carbon dioxide: air bubbling +!Sample_treatment_protocol_ch1 = Samples collected over multiple time points over the course 1 day. +!Sample_growth_protocol_ch1 = Cultures were grown in a photobioreactor on a 12 h light / 12 h dark cycle in HSM media with air bubbling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Total RNA was purified by extraction with Trizol reagent. +!Sample_extract_protocol_ch1 = ~2 ug total RNA was used as starting material for rRNA-depletion by RiboZero Plant Leaf kit. The resulting RNA was then used to generate strand-specific Illumina libraries. +!Sample_description = Diurnally grown culture sampled 13 h after the dark to light transition and 1 h into the dark phase. +!Sample_data_processing = Basecalling performed using Illumina RTA software. +!Sample_data_processing = Conversion of qseq to fastq format and demultiplexing by in-house scripts +!Sample_data_processing = Removal of contaminating rRNA reads by alignment to rRNA+snoRNA.fasta with RNA-STAR (STAR_2.4.0j). Unmapped reads selected for further analysis with "--outReadsUnmapped Fastx" option of STAR. +!Sample_data_processing = Alignment to C.reinhardtii nuclear genome (Phytozome v5.5) plus chloroplast genome (CPv4) plus mitochondrial genome (MTv4) by RNA-STAR (STAR_2.4.0j) with default parameters except --alignIntronMax 5000 +!Sample_data_processing = SAM alignments sorted and converted to BAM format by samtools (v1.3). +!Sample_data_processing = Counts per gene and FPKMs calculated by cuffdiff (v2.0.2) with "--multi-read-correct --max-bundle-frags 1000000000 --library-type fr-firststrand" +!Sample_data_processing = Genome_build: Cre.nuc.v5.5.cp.v4.4.mt.v4.4 +!Sample_data_processing = Supplementary_files_format_and_content: tab-delimited text files (.tsv) containing transcript abundance determinations calculated as FPKMs +!Sample_platform_id = GPL15922 +!Sample_contact_name = Sean,D.,Gallaher +!Sample_contact_laboratory = Sabeeha Merchant +!Sample_contact_department = Chem & BioChem +!Sample_contact_institute = UCLA +!Sample_contact_address = 607 Charle E. Young Drive East +!Sample_contact_city = Los Angeles +!Sample_contact_state = California +!Sample_contact_zip/postal_code = 90095 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN08801691 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX3853422 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE112394 +!Sample_data_row_count = 0 +^SERIES = GSE40031 +!Series_title = Retrograde bilin signaling enables Chlamydomonas greening and phototrophic survival +!Series_geo_accession = GSE40031 +!Series_status = Public on Jan 10 2013 +!Series_submission_date = Aug 10 2012 +!Series_last_update_date = May 15 2019 +!Series_pubmed_id = 23345435 +!Series_summary = Here we show that the phytochrome-less chlorophyte Chlamydomonas reinhardtii retains a functional pathway to synthesize the linear tetrapyrrole (bilin) precursor of the phytochrome chromophore. Reverse genetic, metabolic inactivation and bilin rescue experiments establish that this pathway is needed for heme iron acquisition and for the diurnal transition to phototrophic growth. RNA-Seq measurements reveal a bilin-dependent signaling network that is necessary for the heterotrophic to phototrophic transition. These results imply the presence of a novel bilin sensor pathway that may be widely distributed amongst oxygenic photosynthetic organisms. +!Series_overall_design = We isolated RNA from heterotrophic suspension cultures of 4A+ WT and the hmox1 mutant grown in the presence or absence of 0.1 mM BV IXα before and after transfer to low light. +!Series_type = Expression profiling by high throughput sequencing +!Series_contributor = Deqiang,,Duanmu +!Series_contributor = David,,Casero +!Series_contributor = Rachel,M,Dent +!Series_contributor = Sean,,Gallaher +!Series_contributor = Wenqiang,,Yang +!Series_contributor = Nathan,C,Rockwell +!Series_contributor = Shelley,S,Martin +!Series_contributor = Matteo,,Pellegrini +!Series_contributor = Krishna,K,Niyogi +!Series_contributor = Sabeeha,S,Merchant +!Series_contributor = Arthur,R,Grossman +!Series_contributor = J,C,Lagarias +!Series_sample_id = GSM983943 +!Series_sample_id = GSM983944 +!Series_sample_id = GSM983945 +!Series_sample_id = GSM983946 +!Series_sample_id = GSM983947 +!Series_sample_id = GSM983948 +!Series_sample_id = GSM983949 +!Series_sample_id = GSM983950 +!Series_sample_id = GSM983951 +!Series_sample_id = GSM983952 +!Series_sample_id = GSM983953 +!Series_sample_id = GSM983954 +!Series_sample_id = GSM983955 +!Series_sample_id = GSM983956 +!Series_sample_id = GSM983957 +!Series_sample_id = GSM983958 +!Series_contact_name = Sabeeha,,Merchant +!Series_contact_email = merchant@chem.ucla.edu +!Series_contact_phone = 310-825-8300 +!Series_contact_department = Department of Chemistry and Biochemistry +!Series_contact_institute = University of California Los Angeles +!Series_contact_address = 607 Charles E. Young Drive East +!Series_contact_city = Los Angeles +!Series_contact_state = California +!Series_contact_zip/postal_code = 90095-1569 +!Series_contact_country = USA +!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE40nnn/GSE40031/suppl/GSE40031_JLDD_ExpressionEstimates_ALL.txt.gz +!Series_platform_id = GPL15922 +!Series_platform_taxid = 3055 +!Series_sample_taxid = 3055 +!Series_relation = BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA172421 +!Series_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP014795 +^SERIES = GSE44611 +!Series_title = Changes in membrane lipid composition during Iron depletion and starvation in Chlamydomonas reinhardtii +!Series_geo_accession = GSE44611 +!Series_status = Public on Feb 20 2014 +!Series_submission_date = Feb 25 2013 +!Series_last_update_date = May 15 2019 +!Series_pubmed_id = 23983122 +!Series_summary = C. reinhardtii cells exposed to abiotic stresses (e.g. iron-, nitrogen-, zinc- or phosphorus-deficiency) accumulate TAGs which are stored in lipid droplets. Here, we report that iron starvation leads to formation of lipids bodies and accumulation of TAGs. This occurs between 12 and 24 h of iron-starvation. C. reinhardtii cells deprived for iron have more saturated FA, due to the loss of functional FA desaturases, which are diiron enzymes. The abundance of a plastid ACP-acyl desaturase (FAB2) is significantly decreased to the same degree as observed for ferredoxin, which is a substrate of the desaturases. The increase in saturated FA (C16:0 and C18:0) is concomitant with the decrease in saturated FA (C16:4, C18:3 or C18:4). This pattern was observed for MGDG, DGTS or DGDG. When we monitored the absolute levels of glycerolipids, MGDG content dropped significantly after only 2 h of iron-starvation. On the other hand, DGTS and DGDG contents gradually decrease until a minimum is reached after 24-48 h of iron-deprivation. RNA-Seq analysis of iron-starved C. reinhardtii cells revealed significant changes in many transcripts coding for enzymes involved in FA metabolism. The mRNA abundances of genes coding for components involved in TAG accumulation (DGAT or MLDP) are increased. A more dramatic increase at the transcript level has been observed for many lipases, suggesting that a major remodeling of lipid membranes occurs during iron-starvation in C. reinhardtii. +!Series_overall_design = Sampling of Chlamydomonas CC-4532 (2137) cells cultivated photoheterotrophically (TAP) under iron-starvation condition (0 uM Fe-EDTA). Samples were collected from biological duplicates after washing in TAP medium lacking Fe at 0, 0.5, 1, 2, 4, 8, 12, 24 and 48 hours. +!Series_type = Expression profiling by high throughput sequencing +!Series_contributor = Eugen,I,Urzica +!Series_contributor = Astrid,,Vieler +!Series_contributor = Anne,,Hong-Hermesdorf +!Series_contributor = M,D,Page +!Series_contributor = David,,Casero +!Series_contributor = Sean,D,Gallaher +!Series_contributor = Janette,,Kropat +!Series_contributor = Matteo,,Pellegrini +!Series_contributor = Christoph,,Benning +!Series_contributor = Sabeeha,S,Merchant +!Series_sample_id = GSM1087792 +!Series_sample_id = GSM1087793 +!Series_sample_id = GSM1087794 +!Series_sample_id = GSM1087795 +!Series_sample_id = GSM1087796 +!Series_sample_id = GSM1087797 +!Series_sample_id = GSM1087798 +!Series_sample_id = GSM1087799 +!Series_sample_id = GSM1087800 +!Series_contact_name = Sabeeha,,Merchant +!Series_contact_email = merchant@chem.ucla.edu +!Series_contact_phone = 310-825-8300 +!Series_contact_department = Department of Chemistry and Biochemistry +!Series_contact_institute = University of California Los Angeles +!Series_contact_address = 607 Charles E. Young Drive East +!Series_contact_city = Los Angeles +!Series_contact_state = California +!Series_contact_zip/postal_code = 90095-1569 +!Series_contact_country = USA +!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE44nnn/GSE44611/suppl/GSE44611_ExpressionUrzicaTimeLong.txt.gz +!Series_platform_id = GPL15922 +!Series_platform_taxid = 3055 +!Series_sample_taxid = 3055 +!Series_relation = BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA190650 +!Series_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP018835 +^SERIES = GSE55253 +!Series_title = The Path to Triacylglyceride Obesity in the sta6 Strain of Chlamydomonas reinhardtii +!Series_geo_accession = GSE55253 +!Series_status = Public on Mar 09 2014 +!Series_submission_date = Feb 21 2014 +!Series_last_update_date = May 15 2019 +!Series_pubmed_id = 24585881 +!Series_summary = When the sta6 (starch-null) strain of the green microalga Chlamydomonas reinhardtii is nitrogen-starved in acetate and then "boosted" after two days with additional acetate, the cells become "obese" after eight days, with triacylglyceride-filled lipid bodies filling their cytoplasm and chloroplasts. To assess the transcriptional correlates of this response, sta6 and the starch-forming cw15 strain were subjected to RNA-Seq analysis during the two days prior and two days post boost, and the data were compared with published reports using other strains and growth conditions. During the two hours post boost, ~425 genes are up-regulated ≥2-fold and ~875 genes are down-regulated ≥2-fold in each strain. Expression of a small subset of "sensitive" genes, encoding enzymes in the glyoxylate and Calvin Benson cycles, gluconeogenesis, and the pentose phosphate pathway, is responsive to culture conditions and genetic background as well as to boost. Four genes--encoding a diacylglycerol acyltransferase (DGTT2), a glycerol-3-P dehydrogenase (GPD3), and two candidate lipases (Cre03.g155250 and Cre17.g735600)--are selectively up-regulated in sta6. Although the bulk rate of acetate depletion from the medium is not boost-enhanced, three candidate acetate permease-encoding genes in the GPR1_FUN34_YaaH superfamily are boost-up-regulated, and 13 of the "sensitive" genes are strongly responsive to the cell's acetate status. A cohort of 64 autophagy-related genes is down-regulated by boost. Our results indicate that the boost serves both to avert an autophagy program and to prolong the operation of key pathways that shuttle carbon from acetate into storage lipid, the combined outcome being enhanced TAG accumulation, notably in sta6. +!Series_overall_design = Here we report studies on gene-expression patterns during the path to obesity. The Merchant/Pellegrini and Los Alamos laboratories recently generated and analyzed RNA-Seq transcriptomes of cw15, sta6, and several complemented sta6 strains during two days of N-starvation (0→48 h). In collaboration with these groups, the Goodenough lab generated a second pair of transcriptomes using cw15 and sta6, tracing 0→48 h gene expression patterns under a different set of culture conditions and taking the time course out to 96 h, with an intervening acetate boost. Analysis of these data was deeply informed by cross-comparisons with the Blaby et al. data. Three additional RNA-Seq studies of wild-type strains were also considered. +!Series_type = Expression profiling by high throughput sequencing +!Series_contributor = Ursula,,Goodenough +!Series_contributor = Ian,,Blaby +!Series_contributor = David,,Casero +!Series_contributor = Sean,D,Gallaher +!Series_contributor = Carrie,,Goodson +!Series_contributor = Shannon,,Johnson +!Series_contributor = Jae,H,Lee +!Series_contributor = Sabeeha,S,Merchant +!Series_contributor = Matteo,,Pellegrini +!Series_contributor = Robyn,,Roth +!Series_contributor = Jannette,,Rusch +!Series_contributor = Manmilan,,Singh +!Series_contributor = James,G,Umen +!Series_contributor = Taylor,L,Weiss +!Series_contributor = Tuya,,Wulan +!Series_sample_id = GSM1332630 +!Series_sample_id = GSM1332631 +!Series_sample_id = GSM1332632 +!Series_sample_id = GSM1332633 +!Series_sample_id = GSM1332634 +!Series_sample_id = GSM1332635 +!Series_sample_id = GSM1332636 +!Series_sample_id = GSM1332637 +!Series_sample_id = GSM1332638 +!Series_sample_id = GSM1332639 +!Series_sample_id = GSM1332640 +!Series_sample_id = GSM1332641 +!Series_sample_id = GSM1332642 +!Series_sample_id = GSM1332643 +!Series_sample_id = GSM1332644 +!Series_sample_id = GSM1332645 +!Series_sample_id = GSM1332646 +!Series_sample_id = GSM1332647 +!Series_sample_id = GSM1332648 +!Series_sample_id = GSM1332649 +!Series_sample_id = GSM1332650 +!Series_sample_id = GSM1332651 +!Series_sample_id = GSM1332652 +!Series_sample_id = GSM1332653 +!Series_sample_id = GSM1332654 +!Series_sample_id = GSM1332655 +!Series_sample_id = GSM1332656 +!Series_sample_id = GSM1332657 +!Series_sample_id = GSM1332658 +!Series_sample_id = GSM1332659 +!Series_sample_id = GSM1332660 +!Series_sample_id = GSM1332661 +!Series_sample_id = GSM1332662 +!Series_sample_id = GSM1332663 +!Series_contact_name = Sabeeha,,Merchant +!Series_contact_email = merchant@chem.ucla.edu +!Series_contact_phone = 310-825-8300 +!Series_contact_department = Department of Chemistry and Biochemistry +!Series_contact_institute = University of California Los Angeles +!Series_contact_address = 607 Charles E. Young Drive East +!Series_contact_city = Los Angeles +!Series_contact_state = California +!Series_contact_zip/postal_code = 90095-1569 +!Series_contact_country = USA +!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE55nnn/GSE55253/suppl/GSE55253_Expression_GEO_2014Feb.txt.gz +!Series_platform_id = GPL15922 +!Series_platform_taxid = 3055 +!Series_sample_taxid = 3055 +!Series_relation = BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA239005 +!Series_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP038751 +^SERIES = GSE58786 +!Series_title = RNAseq Analysis of Transcriptomic Response to Zn Resupply in Chlamydomonas reinhardtii +!Series_geo_accession = GSE58786 +!Series_status = Public on Nov 01 2014 +!Series_submission_date = Jun 24 2014 +!Series_last_update_date = May 15 2019 +!Series_pubmed_id = 25344811 +!Series_summary = Zn-limited cells accumulate Cu in intracellular structures in a reversable manner. We used RNAseq analysis to monitor gene expression in Zn-limited cells, and during a time course (0 - 24 h) after Zn resupply. +!Series_overall_design = Comparison of Chlamydomonas reinhardtii gene expression when Zn deficient cells are resupplied with 2.5 µM Zn. Time points 0 (before resupply), 1.5, 3, 4.5, 12, and 24 hours after resupply. Four biological replicates per condition. +!Series_type = Expression profiling by high throughput sequencing +!Series_contributor = Anne,,Hong-Hermesdorf +!Series_contributor = Marcus,,Miethke +!Series_contributor = Sean,D,Gallaher +!Series_contributor = Janette,,Kropat +!Series_contributor = Sabeeha,S,Merchant +!Series_sample_id = GSM1419589 +!Series_sample_id = GSM1419590 +!Series_sample_id = GSM1419591 +!Series_sample_id = GSM1419592 +!Series_sample_id = GSM1419593 +!Series_sample_id = GSM1419594 +!Series_sample_id = GSM1419595 +!Series_sample_id = GSM1419596 +!Series_contact_name = Sean,D.,Gallaher +!Series_contact_laboratory = Sabeeha Merchant +!Series_contact_department = Chem & BioChem +!Series_contact_institute = UCLA +!Series_contact_address = 607 Charle E. Young Drive East +!Series_contact_city = Los Angeles +!Series_contact_state = California +!Series_contact_zip/postal_code = 90095 +!Series_contact_country = USA +!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE58nnn/GSE58786/suppl/GSE58786_genes.fpkm_tracking.txt.gz +!Series_platform_id = GPL15922 +!Series_platform_taxid = 3055 +!Series_sample_taxid = 3055 +!Series_relation = BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA253485 +!Series_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP043537 +^SERIES = GSE59629 +!Series_title = Lineage-Specific Chromatin Signatures Reveal a Master Lipid Switch in Microalgae +!Series_geo_accession = GSE59629 +!Series_status = Public on Jul 28 2015 +!Series_submission_date = Jul 21 2014 +!Series_last_update_date = May 15 2019 +!Series_summary = Alga-derived lipids represent an attractive potential source of biofuels. However, lipid accumulation in algae is a stress response tightly coupled to growth arrest, thereby imposing a major limitation on productivity. To identify master regulators of lipid accumulation and decipher the regulation of lipid biosynthetic pathway, we performed an integrative chromatin signature and transcriptomic analysis in the alga Chlamydomonas reinhardtii. Genome-wide histone modification profiling revealed remarkable differences in functional chromatin states between algae and higher eukaryotes and uncovered regulatory components at the core of lipid accumulation pathways. We identified the transcription factor PSR1 as a pivotal master switch that triggers cytosolic lipid hyper-accumulation an order of magnitude higher than stress regimens have achieved. Dissection of the PSR1 target network corroborates its central role in coordinating multiple stress responses. The comprehensive maps of functional chromatin signatures in a major clade of eukaryotic life and the discovery of a central regulator of algal lipid metabolism will facilitate targeted engineering strategies in microalgae. +!Series_overall_design = 1. Genome-wide H3K4me3 time series profiling (at 0 hr, 10 min, 30 min, 1 hr, 2hr, 6 hr, 8 hr, 24 hr and 48 hr after nitrogen starvation) was performed to determine time point to capture maximal chromatin changes. +!Series_overall_design = +!Series_overall_design = 2. Genome-wide H3K4me3, H3K27ac, H3K9me3, H3K27me3, H3K36me3 and Pol II profiling were performed at 0 hr, 1 hr after nitrogen starvation and 1 hr after sulfur starvation to determine chromatin signatures. Genome-wide H3K4me2 profiling was performed at 0 hr before starvation. +!Series_overall_design = +!Series_overall_design = 3. Transcriptome time series profiling (at 0 hr, 10 min, 30 min, 1 hr, 2hr, 6 hr, 8 hr, 24 hr and 48 hr after nitrogen and sulfur starvation separately) for chromatin signature characterization and integrative analysis. +!Series_overall_design = +!Series_overall_design = 4. Genome-wide PSR1 binding profiling was performed with polyclonal antibody against PSR1 peptide A region and PSR1 peptide B region individually. (At 30 min and 1 hr after nitrogen starvation, and 1 hr, 2 hr and 6 hr after sulfur starvation.) +!Series_overall_design = +!Series_overall_design = Please note that the following reference genome and gene models used in these experiments are linked below; +!Series_overall_design = C.reinhardtii_v5.3_genomic_scaffold_plastids.fasta.gz +!Series_overall_design = reference_gene_model.gtf.gz +!Series_overall_design = These are based off Phytozome (http://www.phytozome.net/) which does not provide access to earlier version data. +!Series_type = Genome binding/occupancy profiling by high throughput sequencing +!Series_type = Expression profiling by high throughput sequencing +!Series_contributor = Chia-Lin,,Wei +!Series_contributor = Chew Yee,,Ngan +!Series_contributor = Chee-Hong,,Wong +!Series_sample_id = GSM1440685 +!Series_sample_id = GSM1440686 +!Series_sample_id = GSM1440687 +!Series_sample_id = GSM1440688 +!Series_sample_id = GSM1440689 +!Series_sample_id = GSM1440690 +!Series_sample_id = GSM1440691 +!Series_sample_id = GSM1440692 +!Series_sample_id = GSM1440693 +!Series_sample_id = GSM1440694 +!Series_sample_id = GSM1440695 +!Series_sample_id = GSM1440696 +!Series_sample_id = GSM1440697 +!Series_sample_id = GSM1440698 +!Series_sample_id = GSM1440699 +!Series_sample_id = GSM1440700 +!Series_sample_id = GSM1440701 +!Series_sample_id = GSM1440702 +!Series_sample_id = GSM1440703 +!Series_sample_id = GSM1440704 +!Series_sample_id = GSM1440705 +!Series_sample_id = GSM1440706 +!Series_sample_id = GSM1440707 +!Series_sample_id = GSM1440708 +!Series_sample_id = GSM1440709 +!Series_sample_id = GSM1440710 +!Series_sample_id = GSM1440711 +!Series_sample_id = GSM1440712 +!Series_sample_id = GSM1440713 +!Series_sample_id = GSM1440714 +!Series_sample_id = GSM1440715 +!Series_sample_id = GSM1440716 +!Series_sample_id = GSM1440717 +!Series_sample_id = GSM1440718 +!Series_sample_id = GSM1440719 +!Series_sample_id = GSM1440720 +!Series_sample_id = GSM1440721 +!Series_sample_id = GSM1440722 +!Series_sample_id = GSM1440723 +!Series_sample_id = GSM1440724 +!Series_sample_id = GSM1440725 +!Series_sample_id = GSM1440726 +!Series_sample_id = GSM1440727 +!Series_sample_id = GSM1440728 +!Series_sample_id = GSM1440729 +!Series_sample_id = GSM1440730 +!Series_sample_id = GSM1440731 +!Series_sample_id = GSM1440732 +!Series_sample_id = GSM1440733 +!Series_sample_id = GSM1440734 +!Series_sample_id = GSM1440735 +!Series_sample_id = GSM1440736 +!Series_sample_id = GSM1440737 +!Series_sample_id = GSM1440738 +!Series_sample_id = GSM1440739 +!Series_sample_id = GSM1440740 +!Series_sample_id = GSM1440741 +!Series_sample_id = GSM1440742 +!Series_sample_id = GSM1440743 +!Series_sample_id = GSM1440744 +!Series_sample_id = GSM1440745 +!Series_sample_id = GSM1440746 +!Series_sample_id = GSM1440747 +!Series_sample_id = GSM1440748 +!Series_sample_id = GSM1440749 +!Series_sample_id = GSM1440750 +!Series_sample_id = GSM1440751 +!Series_sample_id = GSM1440752 +!Series_sample_id = GSM1440753 +!Series_sample_id = GSM1440754 +!Series_sample_id = GSM1440755 +!Series_sample_id = GSM1440756 +!Series_sample_id = GSM1440757 +!Series_sample_id = GSM1440758 +!Series_sample_id = GSM1440759 +!Series_sample_id = GSM1440760 +!Series_sample_id = GSM1440761 +!Series_sample_id = GSM1440762 +!Series_sample_id = GSM1440763 +!Series_sample_id = GSM1440764 +!Series_sample_id = GSM1440765 +!Series_sample_id = GSM1440766 +!Series_sample_id = GSM1440767 +!Series_sample_id = GSM1440768 +!Series_sample_id = GSM1440769 +!Series_sample_id = GSM1440770 +!Series_sample_id = GSM1440771 +!Series_sample_id = GSM1440772 +!Series_sample_id = GSM1440773 +!Series_sample_id = GSM1440774 +!Series_sample_id = GSM1440775 +!Series_sample_id = GSM1440776 +!Series_sample_id = GSM1440777 +!Series_sample_id = GSM1440778 +!Series_sample_id = GSM1440779 +!Series_sample_id = GSM1440780 +!Series_sample_id = GSM1440781 +!Series_sample_id = GSM1440782 +!Series_sample_id = GSM1440783 +!Series_sample_id = GSM1440784 +!Series_sample_id = GSM1440785 +!Series_sample_id = GSM1440786 +!Series_sample_id = GSM1440787 +!Series_sample_id = GSM1440788 +!Series_sample_id = GSM1440789 +!Series_sample_id = GSM1440790 +!Series_sample_id = GSM1440791 +!Series_sample_id = GSM1440792 +!Series_sample_id = GSM1440793 +!Series_sample_id = GSM1440794 +!Series_sample_id = GSM1440795 +!Series_sample_id = GSM1440796 +!Series_contact_name = Chia-Lin,,Wei +!Series_contact_email = CWei@lbl.gov +!Series_contact_phone = +1 (925) 927-2593 +!Series_contact_laboratory = Sequencing Technologies +!Series_contact_department = Genomic Technologies +!Series_contact_institute = DOE Joint Genome Institute +!Series_contact_address = 2800 Mitchell Drive +!Series_contact_city = Walnut Creek +!Series_contact_state = California +!Series_contact_zip/postal_code = 94598 +!Series_contact_country = USA +!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE59nnn/GSE59629/suppl/GSE59629_C.reinhardtii_v5.3_genomic_scaffold_plastids.fasta.gz +!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE59nnn/GSE59629/suppl/GSE59629_Cre4A+Baseline_16states_genome_segmentation.bed.gz +!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE59nnn/GSE59629/suppl/GSE59629_Cre4A+Nitrogen_starvation_1hr_16states_genome_segmentation.bed.gz +!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE59nnn/GSE59629/suppl/GSE59629_Cre4A+Sulfur_starvation_1hr_16states_genome_segmentation.bed.gz +!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE59nnn/GSE59629/suppl/GSE59629_RAW.tar +!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE59nnn/GSE59629/suppl/GSE59629_RNA-Seq_Transcripts_and_Annotation.txt.gz +!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE59nnn/GSE59629/suppl/GSE59629_emissions_16.txt.gz +!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE59nnn/GSE59629/suppl/GSE59629_master_gene_model.gtf.gz +!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE59nnn/GSE59629/suppl/GSE59629_reference_gene_model.gtf.gz +!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE59nnn/GSE59629/suppl/GSE59629_transitions_16.txt.gz +!Series_citation = Nature Plants 1, Article number: 15107 (2015) doi:10.1038/nplants.2015.107 Lineage-specific chromatin signatures reveal a regulator of lipid metabolism in microalgae. Chew Yee Ngan, Chee-Hong Wong, Cindy Choi, Yuko Yoshinaga, Katherine Louie, Jing Jia, Cindy Chen, Benjamin Bowen, Haoyu Cheng, Lauriebeth Leonelli, Rita Kuo, Richard Baran, José G. García-Cerdán, Abhishek Pratap, Mei Wang, Joanne Lim, Hope Tice, Chris Daum, Jian Xu, Trent Northen, Axel Visel, James Bristow, Krishna K. Niyogi & Chia-Lin Wei +!Series_platform_id = GPL15922 +!Series_platform_id = GPL18983 +!Series_platform_taxid = 3055 +!Series_sample_taxid = 3055 +!Series_relation = BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA255778 +!Series_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP044681 +^SERIES = GSE62690 +!Series_title = N6-Methyldeoxyadenosine Marks Active Transcription Start Sites in Chlamydomonas +!Series_geo_accession = GSE62690 +!Series_status = Public on Apr 30 2015 +!Series_submission_date = Oct 24 2014 +!Series_last_update_date = May 15 2019 +!Series_pubmed_id = 25936837 +!Series_summary = N6-methyldeoxyadenosine (6mA or m6A) is a DNA modification preserved in prokaryotes to eukaryotes. It is widespread in bacteria, and functions in DNA mismatch repair, chromosome segregation, and virulence regulation. In contrast, the distribution and function of 6mA in eukaryotes have been unclear. Here we present a comprehensive analysis of the 6mA landscape in the genome of Chlamydomonas using new sequencing approaches. We identified the 6mA modification in 84% of genes in Chlamydomonas. We found that 6mA mainly locates at ApT dinucleotides around transcription start sites (TSS) with a bimodal distribution, and appears to mark active genes. A periodic pattern of 6mA deposition was also observed at base resolution, which is associated with nucleosome distribution near the TSS, suggesting a possible role in nucleosome positioning. The new genome-wide mapping of 6mA and its unique distribution in the Chlamydomonas genome suggest potential regulatory roles of 6mA in gene expression in eukaryotic organisms. +!Series_overall_design = Multiple sequencing methods are developed to profile the distribution of 6mA in Chlamydomonas including MeDIP-Seq, enzyme-treated DNA-Seq, MNase-Seq and RNA-Seq. +!Series_type = Methylation profiling by high throughput sequencing +!Series_type = Expression profiling by high throughput sequencing +!Series_type = Other +!Series_type = Genome binding/occupancy profiling by high throughput sequencing +!Series_contributor = Guan-Zheng,,Luo +!Series_contributor = Ye,,Fu +!Series_contributor = Chuan,,He +!Series_sample_id = GSM1666091 +!Series_sample_id = GSM1666092 +!Series_sample_id = GSM1666093 +!Series_sample_id = GSM1666094 +!Series_sample_id = GSM1666095 +!Series_sample_id = GSM1666096 +!Series_sample_id = GSM1666097 +!Series_sample_id = GSM1666098 +!Series_sample_id = GSM1666099 +!Series_sample_id = GSM1666100 +!Series_sample_id = GSM1666101 +!Series_sample_id = GSM1666102 +!Series_sample_id = GSM1666103 +!Series_sample_id = GSM1666104 +!Series_contact_name = Guan-Zheng,,Luo +!Series_contact_department = Chemistry +!Series_contact_institute = UChicago +!Series_contact_address = 929 E 57th St +!Series_contact_city = Chicago +!Series_contact_state = IL +!Series_contact_zip/postal_code = 60637 +!Series_contact_country = USA +!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE62nnn/GSE62690/suppl/GSE62690_RAW.tar +!Series_platform_id = GPL15922 +!Series_platform_taxid = 3055 +!Series_sample_taxid = 3055 +!Series_relation = BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA264813 +!Series_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP049246 +^SERIES = GSE71469 +!Series_title = Chlamydomonas diurnal transcriptome +!Series_geo_accession = GSE71469 +!Series_status = Public on Jul 30 2015 +!Series_submission_date = Jul 29 2015 +!Series_last_update_date = May 15 2019 +!Series_pubmed_id = 26432862 +!Series_summary = We combined a highly synchronous photobioreactor culture system with frequent temporal sampling to characterize genome-wide periodic gene expression in Chlamydomonas. +!Series_overall_design = Synchronous phototrophic cultures of Chlamydomonas reinhardtii were prepared in controlled diurnal bioreactor growth conditions and sampled in two 24-hour replicate time courses at 1-hour and 0.5-hour intervals for Illumina paired-end RNA-Seq. More than ~3 million paired end reads were obtained for each sample. +!Series_type = Expression profiling by high throughput sequencing +!Series_contributor = James,M,Zones +!Series_contributor = Ian,K,Blaby +!Series_contributor = Sabeeha,S,Merchant +!Series_contributor = James,G,Umen +!Series_sample_id = GSM1835200 +!Series_sample_id = GSM1835201 +!Series_sample_id = GSM1835202 +!Series_sample_id = GSM1835203 +!Series_sample_id = GSM1835204 +!Series_sample_id = GSM1835205 +!Series_sample_id = GSM1835206 +!Series_sample_id = GSM1835207 +!Series_sample_id = GSM1835208 +!Series_sample_id = GSM1835209 +!Series_sample_id = GSM1835210 +!Series_sample_id = GSM1835211 +!Series_sample_id = GSM1835212 +!Series_sample_id = GSM1835213 +!Series_sample_id = GSM1835214 +!Series_sample_id = GSM1835215 +!Series_sample_id = GSM1835216 +!Series_sample_id = GSM1835217 +!Series_sample_id = GSM1835218 +!Series_sample_id = GSM1835219 +!Series_sample_id = GSM1835220 +!Series_sample_id = GSM1835221 +!Series_sample_id = GSM1835222 +!Series_sample_id = GSM1835223 +!Series_sample_id = GSM1835224 +!Series_sample_id = GSM1835225 +!Series_sample_id = GSM1835226 +!Series_sample_id = GSM1835227 +!Series_sample_id = GSM1835228 +!Series_sample_id = GSM1835229 +!Series_sample_id = GSM1835230 +!Series_sample_id = GSM1835231 +!Series_sample_id = GSM1835232 +!Series_sample_id = GSM1835233 +!Series_sample_id = GSM1835234 +!Series_sample_id = GSM1835235 +!Series_sample_id = GSM1835236 +!Series_sample_id = GSM1835237 +!Series_sample_id = GSM1835238 +!Series_sample_id = GSM1835239 +!Series_sample_id = GSM1835240 +!Series_sample_id = GSM1835241 +!Series_sample_id = GSM1835242 +!Series_sample_id = GSM1835243 +!Series_sample_id = GSM1835244 +!Series_sample_id = GSM1835245 +!Series_sample_id = GSM1835246 +!Series_sample_id = GSM1835247 +!Series_sample_id = GSM1835248 +!Series_sample_id = GSM1835249 +!Series_sample_id = GSM1835250 +!Series_sample_id = GSM1835251 +!Series_sample_id = GSM1835252 +!Series_sample_id = GSM1835253 +!Series_sample_id = GSM1835254 +!Series_sample_id = GSM1835255 +!Series_contact_name = James,,Umen +!Series_contact_email = jumen@danforthcenter.org +!Series_contact_phone = 314-587-1689 +!Series_contact_laboratory = Umen Laboratory +!Series_contact_institute = Donald Danforth Plant Science Center +!Series_contact_address = 975 N. Warson Rd. +!Series_contact_city = St. Louis +!Series_contact_state = MO +!Series_contact_zip/postal_code = 63141 +!Series_contact_country = USA +!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71469/suppl/GSE71469_ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt.gz +!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71469/suppl/GSE71469_ChlamydomonasSynchronousDiurnalExpressionRPKM.txt.gz +!Series_platform_id = GPL15922 +!Series_platform_taxid = 3055 +!Series_sample_taxid = 3055 +!Series_relation = BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA291337 +!Series_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP061735 +^SERIES = GSE77388 +!Series_title = Bilin-dependent photoacclimation in Chlamydomonas reinhardtii +!Series_geo_accession = GSE77388 +!Series_status = Public on Jan 24 2019 +!Series_submission_date = Jan 29 2016 +!Series_last_update_date = May 15 2019 +!Series_pubmed_id = 23345435 +!Series_summary = Linear tetrapyrrole (bilin)-based phytochrome sensors optimize photosynthetic light capture by mediating massive gene reprogramming in land plants, yet surprisingly, many sequenced chlorophyte (green) algae lack phytochrome genes. Previous studies on the heme oxygenase (hmox1) mutant of Chlamydomonas reinhardtii suggest that bilin biosynthesis in plastids is needed for regulation of a limited nuclear gene network implicated in oxygen detoxification during dark to light transitions. The hmox1 mutant is unable to grow photoautotrophically and poorly acclimates to increased illumination even in the presence of acetate. Here we show that these phenotypes reflect the reduced accumulation of PSI reaction centers as well as a loss of PSI and PSII antennae complexes during photoacclimation. Phenotypically, the hmox1 mutant is similar to the chlorophyll biosynthesis mutants, gun4, crd1 and cth1. However, many of the hmox1 phenotypes can be rescued by the application of exogenous biliverdin IXα, the bilin product of HMOX1; this rescue is independent of photosynthesis but strongly dependent upon blue light. RNA-Seq comparisons of hmox1, 4A+ wild type and two genetically complemented lines also reveal that bilins restore regulation of a small network of photosynthesis-associated nuclear genes. These include genes responsible for chlorophyll biosynthesis (CHLI1/2), PSI light-harvesting (LHCA4) and naphthoquinone metabolism (MEN2), all of which show reduced photoinduction in the hmox1 mutant. We propose that a bilin-based, blue light sensory system is responsible for the maintenance of a functional photosynthetic apparatus in light-grown C. reinhardtii. This critical and possibly ancestral role for bilins may be responsible for retention of bilin biosynthesis in all eukaryotic photosynthetic species. +!Series_overall_design = We isolated RNA from heterotrophic suspension cultures of 4A+ WT and the hmox1 mutant grown in the presence or absence of 0.1 mM BV IXα before and after transfer to low light. +!Series_type = Expression profiling by high throughput sequencing +!Series_contributor = Tyler,M,Wittkopp +!Series_contributor = Deqiang,,Duanmu +!Series_contributor = Stefan,,Schmollinger +!Series_contributor = Wei,,Hu +!Series_contributor = Qiuling,,Fan +!Series_contributor = Ian,K,Blaby +!Series_contributor = David,,Casero +!Series_contributor = Matteo,,Pellegrini +!Series_contributor = Sabeeha,S,Merchant +!Series_contributor = Arthur,R,Grossman +!Series_contributor = J,C,Lagarias +!Series_contributor = Michael,T,Leonard +!Series_contributor = Sean,D,Gallaher +!Series_sample_id = GSM2051194 +!Series_sample_id = GSM2051195 +!Series_sample_id = GSM2051196 +!Series_sample_id = GSM2051197 +!Series_sample_id = GSM2051198 +!Series_sample_id = GSM2051199 +!Series_sample_id = GSM2051200 +!Series_sample_id = GSM2051201 +!Series_sample_id = GSM2051202 +!Series_sample_id = GSM2051203 +!Series_sample_id = GSM2051204 +!Series_sample_id = GSM2051205 +!Series_sample_id = GSM2051206 +!Series_sample_id = GSM2051207 +!Series_sample_id = GSM2051208 +!Series_sample_id = GSM2051209 +!Series_sample_id = GSM2051210 +!Series_sample_id = GSM2051211 +!Series_sample_id = GSM2051212 +!Series_sample_id = GSM2051213 +!Series_contact_name = Sabeeha,,Merchant +!Series_contact_email = merchant@chem.ucla.edu +!Series_contact_phone = 310-825-8300 +!Series_contact_department = Department of Chemistry and Biochemistry +!Series_contact_institute = University of California Los Angeles +!Series_contact_address = 607 Charles E. Young Drive East +!Series_contact_city = Los Angeles +!Series_contact_state = California +!Series_contact_zip/postal_code = 90095-1569 +!Series_contact_country = USA +!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE77nnn/GSE77388/suppl/GSE77388_Lagarias_GEOmetadata_Expression.txt.gz +!Series_platform_id = GPL15922 +!Series_platform_taxid = 3055 +!Series_sample_taxid = 3055 +!Series_relation = BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA310199 +!Series_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP069064 +^SERIES = GSE101944 +!Series_title = Transcriptome analysis of Chlamydomonas reinhardtii chloroplast and mitochondria +!Series_geo_accession = GSE101944 +!Series_status = Public on Nov 27 2017 +!Series_submission_date = Jul 27 2017 +!Series_last_update_date = May 15 2019 +!Series_pubmed_id = 29172250 +!Series_web_link = http://genomes.mcdb.ucla.edu/CreOrganelles/ +!Series_summary = Here, we report on the transcriptome of the organelles of the micro-alga, Chlamydomonas reinhardtii, sampled under a number of different conditions. The preparation of the RNA-Seq libraries and their analysis were performed using protocols optimized for organellar transcripts. Samples include growth in media +/– Fe, growth in media +/– Cu, diurnal growth samples collected in dark and light, and the sexual cycle. +!Series_overall_design = RNA-Seq libraries were prepared from Chlamydomonas reinhardtii sampled under 12 different conditions including: diurnal growth in light, diurnal growth in dark, +Fe, –Fe, +Cu, –Cu, mt+ vegetative, mt– vegetative, mt+ gamete, mt– gamete, zygote, and post-germination. +!Series_type = Expression profiling by high throughput sequencing +!Series_contributor = Sean,D,Gallaher +!Series_contributor = Daniela,,Strenkert +!Series_sample_id = GSM2719230 +!Series_sample_id = GSM2719231 +!Series_sample_id = GSM2719232 +!Series_sample_id = GSM2719233 +!Series_sample_id = GSM2719234 +!Series_sample_id = GSM2719235 +!Series_sample_id = GSM2719236 +!Series_sample_id = GSM2719237 +!Series_sample_id = GSM2719238 +!Series_sample_id = GSM2719239 +!Series_sample_id = GSM2719240 +!Series_sample_id = GSM2719241 +!Series_sample_id = GSM2719242 +!Series_sample_id = GSM2719243 +!Series_contact_name = Sean,D.,Gallaher +!Series_contact_laboratory = Sabeeha Merchant +!Series_contact_department = Chem & BioChem +!Series_contact_institute = UCLA +!Series_contact_address = 607 Charle E. Young Drive East +!Series_contact_city = Los Angeles +!Series_contact_state = California +!Series_contact_zip/postal_code = 90095 +!Series_contact_country = USA +!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE101nnn/GSE101944/suppl/GSE101944_Cre.nuc.v5.5.cp.mt.v4.4.gff3.gz +!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE101nnn/GSE101944/suppl/GSE101944_fpkms.all.tsv.gz +!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE101nnn/GSE101944/suppl/GSE101944_fpkms.copper.tsv.gz +!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE101nnn/GSE101944/suppl/GSE101944_fpkms.diurnal.tsv.gz +!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE101nnn/GSE101944/suppl/GSE101944_fpkms.iron_PAvsRZ.tsv.gz +!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE101nnn/GSE101944/suppl/GSE101944_fpkms.sexual.tsv.gz +!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE101nnn/GSE101944/suppl/GSE101944_rRNA+snoRNA.fasta.gz +!Series_platform_id = GPL15922 +!Series_platform_taxid = 3055 +!Series_sample_taxid = 3055 +!Series_relation = BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA395986 +!Series_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP113670 +^SERIES = GSE112394 +!Series_title = Transcriptomics analysis of the Chlamydomonas reinhardtii diurnal cycle. +!Series_geo_accession = GSE112394 +!Series_status = Public on Jan 03 2019 +!Series_submission_date = Mar 27 2018 +!Series_last_update_date = Feb 19 2019 +!Series_pubmed_id = 30659148 +!Series_summary = Here, we report a transcriptomics analysis on a day in the life of Chlamydomonas reinhardtii. Cultures of this unicellular alga were grown in photobioreactors on a 12 h light / 12 h dark cycle. Samples were collected at regular intervals and subjected to a transcriptomics analysis by RNA-Seq. +!Series_overall_design = RNA-Seq libraries were prepared from synchronized cultures of Chlamydomonas reinhardtii sampled at regular intervals over the course of a diurnal cycle. Light intensity during the day was 200 PFD. +!Series_type = Expression profiling by high throughput sequencing +!Series_contributor = Sean,D,Gallaher +!Series_contributor = Daniela,,Strenkert +!Series_sample_id = GSM3069464 +!Series_sample_id = GSM3069465 +!Series_sample_id = GSM3069466 +!Series_sample_id = GSM3069467 +!Series_sample_id = GSM3069468 +!Series_sample_id = GSM3069469 +!Series_sample_id = GSM3069470 +!Series_sample_id = GSM3069471 +!Series_sample_id = GSM3069472 +!Series_sample_id = GSM3069473 +!Series_sample_id = GSM3069474 +!Series_sample_id = GSM3069475 +!Series_sample_id = GSM3069476 +!Series_sample_id = GSM3069477 +!Series_sample_id = GSM3069478 +!Series_sample_id = GSM3069479 +!Series_contact_name = Sean,D.,Gallaher +!Series_contact_laboratory = Sabeeha Merchant +!Series_contact_department = Chem & BioChem +!Series_contact_institute = UCLA +!Series_contact_address = 607 Charle E. Young Drive East +!Series_contact_city = Los Angeles +!Series_contact_state = California +!Series_contact_zip/postal_code = 90095 +!Series_contact_country = USA +!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE112nnn/GSE112394/suppl/GSE112394_Cre.nuc.v5.5.cp.mt.v4.4.gff3.gz +!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE112nnn/GSE112394/suppl/GSE112394_diurnal.cuffdiff_analysis.tar.gz +!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE112nnn/GSE112394/suppl/GSE112394_fpkms.tsv.gz +!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE112nnn/GSE112394/suppl/GSE112394_rRNA+snoRNA.fasta.gz +!Series_platform_id = GPL15922 +!Series_platform_taxid = 3055 +!Series_sample_taxid = 3055 +!Series_relation = BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA445880 +!Series_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP136557 diff --git a/docsrc/content/data/GSE71469_family.soft b/docsrc/content/data/GSE71469_family.soft new file mode 100644 index 00000000..43284889 --- /dev/null +++ b/docsrc/content/data/GSE71469_family.soft @@ -0,0 +1,2793 @@ +^DATABASE = GeoMiame +!Database_name = Gene Expression Omnibus (GEO) +!Database_institute = NCBI NLM NIH +!Database_web_link = http://www.ncbi.nlm.nih.gov/geo +!Database_email = geo@ncbi.nlm.nih.gov +^SERIES = GSE71469 +!Series_title = Chlamydomonas diurnal transcriptome +!Series_geo_accession = GSE71469 +!Series_status = Public on Jul 30 2015 +!Series_submission_date = Jul 29 2015 +!Series_last_update_date = May 15 2019 +!Series_pubmed_id = 26432862 +!Series_summary = We combined a highly synchronous photobioreactor culture system with frequent temporal sampling to characterize genome-wide periodic gene expression in Chlamydomonas. +!Series_overall_design = Synchronous phototrophic cultures of Chlamydomonas reinhardtii were prepared in controlled diurnal bioreactor growth conditions and sampled in two 24-hour replicate time courses at 1-hour and 0.5-hour intervals for Illumina paired-end RNA-Seq. More than ~3 million paired end reads were obtained for each sample. +!Series_type = Expression profiling by high throughput sequencing +!Series_contributor = James,M,Zones +!Series_contributor = Ian,K,Blaby +!Series_contributor = Sabeeha,S,Merchant +!Series_contributor = James,G,Umen +!Series_sample_id = GSM1835200 +!Series_sample_id = GSM1835201 +!Series_sample_id = GSM1835202 +!Series_sample_id = GSM1835203 +!Series_sample_id = GSM1835204 +!Series_sample_id = GSM1835205 +!Series_sample_id = GSM1835206 +!Series_sample_id = GSM1835207 +!Series_sample_id = GSM1835208 +!Series_sample_id = GSM1835209 +!Series_sample_id = GSM1835210 +!Series_sample_id = GSM1835211 +!Series_sample_id = GSM1835212 +!Series_sample_id = GSM1835213 +!Series_sample_id = GSM1835214 +!Series_sample_id = GSM1835215 +!Series_sample_id = GSM1835216 +!Series_sample_id = GSM1835217 +!Series_sample_id = GSM1835218 +!Series_sample_id = GSM1835219 +!Series_sample_id = GSM1835220 +!Series_sample_id = GSM1835221 +!Series_sample_id = GSM1835222 +!Series_sample_id = GSM1835223 +!Series_sample_id = GSM1835224 +!Series_sample_id = GSM1835225 +!Series_sample_id = GSM1835226 +!Series_sample_id = GSM1835227 +!Series_sample_id = GSM1835228 +!Series_sample_id = GSM1835229 +!Series_sample_id = GSM1835230 +!Series_sample_id = GSM1835231 +!Series_sample_id = GSM1835232 +!Series_sample_id = GSM1835233 +!Series_sample_id = GSM1835234 +!Series_sample_id = GSM1835235 +!Series_sample_id = GSM1835236 +!Series_sample_id = GSM1835237 +!Series_sample_id = GSM1835238 +!Series_sample_id = GSM1835239 +!Series_sample_id = GSM1835240 +!Series_sample_id = GSM1835241 +!Series_sample_id = GSM1835242 +!Series_sample_id = GSM1835243 +!Series_sample_id = GSM1835244 +!Series_sample_id = GSM1835245 +!Series_sample_id = GSM1835246 +!Series_sample_id = GSM1835247 +!Series_sample_id = GSM1835248 +!Series_sample_id = GSM1835249 +!Series_sample_id = GSM1835250 +!Series_sample_id = GSM1835251 +!Series_sample_id = GSM1835252 +!Series_sample_id = GSM1835253 +!Series_sample_id = GSM1835254 +!Series_sample_id = GSM1835255 +!Series_contact_name = James,,Umen +!Series_contact_email = jumen@danforthcenter.org +!Series_contact_phone = 314-587-1689 +!Series_contact_laboratory = Umen Laboratory +!Series_contact_institute = Donald Danforth Plant Science Center +!Series_contact_address = 975 N. Warson Rd. +!Series_contact_city = St. Louis +!Series_contact_state = MO +!Series_contact_zip/postal_code = 63141 +!Series_contact_country = USA +!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71469/suppl/GSE71469_ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt.gz +!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE71nnn/GSE71469/suppl/GSE71469_ChlamydomonasSynchronousDiurnalExpressionRPKM.txt.gz +!Series_platform_id = GPL15922 +!Series_platform_taxid = 3055 +!Series_sample_taxid = 3055 +!Series_relation = BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA291337 +!Series_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP061735 +^PLATFORM = GPL15922 +!Platform_title = Illumina HiSeq 2000 (Chlamydomonas reinhardtii) +!Platform_geo_accession = GPL15922 +!Platform_status = Public on Aug 10 2012 +!Platform_submission_date = Aug 10 2012 +!Platform_last_update_date = Apr 24 2015 +!Platform_technology = high-throughput sequencing +!Platform_distribution = virtual +!Platform_organism = Chlamydomonas reinhardtii +!Platform_taxid = 3055 +!Platform_contact_name = ,,GEO +!Platform_contact_country = USA +!Platform_data_row_count = 0 +^SAMPLE = GSM1835200 +!Sample_title = 1_1 +!Sample_geo_accession = GSM1835200 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 1 +!Sample_characteristics_ch1 = protocol: light +!Sample_characteristics_ch1 = time (zeitgeber): ZT1 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941585 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122839 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835201 +!Sample_title = 2_1 +!Sample_geo_accession = GSM1835201 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 1 +!Sample_characteristics_ch1 = protocol: light +!Sample_characteristics_ch1 = time (zeitgeber): ZT2 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941586 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122840 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835202 +!Sample_title = 3_1 +!Sample_geo_accession = GSM1835202 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 1 +!Sample_characteristics_ch1 = protocol: light +!Sample_characteristics_ch1 = time (zeitgeber): ZT3 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941587 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122841 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835203 +!Sample_title = 4_1 +!Sample_geo_accession = GSM1835203 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 1 +!Sample_characteristics_ch1 = protocol: light +!Sample_characteristics_ch1 = time (zeitgeber): ZT4 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941588 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122842 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835204 +!Sample_title = 5_1 +!Sample_geo_accession = GSM1835204 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 1 +!Sample_characteristics_ch1 = protocol: light +!Sample_characteristics_ch1 = time (zeitgeber): ZT5 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941589 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122843 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835205 +!Sample_title = 6_1 +!Sample_geo_accession = GSM1835205 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 1 +!Sample_characteristics_ch1 = protocol: light +!Sample_characteristics_ch1 = time (zeitgeber): ZT6 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941590 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122844 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835206 +!Sample_title = 7_1 +!Sample_geo_accession = GSM1835206 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 1 +!Sample_characteristics_ch1 = protocol: light +!Sample_characteristics_ch1 = time (zeitgeber): ZT7 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941591 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122845 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835207 +!Sample_title = 8_1 +!Sample_geo_accession = GSM1835207 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 1 +!Sample_characteristics_ch1 = protocol: light +!Sample_characteristics_ch1 = time (zeitgeber): ZT8 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941592 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122846 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835208 +!Sample_title = 9_1 +!Sample_geo_accession = GSM1835208 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 1 +!Sample_characteristics_ch1 = protocol: light +!Sample_characteristics_ch1 = time (zeitgeber): ZT9 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941593 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122847 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835209 +!Sample_title = 10_1 +!Sample_geo_accession = GSM1835209 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 1 +!Sample_characteristics_ch1 = protocol: light +!Sample_characteristics_ch1 = time (zeitgeber): ZT10 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941594 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122848 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835210 +!Sample_title = 11_1 +!Sample_geo_accession = GSM1835210 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 1 +!Sample_characteristics_ch1 = protocol: light +!Sample_characteristics_ch1 = time (zeitgeber): ZT11 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941595 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122849 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835211 +!Sample_title = 11.5_1 +!Sample_geo_accession = GSM1835211 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 1 +!Sample_characteristics_ch1 = protocol: light +!Sample_characteristics_ch1 = time (zeitgeber): ZT11.5 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941596 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122850 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835212 +!Sample_title = 12_1 +!Sample_geo_accession = GSM1835212 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 1 +!Sample_characteristics_ch1 = protocol: light +!Sample_characteristics_ch1 = time (zeitgeber): ZT12 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941597 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122851 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835213 +!Sample_title = 12.5_1 +!Sample_geo_accession = GSM1835213 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 1 +!Sample_characteristics_ch1 = protocol: dark +!Sample_characteristics_ch1 = time (zeitgeber): ZT12.5 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941598 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122852 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835214 +!Sample_title = 13_1 +!Sample_geo_accession = GSM1835214 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 1 +!Sample_characteristics_ch1 = protocol: dark +!Sample_characteristics_ch1 = time (zeitgeber): ZT13 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941599 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122853 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835215 +!Sample_title = 13.5_1 +!Sample_geo_accession = GSM1835215 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 1 +!Sample_characteristics_ch1 = protocol: dark +!Sample_characteristics_ch1 = time (zeitgeber): ZT13.5 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941600 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122854 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835216 +!Sample_title = 14_1 +!Sample_geo_accession = GSM1835216 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 1 +!Sample_characteristics_ch1 = protocol: dark +!Sample_characteristics_ch1 = time (zeitgeber): ZT14 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941601 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122855 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835217 +!Sample_title = 14.5_1 +!Sample_geo_accession = GSM1835217 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 1 +!Sample_characteristics_ch1 = protocol: dark +!Sample_characteristics_ch1 = time (zeitgeber): ZT14.5 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941602 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122856 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835218 +!Sample_title = 15_1 +!Sample_geo_accession = GSM1835218 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 1 +!Sample_characteristics_ch1 = protocol: dark +!Sample_characteristics_ch1 = time (zeitgeber): ZT15 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941603 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122857 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835219 +!Sample_title = 16_1 +!Sample_geo_accession = GSM1835219 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 1 +!Sample_characteristics_ch1 = protocol: dark +!Sample_characteristics_ch1 = time (zeitgeber): ZT16 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941604 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122858 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835220 +!Sample_title = 17_1 +!Sample_geo_accession = GSM1835220 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 1 +!Sample_characteristics_ch1 = protocol: dark +!Sample_characteristics_ch1 = time (zeitgeber): ZT17 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941605 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122859 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835221 +!Sample_title = 18_1 +!Sample_geo_accession = GSM1835221 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 1 +!Sample_characteristics_ch1 = protocol: dark +!Sample_characteristics_ch1 = time (zeitgeber): ZT18 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941606 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122860 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835222 +!Sample_title = 19_1 +!Sample_geo_accession = GSM1835222 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 1 +!Sample_characteristics_ch1 = protocol: dark +!Sample_characteristics_ch1 = time (zeitgeber): ZT19 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941607 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122861 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835223 +!Sample_title = 20_1 +!Sample_geo_accession = GSM1835223 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 1 +!Sample_characteristics_ch1 = protocol: dark +!Sample_characteristics_ch1 = time (zeitgeber): ZT20 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941608 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122862 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835224 +!Sample_title = 21_1 +!Sample_geo_accession = GSM1835224 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 1 +!Sample_characteristics_ch1 = protocol: dark +!Sample_characteristics_ch1 = time (zeitgeber): ZT21 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941609 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122863 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835225 +!Sample_title = 22_1 +!Sample_geo_accession = GSM1835225 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 1 +!Sample_characteristics_ch1 = protocol: dark +!Sample_characteristics_ch1 = time (zeitgeber): ZT22 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941610 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122864 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835226 +!Sample_title = 23_1 +!Sample_geo_accession = GSM1835226 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 1 +!Sample_characteristics_ch1 = protocol: dark +!Sample_characteristics_ch1 = time (zeitgeber): ZT23 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941611 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122865 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835227 +!Sample_title = 24_1 +!Sample_geo_accession = GSM1835227 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 1 +!Sample_characteristics_ch1 = protocol: dark +!Sample_characteristics_ch1 = time (zeitgeber): ZT24 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941612 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122866 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835228 +!Sample_title = 1_2 +!Sample_geo_accession = GSM1835228 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 2 +!Sample_characteristics_ch1 = protocol: light +!Sample_characteristics_ch1 = time (zeitgeber): ZT1 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941613 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122867 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835229 +!Sample_title = 2_2 +!Sample_geo_accession = GSM1835229 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 2 +!Sample_characteristics_ch1 = protocol: light +!Sample_characteristics_ch1 = time (zeitgeber): ZT2 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941614 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122868 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835230 +!Sample_title = 3_2 +!Sample_geo_accession = GSM1835230 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 2 +!Sample_characteristics_ch1 = protocol: light +!Sample_characteristics_ch1 = time (zeitgeber): ZT3 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941616 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122869 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835231 +!Sample_title = 4_2 +!Sample_geo_accession = GSM1835231 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 2 +!Sample_characteristics_ch1 = protocol: light +!Sample_characteristics_ch1 = time (zeitgeber): ZT4 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941617 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122870 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835232 +!Sample_title = 5_2 +!Sample_geo_accession = GSM1835232 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 2 +!Sample_characteristics_ch1 = protocol: light +!Sample_characteristics_ch1 = time (zeitgeber): ZT5 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941618 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122871 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835233 +!Sample_title = 6_2 +!Sample_geo_accession = GSM1835233 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 2 +!Sample_characteristics_ch1 = protocol: light +!Sample_characteristics_ch1 = time (zeitgeber): ZT6 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941619 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122872 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835234 +!Sample_title = 7_2 +!Sample_geo_accession = GSM1835234 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 2 +!Sample_characteristics_ch1 = protocol: light +!Sample_characteristics_ch1 = time (zeitgeber): ZT7 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941620 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122873 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835235 +!Sample_title = 8_2 +!Sample_geo_accession = GSM1835235 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 2 +!Sample_characteristics_ch1 = protocol: light +!Sample_characteristics_ch1 = time (zeitgeber): ZT8 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941621 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122874 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835236 +!Sample_title = 9_2 +!Sample_geo_accession = GSM1835236 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 2 +!Sample_characteristics_ch1 = protocol: light +!Sample_characteristics_ch1 = time (zeitgeber): ZT9 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941622 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122875 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835237 +!Sample_title = 10_2 +!Sample_geo_accession = GSM1835237 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 2 +!Sample_characteristics_ch1 = protocol: light +!Sample_characteristics_ch1 = time (zeitgeber): ZT10 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941615 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122876 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835238 +!Sample_title = 11_2 +!Sample_geo_accession = GSM1835238 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 2 +!Sample_characteristics_ch1 = protocol: light +!Sample_characteristics_ch1 = time (zeitgeber): ZT11 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941623 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122877 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835239 +!Sample_title = 11.5_2 +!Sample_geo_accession = GSM1835239 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 2 +!Sample_characteristics_ch1 = protocol: light +!Sample_characteristics_ch1 = time (zeitgeber): ZT11.5 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941624 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122878 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835240 +!Sample_title = 12_2 +!Sample_geo_accession = GSM1835240 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 2 +!Sample_characteristics_ch1 = protocol: light +!Sample_characteristics_ch1 = time (zeitgeber): ZT12 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941625 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122879 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835241 +!Sample_title = 12.5_2 +!Sample_geo_accession = GSM1835241 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 2 +!Sample_characteristics_ch1 = protocol: dark +!Sample_characteristics_ch1 = time (zeitgeber): ZT12.5 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941626 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122880 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835242 +!Sample_title = 13_2 +!Sample_geo_accession = GSM1835242 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 2 +!Sample_characteristics_ch1 = protocol: dark +!Sample_characteristics_ch1 = time (zeitgeber): ZT13 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941627 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122881 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835243 +!Sample_title = 13.5_2 +!Sample_geo_accession = GSM1835243 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 2 +!Sample_characteristics_ch1 = protocol: dark +!Sample_characteristics_ch1 = time (zeitgeber): ZT13.5 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941628 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122882 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835244 +!Sample_title = 14_2 +!Sample_geo_accession = GSM1835244 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 2 +!Sample_characteristics_ch1 = protocol: dark +!Sample_characteristics_ch1 = time (zeitgeber): ZT14 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941629 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122883 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835245 +!Sample_title = 14.5_2 +!Sample_geo_accession = GSM1835245 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 2 +!Sample_characteristics_ch1 = protocol: dark +!Sample_characteristics_ch1 = time (zeitgeber): ZT14.5 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941630 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122884 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835246 +!Sample_title = 15_2 +!Sample_geo_accession = GSM1835246 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 2 +!Sample_characteristics_ch1 = protocol: dark +!Sample_characteristics_ch1 = time (zeitgeber): ZT15 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941631 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122885 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835247 +!Sample_title = 16_2 +!Sample_geo_accession = GSM1835247 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 2 +!Sample_characteristics_ch1 = protocol: dark +!Sample_characteristics_ch1 = time (zeitgeber): ZT16 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941632 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122886 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835248 +!Sample_title = 17_2 +!Sample_geo_accession = GSM1835248 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 2 +!Sample_characteristics_ch1 = protocol: dark +!Sample_characteristics_ch1 = time (zeitgeber): ZT17 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941633 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122887 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835249 +!Sample_title = 18_2 +!Sample_geo_accession = GSM1835249 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 2 +!Sample_characteristics_ch1 = protocol: dark +!Sample_characteristics_ch1 = time (zeitgeber): ZT18 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941634 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122888 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835250 +!Sample_title = 19_2 +!Sample_geo_accession = GSM1835250 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 2 +!Sample_characteristics_ch1 = protocol: dark +!Sample_characteristics_ch1 = time (zeitgeber): ZT19 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941635 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122889 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835251 +!Sample_title = 20_2 +!Sample_geo_accession = GSM1835251 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 2 +!Sample_characteristics_ch1 = protocol: dark +!Sample_characteristics_ch1 = time (zeitgeber): ZT20 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941636 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122890 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835252 +!Sample_title = 21_2 +!Sample_geo_accession = GSM1835252 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 2 +!Sample_characteristics_ch1 = protocol: dark +!Sample_characteristics_ch1 = time (zeitgeber): ZT21 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941637 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122891 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835253 +!Sample_title = 22_2 +!Sample_geo_accession = GSM1835253 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 2 +!Sample_characteristics_ch1 = protocol: dark +!Sample_characteristics_ch1 = time (zeitgeber): ZT22 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941638 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122892 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835254 +!Sample_title = 23_2 +!Sample_geo_accession = GSM1835254 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 2 +!Sample_characteristics_ch1 = protocol: dark +!Sample_characteristics_ch1 = time (zeitgeber): ZT23 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941639 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122893 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 +^SAMPLE = GSM1835255 +!Sample_title = 24_2 +!Sample_geo_accession = GSM1835255 +!Sample_status = Public on Jul 30 2015 +!Sample_submission_date = Jul 29 2015 +!Sample_last_update_date = May 15 2019 +!Sample_type = SRA +!Sample_channel_count = 1 +!Sample_source_name_ch1 = Synchronized diurnal cullture +!Sample_organism_ch1 = Chlamydomonas reinhardtii +!Sample_taxid_ch1 = 3055 +!Sample_characteristics_ch1 = strain: 6145c (CC-2895) +!Sample_characteristics_ch1 = replicate time course: Replicate 2 +!Sample_characteristics_ch1 = protocol: dark +!Sample_characteristics_ch1 = time (zeitgeber): ZT24 +!Sample_treatment_protocol_ch1 = 30 mL of bioreactor culture was sampled at indicated times and collected by centrifugation. +!Sample_growth_protocol_ch1 = Cells were innoculated from a plate into a 400 mL PSI FMT-150 photobioreactor cuvette containing HSM medium and grown in 12:12 light-dark conditions (125 uE red light, 125 uE blue light) at 28 degrees C. The culture was grown to a density corresponding to OD680=0.3 (~2-3e6 daughter cells/mL) and maintained at this density for 3-4 days before sampling. +!Sample_molecule_ch1 = total RNA +!Sample_extract_protocol_ch1 = Cell pellets were resuspended in 0.25 mL RNase-free water and then mixed with 0.25 mL warmed (70 C) lysis buffer (50 mM Tris-HCl pH 8.0, 200 mM NaCl, 20 mM EDTA, 2% SDS, 1 mg/mL Proteinase K). 10 mL TRIzol was then added and samples were mixed, flash frozen in liquid nitrogen, and stored at -80 C. Samples were later thawed and transfered to 15 mL MaXtract HD tubes followed by extraction with 2 mL chloroform. The aqueous phase was mixed with 1.5 volcumes 100% ethanol and applied to a MicroRNeasy column under vacuum. Washing, DNase treatment, and elution were performed according to manufacturer's instructions (RNase-free DNase Set). +!Sample_extract_protocol_ch1 = Plate-based RNASeq with polyA selection sample prep was performed on the PerkinElmer Sciclone NGS robotic liquid handling system, where purified mRNA is converted into cDNA library templates of known strand origin for sequencing on the Illumina Sequencer platform. The DynaBead kit (Invitrogen) was used to select and purify poly-A containing mRNA from 5 µg of total RNA per sample. The mRNA was chemically fragmented with 10X fragmentation solution (Ambion) at 70°C for 3 minutes to generate fragments ranging in size between 250 to 300bp. The fragmented RNA was purified using AMpure SPRI beads (Agencourt) using a ratio of 160:100 beads volume: RNA sample volume. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) and random hexamer primers (MBI Fermentas) with Actinomycin D in the master-mix to inhibit DNA dependent DNA synthesis. First-strand synthesis thermocycler conditions were 42°C for 50 minutes and an inactivation step at 70°C for 10 minutes. This was followed by another purification using AMpure SPRI beads at a ratio of 140:100 beads volume:cDNA volume. Second-strand cDNA synthesis was performed using DNA Polymerase I (Invitrogen), RNase H (Invitrogen), and a nucleotide mix containing dUTP (Roche). The second-strand synthesis was done at 16°C for 60 minutes. The double stranded cDNA fragments were purified using AMpure SPRI beads at a ratio of 75:100 beads volume: cDNA volume followed by a second purification using a bead:cDNA ratio of 140:100. cDNA fragments were end repaired, phosphorylated and A-tailed using a Kapa Biosystems kit followed by ligation to Illumina barcoded sequencing adapters. AmpErase UNG (Uracil N-glycosylase, Applied Biosystems) was added to the double stranded cDNA library fragments and incubated at 37°C for 15 minutes to cleave and degrade the strand containing dUTP. The single stranded cDNA was then enriched using 10 cycles of PCR with Illumina TruSeq primers and purified using AMpure SPRI beads at a ratio of 90:100 beads volume: cDNA volume to create the final cDNA library. Libraries were quantified using KAPA Biosystem’s next-generation sequencing library qPCR kit using a Roche LightCycler 480 real-time PCR instrument. The libraries were then prepared for sequencing on the Illumina HiSeq sequencing platform utilizing a TruSeq paired-end cluster kit, v3, and Illumina’s cBot instrument to generate clustered flowcells for sequencing. Sequencing of the flowcells was performed on the Illumina HiSeq2000 sequencer using a TruSeq SBS sequencing kit with 200 cycles, v3, following a 2x100 indexed run recipe. +!Sample_data_processing = Quality control of RNA-Seq samples was performed on the raw paired-end reads using Trimmomatic to remove contaminating Illumina adapter sequences and low quality sequences (average Q20 over 4 base slide window<20). +!Sample_data_processing = Reads were aligned to the Chlamydomonas reinhardtii genome version 5 assembly with STAR version 20201 using standard presets except for intron size that was set between 20 and 3,000 bp (--alignIntronMin 20 & --alignIntronMax 3000). +!Sample_data_processing = Uniquely mapping reads were assigned to 17,737 version 5.3.1 primary transcripts using HT-Seq version 0.5.4p3 (htseq-count --mode intersection-nonempty --type exon --stranded=no). +!Sample_data_processing = One read was added to each sample/gene locus and samples were normalized by library size (# uniquely-mapping reads). Differential expression analysis was performed using DESeq2 version 1.4.5 comparing samples to mean expression of all samples. HTSFilter version 1.4.0 was used to establish a low-expression filter of 1.061 reads/million (RPM) and genes with less that 1.061 RPM average expression were excluded from multiple testing correction (FDR). Genes with an absolute fold-change ≥ 2 compared to the mean expression and with a FDR < 0.05 in at least one sample were considered differentially expressed. Expression estimates were then length normalized by primary transcript length into RPKMs. +!Sample_data_processing = Expression estimates were transformed to into standard deviation/mean (z-score). Then K-means Support clustering was performed by MeV version 4.9 on differentially expressed genes to obtain 6 groups of genes with similar expression patterns. These gene sets were then clustered again to obtain a total of 18 groups of differentially-expressed genes. +!Sample_data_processing = Genome_build: Chlamydomonas reinhardtii version 5. +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionHTSeqCounts.txt - Tab-delimited text file, HTSeq read counts +!Sample_data_processing = Supplementary_files_format_and_content: ChlamydomonasSynchronousDiurnalExpressionRPKM.txt - Tab-delimited text file, RPKM expression estimates +!Sample_platform_id = GPL15922 +!Sample_contact_name = James,,Umen +!Sample_contact_email = jumen@danforthcenter.org +!Sample_contact_phone = 314-587-1689 +!Sample_contact_laboratory = Umen Laboratory +!Sample_contact_institute = Donald Danforth Plant Science Center +!Sample_contact_address = 975 N. Warson Rd. +!Sample_contact_city = St. Louis +!Sample_contact_state = MO +!Sample_contact_zip/postal_code = 63141 +!Sample_contact_country = USA +!Sample_instrument_model = Illumina HiSeq 2000 +!Sample_library_selection = cDNA +!Sample_library_source = transcriptomic +!Sample_library_strategy = RNA-Seq +!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03941640 +!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1122894 +!Sample_supplementary_file_1 = NONE +!Sample_series_id = GSE71469 +!Sample_data_row_count = 0 diff --git a/docsrc/tools/templates/template.cshtml b/docsrc/tools/templates/template.cshtml index 08d7796a..02d59339 100644 --- a/docsrc/tools/templates/template.cshtml +++ b/docsrc/tools/templates/template.cshtml @@ -121,6 +121,7 @@ } +
  • GEO Metadata (SOFT)
  • GFF3 @if (Properties.Dictionary.ContainsKey("page-source") && Properties["page-source"].ToString().EndsWith("GFF3.fsx")) @@ -152,6 +153,7 @@
  • BioItems
  • BioCollections
  • Clustal
    • +
  • GEO Metadata (SOFT)
    • } From 425fbb93b41700eeece8f8ab063c9c37b15124bd Mon Sep 17 00:00:00 2001 From: kMutagene Date: Tue, 17 Mar 2020 10:39:13 +0100 Subject: [PATCH 06/11] Add DSL for fasterq-dump in SRATools BioContainer API --- .../BioFSharp.BioContainers.fsx | 35 ++- src/BioFSharp.BioContainers/SRAToolkit.fs | 213 +++++++++++++++++- 2 files changed, 241 insertions(+), 7 deletions(-) diff --git a/src/BioFSharp.BioContainers/BioFSharp.BioContainers.fsx b/src/BioFSharp.BioContainers/BioFSharp.BioContainers.fsx index 543faa79..8f66ba69 100644 --- a/src/BioFSharp.BioContainers/BioFSharp.BioContainers.fsx +++ b/src/BioFSharp.BioContainers/BioFSharp.BioContainers.fsx @@ -17,6 +17,7 @@ #load "ClustalO.fs" #load "HMMER.fs" #load "LastAlign.fs" +#load "SRAToolkit.fs" open System.Threading open System.Threading @@ -424,8 +425,6 @@ open BioFSharp.BioContainers.BioContainer open BioFSharp.BioContainers.BioContainerIO open Blast -let client = Docker.connect "npipe://./pipe/docker_engine" - let ImageBlast = Docker.DockerId.ImageId "blast" let blastContext = @@ -434,9 +433,9 @@ let blastContext = let paramz = [ - MakeDbParams.DbType Protein - MakeDbParams.Input @"C:\Users\Kevin\source\repos\CsbScaffold\Docker\data\Chlamy_Cp.fastA" - MakeDbParams.Output@"C:\Users\Kevin\source\repos\CsbScaffold\Docker\data\Chlamy_Cp.fastA" + MakeBlastDbParams.DbType Protein + MakeBlastDbParams.Input @"C:\Users\Kevin\source\repos\CsbScaffold\Docker\data\Chlamy_Cp.fastA" + MakeBlastDbParams.Output@"C:\Users\Kevin\source\repos\CsbScaffold\Docker\data\Chlamy_Cp.fastA" ] let outputFormat= @@ -577,4 +576,28 @@ let alignParams = runLastAlignAsync lastAlignContext alignParams |> Async.RunSynchronously -|> fun x -> File.WriteAllLines(@"C:\Users\kevin\Desktop\Microbiology_CrossGenomics\Data\Genomes\GenomeAlignment.maf",x.Split([|"\r\n";"\r";"\n"|],StringSplitOptions.None)) \ No newline at end of file +|> fun x -> File.WriteAllLines(@"C:\Users\kevin\Desktop\Microbiology_CrossGenomics\Data\Genomes\GenomeAlignment.maf",x.Split([|"\r\n";"\r";"\n"|],StringSplitOptions.None)) + + +open SRATools + +let sraImage = Docker.ImageId "quay.io/biocontainers/sra-tools:2.10.3--pl526haddd2b5_0" + +let sraContext = + BioContainer.initBcContextWithMountAsync client sraImage @"C:\Users\kevin\Downloads\CsbScaffold-master\MetaIndexing_New\data" + |> Async.RunSynchronously + +let FQDOptions = + [ + FasterQDumpParams.OutDirectory @"C:\Users\kevin\Downloads\CsbScaffold-master\MetaIndexing_New\data\lol" + FasterQDumpParams.TempDirectory @"C:\Users\kevin\Downloads\CsbScaffold-master\MetaIndexing_New\data\lol\tmp" + FasterQDumpParams.Split SplitOptions.Split3 + FasterQDumpParams.PrintDetails + FasterQDumpParams.ShowProgress + ] + +runFasterQDump sraContext FQDOptions "SRR000001" + +sraContext +|> BioContainer.disposeAsync +|> Async.RunSynchronously \ No newline at end of file diff --git a/src/BioFSharp.BioContainers/SRAToolkit.fs b/src/BioFSharp.BioContainers/SRAToolkit.fs index caae7e6f..d379023a 100644 --- a/src/BioFSharp.BioContainers/SRAToolkit.fs +++ b/src/BioFSharp.BioContainers/SRAToolkit.fs @@ -1 +1,212 @@ -namespace BioFSharp.BioContainers \ No newline at end of file +namespace BioFSharp.BioContainers +open BioContainer + +module SRATools = + + //type PrefetchParams = + // |Placeholder + + // static member makeCmd = function + // |Placeholder -> [""] + + // static member makeCmdWith (m:MountInfo) = function + // |Placeholder -> [""] + + + + + //let runPrefetchAsync (bcContext:BioContainer.BcContext) (opt:PrefetchParams list) = + + // let cmds = (opt |> List.map (PrefetchParams.makeCmdWith bcContext.Mount)) + // let tp = "prefetch"::(cmds |> List.concat) + + // printfn "Starting process prefetch\r\nparameters:" + // cmds |> List.iter (fun op -> printfn "\t%s" (String.concat " " op)) + + // async { + // let! res = BioContainer.execAsync bcContext tp + // return res + // } + + type SplitOptions = + ///Split spots into reads + |SplitSpot + ///Write reads into different files + |SplitFiles + ///Writes single reads into special file + |Split3 + ///Writes whole spots into one file + |ConcatenateReads + + static member make = function + |SplitSpot -> "--split-spot" + |SplitFiles -> "--split-files" + |Split3 -> "--split-3" + |ConcatenateReads -> "--concatenate-read" + + //type FastQDumpParams = + // |Placeholder + + // static member makeCmd = function + // |Placeholder -> [""] + + // static member makeCmdWith (m:MountInfo) = function + // |Placeholder -> [""] + + + + + //let runFastQDumpAsync (bcContext:BioContainer.BcContext) (opt:FastQDumpParams list) = + + // let cmds = (opt |> List.map (FastQDumpParams.makeCmdWith bcContext.Mount)) + // let tp = "fastq-dump"::(cmds |> List.concat) + + // printfn "Starting process fastq-dump\r\nparameters:" + // cmds |> List.iter (fun op -> printfn "\t%s" (String.concat " " op)) + + // async { + // let! res = BioContainer.execAsync bcContext tp + // return res + // } + + + ///DSL for command line arguments for the fasterq-dump tool contained in the SRA Toolkit + type FasterQDumpParams = + ///full path of outputfile (overrides usage of current directory and given accession) + |OutFile of string + ///path for outputfile (overrides usage of current directory, but uses given accession) + |OutDirectory of string + ///path to directory for temp. files (dflt=current dir.) + |TempDirectory of string + //size of file-buffer (dflt=1MB) + |BufferSize of string + ///Determine how to handle paired reads + |Split of SplitOptions + ///size of cursor-cache (dflt=10MB, takes number or number and unit) + |CursorCacheSize of string + ///memory limit for sorting (dflt=100MB, takes number or number and unit) + |SortingMemoryLimit of string + ///how many threads to use (dflt=6) + |Threads of int + ///show progress (not possible if stdout used) + |ShowProgress + ///print details of all options selected + |PrintDetails + ///print output to stdout + |StdOut + //force overwrite of existing file(s) + |Force + ///use rowid as name (avoids using the name column) + |RowIdAsName + ///skip technical reads + |SkipTechnical + ///explicitly include technical reads + |IncludeTechnical + ///include read-number in defline + |PrintReadNumber + ///filter by sequence-lenght + |MinReadLength of int + ///which seq-table to use in case of pacbio + |PacBioTableName of string + ///terminate on invalid read + |Strict + ///filter output by matching against given bases + |FilterBases of string + ///append to output-file, instead of overwriting it + |AppendOutput + ///path to ngc file + |NGCFilePath of string + ///path to permission file + |PermissionFilePath of string + ///location in cloud + |CloudLocation of string + //path to cart file + |CartPath of string + ///disable multithreading + |DisableMultiThreading + //Display the version of the program + |Version + //Logging level as number or enum string. One of (fatal|sys|int|err|warn|info|debug) or (0-6) Current/default is warn + |LogLevel of string + ///Read more options and parameters from the file. + |OptionFilePath of string + + static member makeCmd = function + |OutFile o -> ["-o"; o] + |OutDirectory o -> ["-O"; o] + |TempDirectory t -> ["-t"; t] + |NGCFilePath n -> ["--ngc"; n] + |PermissionFilePath p -> ["--perm"; p] + |CartPath c -> ["--cart"; c] + |OptionFilePath o -> ["option-file"; o] + |Split so -> [SplitOptions.make so] + |Threads t -> ["-e"; string t] + |MinReadLength l -> ["-M"; string l] + |FilterBases b -> ["-B"; b] + |BufferSize b -> ["-b"; b] + |CursorCacheSize c -> ["-c"; c] + |SortingMemoryLimit m -> ["-m"; m] + |ShowProgress -> ["-p"] + |PrintDetails -> ["-x"] + |StdOut -> ["-Z"] + |Force -> ["-f"] + |RowIdAsName -> ["-N"] + |PrintReadNumber -> ["-P"] + |AppendOutput -> ["-A"] + |Version -> ["-V"] + |LogLevel l -> ["-L"; l] + |SkipTechnical -> ["--skip-technical"] + |IncludeTechnical -> ["--include-technical"] + |PacBioTableName t -> ["--table"; t] + |Strict -> ["--strict"] + |CloudLocation c -> ["--location"; c] + |DisableMultiThreading -> ["--disable-multithreading"] + + static member makeCmdWith (m:MountInfo) = function + |OutFile o -> ["-o"; MountInfo.containerPathOf m o] + |OutDirectory o -> ["-O"; MountInfo.containerPathOf m o] + |TempDirectory t -> ["-t"; MountInfo.containerPathOf m t] + |NGCFilePath n -> ["--ngc" ; MountInfo.containerPathOf m n] + |PermissionFilePath p -> ["--perm" ; MountInfo.containerPathOf m p] + |CartPath c -> ["--cart" ; MountInfo.containerPathOf m c] + |OptionFilePath o -> ["option-file"; MountInfo.containerPathOf m o] + |Split so -> [SplitOptions.make so] + |Threads t -> ["-e"; string t] + |MinReadLength l -> ["-M"; string l] + |FilterBases b -> ["-B"; b] + |BufferSize b -> ["-b"; b] + |CursorCacheSize c -> ["-c"; c] + |SortingMemoryLimit m -> ["-m"; m] + |ShowProgress -> ["-p"] + |PrintDetails -> ["-x"] + |StdOut -> ["-Z"] + |Force -> ["-f"] + |RowIdAsName -> ["-N"] + |PrintReadNumber -> ["-P"] + |AppendOutput -> ["-A"] + |Version -> ["-V"] + |LogLevel l -> ["-L"; l] + |SkipTechnical -> ["--skip-technical"] + |IncludeTechnical -> ["--include-technical"] + |PacBioTableName t -> ["--table"; t] + |Strict -> ["--strict"] + |CloudLocation c -> ["--location"; c] + |DisableMultiThreading -> ["--disable-multithreading"] + + + let runFasterQDumpAsync (bcContext:BioContainer.BcContext) (opt:FasterQDumpParams list) (accession:string) = + + let cmds = (opt |> List.map (FasterQDumpParams.makeCmdWith bcContext.Mount)) + let tp = "fasterq-dump"::(cmds |> List.concat)@[accession] + + printfn "Starting process fasterq-dump\r\nparameters:" + cmds |> List.iter (fun op -> printfn "\t%s" (String.concat " " op)) + + async { + let! res = BioContainer.execAsync bcContext tp + return res + } + + let runFasterQDump (bcContext:BioContainer.BcContext) (opt:FasterQDumpParams list) (accession:string) = + runFasterQDumpAsync bcContext opt accession + |> Async.RunSynchronously \ No newline at end of file From b08f307f203eea4c2a84cce10f1a72d05453806b Mon Sep 17 00:00:00 2001 From: kMutagene Date: Mon, 23 Mar 2020 08:30:04 +0100 Subject: [PATCH 07/11] Add DSL for prefetch in SRATools BioContainer API and improve fasterq-dump DSL --- src/BioFSharp.BioContainers/SRAToolkit.fs | 146 +++++++++++++++++++--- 1 file changed, 127 insertions(+), 19 deletions(-) diff --git a/src/BioFSharp.BioContainers/SRAToolkit.fs b/src/BioFSharp.BioContainers/SRAToolkit.fs index d379023a..b32208b6 100644 --- a/src/BioFSharp.BioContainers/SRAToolkit.fs +++ b/src/BioFSharp.BioContainers/SRAToolkit.fs @@ -3,30 +3,120 @@ open BioContainer module SRATools = - //type PrefetchParams = - // |Placeholder +// accessions(s) list of accessions to process - // static member makeCmd = function - // |Placeholder -> [""] + type PrefetchForceOptions = + ///Skip download if the object is found on the output path. + | No + ///Download it even if the object is found on the output path. + | Yes + ///Ignore lock files (stale locks or if it is currently being downloaded: use at your own risk!). + | All - // static member makeCmdWith (m:MountInfo) = function - // |Placeholder -> [""] - + static member make = function + | No -> "no" + | Yes -> "yes" + | All -> "all" + type PrefetchTransportOptions = + ///Use only ascp for file transfer. + | AscpOnly + ///Use only HTTP for file transfer. + | HttpOnly + ///Try ascp first for file transfer, fallback to HTTP. + | TryAscpWithHttpFallback + static member make = function + | AscpOnly -> "ascp" + | HttpOnly -> "http" + | TryAscpWithHttpFallback -> "both" + +//Options: + + type PrefetchParams = + ///specify file type to download. Default: sra + |FileType of string + ///Minimum file size to download in KB (inclusive). + |MinimumFileSize of int + ///Maximum file size to download in KB (exclusive). Default: 20G + |MaximumFileSize of int + ///Force object download one of: no, yes, all. no [default]: skip download if the object if found and complete; yes: download it even if it is found and is complete; all: ignore lock files (stale locks or it is being downloaded by another process: use at your own risk!) + |Force of PrefetchForceOptions + ///Time period in minutes to display download progress (0: no progress), default: 1 + |Progress of int + ///Double-check all refseqs + |CheckAll + ///Write file to FILE when downloading single file + |OutputFile of string + ///Save files to path/ + |OutputDirectory of string + /// to ngc file + |NGCFilePath of string + /// to permission file + |PermissionFilePath of string + ///location in cloud + |CloudLocation of string + /// to cart file + |CartPath of string + ///disable multithreading + |DisableMultiThreading + ///Display the version of the program + |Version + ///Logging level as number or enum string. One of (fatal|sys|int|err|warn|info|debug) or (0-6) Current/default is warn + |LogLevel of string + ///Read more options and parameters from the file. + |OptionFilePath of string - //let runPrefetchAsync (bcContext:BioContainer.BcContext) (opt:PrefetchParams list) = + static member makeCmd = function + |FileType p -> ["--type" ; p] + |MinimumFileSize p -> ["--min_size" ; p |> string] + |MaximumFileSize p -> ["--max_size" ; p |> string] + |Force p -> ["--force" ; p |> PrefetchForceOptions.make] + |Progress p -> ["--progress" ; p |> string] + |CheckAll -> ["--check-all" ; ] + |OutputFile p -> ["--output-file" ; p ] + |OutputDirectory p -> ["--output-directory" ; p ] + |NGCFilePath p -> ["--ngc" ; p ] + |PermissionFilePath p -> ["--perm" ; p ] + |OptionFilePath p -> ["--option-file" ; p ] + |CartPath p -> ["--cart" ; p ] + |CloudLocation p -> ["--location" ; p ] + |DisableMultiThreading -> ["--disable-multithreading" ; ] + |Version -> ["--version" ; ] + |LogLevel p -> ["--log-level" ; p ] - // let cmds = (opt |> List.map (PrefetchParams.makeCmdWith bcContext.Mount)) - // let tp = "prefetch"::(cmds |> List.concat) + + static member makeCmdWith (m:MountInfo) = function + |FileType p -> ["--type" ; p] + |MinimumFileSize p -> ["--min_size" ; p |> string] + |MaximumFileSize p -> ["--max_size" ; p |> string] + |Force p -> ["--force" ; p |> PrefetchForceOptions.make] + |Progress p -> ["--progress" ; p |> string] + |CheckAll -> ["--check-all" ; ] + |OutputFile p -> ["--output-file" ; p |> MountInfo.containerPathOf m] + |OutputDirectory p -> ["--output-directory" ; p |> MountInfo.containerPathOf m] + |NGCFilePath p -> ["--ngc" ; p |> MountInfo.containerPathOf m] + |PermissionFilePath p -> ["--perm" ; p |> MountInfo.containerPathOf m] + |OptionFilePath p -> ["--option-file" ; p |> MountInfo.containerPathOf m] + |CartPath p -> ["--cart" ; p |> MountInfo.containerPathOf m] + |CloudLocation p -> ["--location" ; p ] + |DisableMultiThreading -> ["--disable-multithreading" ; ] + |Version -> ["--version" ; ] + |LogLevel p -> ["--log-level" ; p ] - // printfn "Starting process prefetch\r\nparameters:" - // cmds |> List.iter (fun op -> printfn "\t%s" (String.concat " " op)) - // async { - // let! res = BioContainer.execAsync bcContext tp - // return res - // } + let runPrefetchAsync (bcContext:BioContainer.BcContext) (opt:PrefetchParams list) (accession:string) = + + let cmds = (opt |> List.map (PrefetchParams.makeCmdWith bcContext.Mount)) + let tp = "prefetch"::(cmds |> List.concat)@[accession] + + printfn "Starting process prefetch\r\nparameters:" + cmds |> List.iter (fun op -> printfn "\t%s" (String.concat " " op)) + + async { + let! res = BioContainer.execAsync bcContext tp + return res + } type SplitOptions = ///Split spots into reads @@ -194,7 +284,7 @@ module SRATools = |DisableMultiThreading -> ["--disable-multithreading"] - let runFasterQDumpAsync (bcContext:BioContainer.BcContext) (opt:FasterQDumpParams list) (accession:string) = + let runFasterQDumpOfAccessionAsync (bcContext:BioContainer.BcContext) (opt:FasterQDumpParams list) (accession:string) = let cmds = (opt |> List.map (FasterQDumpParams.makeCmdWith bcContext.Mount)) let tp = "fasterq-dump"::(cmds |> List.concat)@[accession] @@ -207,6 +297,24 @@ module SRATools = return res } - let runFasterQDump (bcContext:BioContainer.BcContext) (opt:FasterQDumpParams list) (accession:string) = - runFasterQDumpAsync bcContext opt accession + let runFasterQDumpOfAccession (bcContext:BioContainer.BcContext) (opt:FasterQDumpParams list) (accession:string) = + runFasterQDumpOfAccessionAsync bcContext opt accession + |> Async.RunSynchronously + + + let runFasterQDumpOfFileAsync (bcContext:BioContainer.BcContext) (opt:FasterQDumpParams list) (sraPath:string) = + + let cmds = (opt |> List.map (FasterQDumpParams.makeCmdWith bcContext.Mount)) + let tp = "fasterq-dump"::(cmds |> List.concat)@[MountInfo.containerPathOf bcContext.Mount sraPath] + + printfn "Starting process fasterq-dump\r\nparameters:" + cmds |> List.iter (fun op -> printfn "\t%s" (String.concat " " op)) + + async { + let! res = BioContainer.execAsync bcContext tp + return res + } + + let runFasterQDumpOfFile (bcContext:BioContainer.BcContext) (opt:FasterQDumpParams list) (accession:string) = + runFasterQDumpOfFileAsync bcContext opt accession |> Async.RunSynchronously \ No newline at end of file From d2cbc0a8691564a487d70d9825867e7eb261d03a Mon Sep 17 00:00:00 2001 From: kMutagene Date: Mon, 23 Mar 2020 08:31:02 +0100 Subject: [PATCH 08/11] Add Full STAR DSL for biocontainer API --- .../BioFSharp.BioContainers.fsproj | 1 + .../BioFSharp.BioContainers.fsx | 48 +- src/BioFSharp.BioContainers/STAR.fs | 1487 +++++++++++++++++ 3 files changed, 1529 insertions(+), 7 deletions(-) create mode 100644 src/BioFSharp.BioContainers/STAR.fs diff --git a/src/BioFSharp.BioContainers/BioFSharp.BioContainers.fsproj b/src/BioFSharp.BioContainers/BioFSharp.BioContainers.fsproj index 7cbe9f1c..ee1602e7 100644 --- a/src/BioFSharp.BioContainers/BioFSharp.BioContainers.fsproj +++ b/src/BioFSharp.BioContainers/BioFSharp.BioContainers.fsproj @@ -39,6 +39,7 @@ + diff --git a/src/BioFSharp.BioContainers/BioFSharp.BioContainers.fsx b/src/BioFSharp.BioContainers/BioFSharp.BioContainers.fsx index 8f66ba69..a1d5ca3e 100644 --- a/src/BioFSharp.BioContainers/BioFSharp.BioContainers.fsx +++ b/src/BioFSharp.BioContainers/BioFSharp.BioContainers.fsx @@ -18,6 +18,8 @@ #load "HMMER.fs" #load "LastAlign.fs" #load "SRAToolkit.fs" +#load "STAR.fs" +#load "FastP.fs" open System.Threading open System.Threading @@ -582,22 +584,54 @@ runLastAlignAsync lastAlignContext alignParams open SRATools let sraImage = Docker.ImageId "quay.io/biocontainers/sra-tools:2.10.3--pl526haddd2b5_0" - + let sraContext = BioContainer.initBcContextWithMountAsync client sraImage @"C:\Users\kevin\Downloads\CsbScaffold-master\MetaIndexing_New\data" |> Async.RunSynchronously let FQDOptions = [ - FasterQDumpParams.OutDirectory @"C:\Users\kevin\Downloads\CsbScaffold-master\MetaIndexing_New\data\lol" - FasterQDumpParams.TempDirectory @"C:\Users\kevin\Downloads\CsbScaffold-master\MetaIndexing_New\data\lol\tmp" - FasterQDumpParams.Split SplitOptions.Split3 + FasterQDumpParams.OutDirectory @"C:\Users\kevin\Downloads\CsbScaffold-master\MetaIndexing_New\data\Testerino" + FasterQDumpParams.TempDirectory @"C:\Users\kevin\Downloads\CsbScaffold-master\MetaIndexing_New\data\Testerino\tmp" + FasterQDumpParams.Split SplitOptions.SplitFiles FasterQDumpParams.PrintDetails FasterQDumpParams.ShowProgress ] - -runFasterQDump sraContext FQDOptions "SRR000001" + +runFasterQDumpOfAccession sraContext FQDOptions "SRR000001" sraContext |> BioContainer.disposeAsync -|> Async.RunSynchronously \ No newline at end of file +|> Async.RunSynchronously + + +open FastP + +let fastPImage = Docker.ImageId "quay.io/biocontainers/fastp:0.20.0--hdbcaa40_0" + + +open STAR + +let STARImage = Docker.ImageId "quay.io/biocontainers/star:2.7.3a--0" + +let starContext = + BioContainer.initBcContextWithMountAsync client STARImage @"C:\Users\kevin\Downloads\CsbScaffold-master\MetaIndexing_New\data" + |> Async.RunSynchronously + +STAR.BasicWorkflows.runBasicGenomeIndexing + 2 + @"C:\Users\kevin\Downloads\CsbScaffold-master\MetaIndexing_New\data\Testerino" + [@"C:\Users\kevin\Downloads\CsbScaffold-master\MetaIndexing_New\data\Chlamydomonas_reinhardtii.Chlamydomonas_reinhardtii_v5.5.dna.toplevel.fa"] + @"C:\Users\kevin\Downloads\CsbScaffold-master\MetaIndexing_New\data\ChlamyGTF.gtf" + starContext + [ + STARParams.GenomeParameters [ + GenomeParams.IndexingOptions[ + GenomeIndexingOptions.SAindexNbases 12 + ] + ] + ] + +starContext +|> BioContainer.disposeAsync +|> Async.RunSynchronously diff --git a/src/BioFSharp.BioContainers/STAR.fs b/src/BioFSharp.BioContainers/STAR.fs new file mode 100644 index 00000000..780c0653 --- /dev/null +++ b/src/BioFSharp.BioContainers/STAR.fs @@ -0,0 +1,1487 @@ +namespace BioFSharp.BioContainers +open BioContainer + +module STAR = + + let inline private handleOptionalSecondParameter (handleFunction1: ('T -> string)) (handleFunction2: ('U -> string)) (parameters: ('T*'U option)) = + let p1,p2 = parameters + match p2 with + |Some v -> + sprintf "%s %s" (handleFunction1 p1) (handleFunction2 v) + |None + -> handleFunction1 p1 + + let inline private handleQuadruples (q: 'A*'B*'C*'D) = + let a,b,c,d = q + sprintf "%s %s %s %s" (string a) (string b) (string c) (string d) + +//### Parameter Files + +//### Variation parameters + +//### Input Files + + +//Run Parameters + + ///type of the STAR run + type RunMode = + ///map reads + |AlignReads + ///generate genome files + |GenomeGenerate + ///input alignments from BAM. Presently only works with --outWigType and --bamRemoveDuplicates. + |InputAlignmentsFromBAM + ///lift-over of GTF files (--sjdbGTFfile) between genome assemblies using chain file(s) from --genomeChainFiles. + |LiftOver + + static member make = function + |AlignReads -> "alignReads" + |GenomeGenerate -> "genomeGenerate" + |InputAlignmentsFromBAM -> "inputAlignmentsFromBAM" + |LiftOver -> "liftOver" + + type RunPermission = + |User_RWX + |All_RWX + + static member make = function + |User_RWX -> "User_RWX" + |All_RWX -> "All_RWX" + + type RunParams = + ///type of the STAR run + |Mode of RunMode + ///number of threads to run STAR + |Threads of int + ///permissions for the directories created at the run-time. + |DirectoryPermissions of RunPermission + ///random number generator seed. + |RNGSeed of int + + static member makeCmd = function + |Mode m -> ["--runMode" ; RunMode.make m] + |Threads t -> ["--runThreadN"; string t] + |DirectoryPermissions p -> ["--runDirPerm"; RunPermission.make p] + |RNGSeed r -> ["--runRNGseed"; string r] + + ///mode of shared memory usage for the genome files. Only used with --runMode alignReads. + type GenomeLoad = + ///load genome into shared and keep it in memory after run + |LoadAndKeep + //load genome into shared but remove it after run + |LoadAndRemove + ///load genome into shared memory and exit, keeping the genome in memory for future runs + |LoadAndExit + ///do not map anything, just remove loaded genome from memory + |Remove + ///do not use shared memory, each job will have its own private copy of the genome + |NoSharedMemory + + static member make = function + |LoadAndKeep -> "LoadAndKeep" + |LoadAndRemove -> "LoadAndRemove" + |LoadAndExit -> "LoadAndExit" + |Remove -> "Remove" + |NoSharedMemory -> "NoSharedMemory" + + ///Genome Indexing Parameters - only used with --runMode genomeGenerate + type GenomeIndexingOptions = + ///=log2(chrBin), where chrBin is the size of the bins for genome storage: each chromosome will occupy an integer number of bins. For a genome with large number of contigs, it is recommended to scale this parameter as min(18, log2[max(GenomeLength/NumberOfReferences,ReadLength)]). + |ChrBinNbits of int + ///length (bases) of the SA pre-indexing string. Typically between 10 and 15. Longer strings will use much more memory, but allow faster searches. For small genomes, the parameter --genomeSAindexNbases must be scaled down to min(14, log2(GenomeLength)/2 - 1). + |SAindexNbases of int + ///suffux array sparsity, i.e. distance between indices: use bigger numbers to decrease needed RAM at the cost of mapping speed reduction + |SAsparseD of int + ///maximum length of the suffixes, has to be longer than read length. -1 = infinite. + |SuffixLengthMax of int + + static member makeCmd = function + //genomeChrBinNbits 18 + |ChrBinNbits i -> ["--genomeChrBinNbits"; string i] + //genomeSAindexNbases 14 + |SAindexNbases i -> ["--genomeSAindexNbases"; string i] + //genomeSAsparseD 1 + |SAsparseD i -> ["--genomeSAsparseD"; string i] + //genomeSuffixLengthMax -1 + |SuffixLengthMax i -> ["--genomeSuffixLengthMax"; string i] + + type GenomeParams = + ///path to the directory where genome files are stored (for --runMode alignReads) or will be generated (for --runMode generateGenome) + |GenomeDirectory of string + ///path(s) to the fasta files with the genome sequences, separated by spaces. These files should be plain text FASTA files, they *cannot* be zipped. Required for the genome generation (--runMode genomeGenerate). Can also be used in the mapping (--runMode alignReads) to add extra (new) sequences to the genome (e.g. spike-ins). + |GenomeFastaFiles of string list + ///chain files for genomic liftover. Only used with --runMode liftOver . + |GenomeChainFiles of string list + ///genome files exact sizes in bytes. Typically, this should not be defined by the user. + |GenomeFileSizes of int list + ///VCF file with consensus SNPs (i.e. alternative allele is the major (AF>0.5) allele) + |GenomeConsensusFile of string + ///mode of shared memory usage for the genome files. Only used with --runMode alignReads. + |Load of GenomeLoad + ///Genome Indexing Parameters - only used with --runMode genomeGenerate + |IndexingOptions of GenomeIndexingOptions list + + static member makeCmd = function + |GenomeDirectory d -> ["--genomeDir"; d] + |GenomeFastaFiles f -> ["--genomeFastaFiles" ; f |> String.concat " " ] + |GenomeChainFiles f -> ["--genomeChainFiles" ; f |> String.concat " "] + |GenomeFileSizes l -> ["--genomeFileSizes" ; l |> List.map string |> String.concat " "] + |GenomeConsensusFile f -> ["--genomeConsensusFile" ; f] + |Load l -> ["--genomeLoad" ; l |> GenomeLoad.make] + |IndexingOptions i -> i |> List.map GenomeIndexingOptions.makeCmd |> List.concat + + static member makeCmdWith (m: MountInfo) = function + |GenomeDirectory d -> ["--genomeDir" ; d |> MountInfo.containerPathOf m ] + |GenomeFastaFiles f -> ["--genomeFastaFiles" ; f |> List.map (MountInfo.containerPathOf m) |> String.concat " " ] + |GenomeChainFiles f -> ["--genomeChainFiles" ; f |> List.map (MountInfo.containerPathOf m) |> String.concat " " ] + |GenomeFileSizes l -> ["--genomeFileSizes" ; l |> List.map string |> List.map (MountInfo.containerPathOf m) |> String.concat " "] + |GenomeConsensusFile f -> ["--genomeConsensusFile" ; f |> MountInfo.containerPathOf m] + |Load l -> ["--genomeLoad" ; l |> GenomeLoad.make] + |IndexingOptions i -> i |> List.map GenomeIndexingOptions.makeCmd |> List.concat + +//### Splice Junctions Database + + ///which files to save when sjdb junctions are inserted on the fly at the mapping step + type SpliceJunctionsDatabaseSaveOptions = + ///only small junction / transcript files + |Basic + ///all files including big Genome, SA and SAindex - this will create a complete genome directory + |All + + static member make = function + |Basic -> "Basic" + |All -> "All" + + type SpliceJunctionsDatabaseParams = + ///path(s) to the files with genomic coordinates (chr start end strand) for the splice junction introns. Multiple files can be supplied wand will be concatenated. + |FileChrStartEnd of string list + ///string: path to the GTF file with annotations + |GTFfile of string + ///prefix for chromosome names in a GTF file (e.g. 'chr' for using ENSMEBL annotations with UCSC genomes) + |GTFchrPrefix of string + /// feature type in GTF file to be used as exons for building transcripts + |GTFfeatureExon of string + ///GTF attribute name for parent transcript ID (default "transcript_id" works for GTF files) + |GTFtagExonParentTranscript of string + ///GTF attribute name for parent gene ID (default "gene_id" works for GTF files) + |GTFtagExonParentGene of string + ///GTF attrbute name for parent gene name + |GTFtagExonParentGeneName of string list + ///GTF attrbute name for parent gene type + |GTFtagExonParentGeneType of string list + ///length of the donor/acceptor sequence on each side of the junctions, ideally = (mate_length - 1) + |Overhang of int + ///extra alignment score for alignmets that cross database junctions + |Score of int + ///which files to save when sjdb junctions are inserted on the fly at the mapping step + |InsertSave of SpliceJunctionsDatabaseSaveOptions + + static member makeCmd = function + |FileChrStartEnd l -> ["--sjdbChrStartEnd" ; l |> String.concat " " ] + |GTFfile f -> ["--sjdbGTFfile" ; f ] + |GTFchrPrefix f -> ["--sjdbGTFchrPrefix" ; f ] + |GTFfeatureExon f -> ["--sjdbGTFfeatureExon" ; f ] + |GTFtagExonParentTranscript f -> ["--sjdbGTFtagExonParentTranscript"; f ] + |GTFtagExonParentGene f -> ["--sjdbGTFtagExonParentGene" ; f ] + |GTFtagExonParentGeneName f -> ["--sjdbGTFtagExonParentGeneName" ; f |> String.concat " " ] + |GTFtagExonParentGeneType f -> ["--sjdbGTFtagExonParentGeneType" ; f |> String.concat " " ] + |Overhang o -> ["--sjdbOverhang" ; string o] + |Score s -> ["--sjdbScore" ; string s] + |InsertSave s -> ["--sjdbInsertSave" ; s |> SpliceJunctionsDatabaseSaveOptions.make ] + + static member makeCmdWith (m: MountInfo) = function + |FileChrStartEnd l -> ["--sjdbChrStartEnd" ; l |> String.concat " " ] + |GTFfile f -> ["--sjdbGTFfile" ; f |> MountInfo.containerPathOf m] + |GTFchrPrefix f -> ["--sjdbGTFchrPrefix" ; f ] + |GTFfeatureExon f -> ["--sjdbGTFfeatureExon" ; f ] + |GTFtagExonParentTranscript f -> ["--sjdbGTFtagExonParentTranscript"; f ] + |GTFtagExonParentGene f -> ["--sjdbGTFtagExonParentGene" ; f ] + |GTFtagExonParentGeneName f -> ["--sjdbGTFtagExonParentGeneName" ; f |> String.concat " " ] + |GTFtagExonParentGeneType f -> ["--sjdbGTFtagExonParentGeneType" ; f |> String.concat " " ] + |Overhang o -> ["--sjdbOverhang" ; string o] + |Score s -> ["--sjdbScore" ; string s] + |InsertSave s -> ["--sjdbInsertSave" ; s |> SpliceJunctionsDatabaseSaveOptions.make ] + +//### Read Parameters + ///format of input read files + type ReadFilesType = + ///FASTA or FASTQ + |FastX + ///SAM or BAM single-end reads; for BAM use --readFilesCommand samtools view + |SAMSingleEnd + ///SAM or BAM paired-end reads; for BAM use --readFilesCommand samtools view + |SAMPairedEnd + + static member make = function + |FastX -> "Fastx" + |SAMSingleEnd -> "SAM SE" + |SAMPairedEnd -> "SAM PE" + + ///lengths of names,sequences,qualities for both mates are the same / not the same. NotEqual is safe in all situations. + type MatesLengths = + ///lengths of names,sequences,qualities for both mates are the same + |Equal + ///lengths of names,sequences,qualities for both mates are not the same. NotEqual is safe in all situations. + |NotEqual + + static member make = function + |Equal -> "Equal" + |NotEqual -> "NotEqual" + + ///clipping options from either end of the mates + type MateClippingOptions = + ///number(s) of bases to clip from 3p of each mate. If one value is given, it will be assumed the same for both mates. + |Bases3p of int * int option + ///number(s) of bases to clip from 5p of each mate. If one value is given, it will be assumed the same for both mates. + |Bases5p of int * int option + ///adapter sequences to clip from 3p of each mate. If one value is given, it will be assumed the same for both mates. + |AdapterSeq3p of string * string option + ///max proportion of mismatches for 3p adpater clipping for each mate. If one value is given, it will be assumed the same for both mates. + |AdapterMisMatchPortion3p of float * float option + ///number of bases to clip from 3p of each mate after the adapter clipping. If one value is given, it will be assumed the same for both mates. + |BasesAfterAdapter3p of int * int option + + static member makeCmd = function + |Bases3p (p1,p2) -> ["--clip3pNbases" ; (p1,p2) |> handleOptionalSecondParameter string string] + |Bases5p (p1,p2) -> ["--clip5pNbases" ; (p1,p2) |> handleOptionalSecondParameter string string] + |AdapterSeq3p (p1,p2) -> ["--clip3pAdapterSeq" ; (p1,p2) |> handleOptionalSecondParameter string string] + |AdapterMisMatchPortion3p (p1,p2) -> ["--clip3pAdapterMMp" ; (p1,p2) |> handleOptionalSecondParameter string string] + |BasesAfterAdapter3p (p1,p2) -> ["--clip3pAfterAdapterNbases"; (p1,p2) |> handleOptionalSecondParameter string string] + + type ReadParams = + ///format of input read files + |InputFormat of ReadFilesType + ///paths to files that contain input read1 (and, if needed, read2) + |FilesIn of string * string option + ///prefix for the read files names, i.e. it will be added in front of the strings in --readFilesIn + |FilesPrefix of string + ///command line to execute for each of the input file. This command should generate FASTA or FASTQ text and send it to stdout For example: zcat - to uncompress .gz files, bzcat - to uncompress .bz2 files, etc. + |FilesCommand of string list + ///number of reads to map from the beginning of the file + |MapNumber of int + ///Equal/NotEqual - lengths of names,sequences,qualities for both mates are the same / not the same. NotEqual is safe in all situations. + |MatesLengthsIn of MatesLengths + ///character(s) separating the part of the read names that will be trimmed in output (read name after space is always trimmed) + |NameSeparator of string + ///number to be subtracted from the ASCII code to get Phred quality score + |QualityScoreBase of int + ///clipping options from either end of the mates + |MateClipping of MateClippingOptions list + + static member makeCmd = function + |MateClipping m -> m |> List.map MateClippingOptions.makeCmd |> List.concat + |NameSeparator s -> ["--readNameSeparator" ; s] + |FilesPrefix p -> ["--readFilesPrefix" ; p] + |InputFormat f -> ["--readFilesType" ; f |> ReadFilesType.make] + |FilesIn (f1,f2) -> ["--readFilesIn" ; (f1,f2) |> handleOptionalSecondParameter string string] + |FilesCommand c -> ["--readFilesCommand" ; c |> String.concat " "] + |MapNumber n -> ["--readMapNumber" ; n |> string] + |MatesLengthsIn m -> ["--readMatesLengthsIn" ; m |> MatesLengths.make] + |QualityScoreBase b -> ["--readQualityScoreBase"; b |> string] + + static member makeCmdWith (m:MountInfo) = function + |MateClipping m -> m |> List.map MateClippingOptions.makeCmd |> List.concat + |NameSeparator s -> ["--readNameSeparator" ; s] + |FilesPrefix p -> ["--readFilesPrefix" ; p] + |InputFormat f -> ["--readFilesType" ; f |> ReadFilesType.make] + |FilesIn (f1,f2) -> ["--readFilesIn" ; (f1,f2) |> handleOptionalSecondParameter ((MountInfo.containerPathOf m) >> string) ((MountInfo.containerPathOf m) >> string)] + |FilesCommand c -> ["--readFilesCommand" ; c |> String.concat " "] + |MapNumber n -> ["--readMapNumber" ; n |> string] + |MatesLengthsIn m -> ["--readMatesLengthsIn" ; m |> MatesLengths.make] + |QualityScoreBase b -> ["--readQualityScoreBase"; b |> string] +//### Limits + + type LimitParams = + ///maximum available RAM (bytes) for genome generation + |GenomeGenerateRAM of int + ///max available buffers size (bytes) for input/output, per thread + |IObufferSize of int + ///max number of junctions for one read (including all multi-mappers) + |OutSAMoneReadBytes of int + ///max size of the SAM record (bytes) for one read. Recommended value: >(2*(LengthMate1+LengthMate2+100)*outFilterMultimapNmax + |OutSJoneRead of int + ///max number of collapsed junctions + |OutSJcollapsed of int + ///maximum available RAM (bytes) for sorting BAM. If =0, it will be set to the genome index size. 0 value can only be used with --genomeLoad NoSharedMemory option. + |BAMsortRAM of int + ///maximum number of junction to be inserted to the genome on the fly at the mapping stage, including those from annotations and those detected in the 1st step of the 2-pass run + |SjdbInsertNsj of int + ///soft limit on the number of reads + |NreadsSoft of int + + static member makeCmd = function + |GenomeGenerateRAM i -> ["--limitGenomeGenerateRAM" ; i |> string] + |IObufferSize i -> ["--limitIObufferSize" ; i |> string] + |OutSAMoneReadBytes i -> ["--limitOutSAMoneReadBytes"; i |> string] + |OutSJoneRead i -> ["--limitOutSJoneRead" ; i |> string] + |OutSJcollapsed i -> ["--limitOutSJcollapsed" ; i |> string] + |BAMsortRAM i -> ["--limitBAMsortRAM" ; i |> string] + |SjdbInsertNsj i -> ["--limitSjdbInsertNsj" ; i |> string] + |NreadsSoft i -> ["--limitNreadsSoft" ; i |> string] + + +//### Output: general + + type OutputSTDOptions = + ///log messages + |Log + ///alignments in SAM format (which normally are output to Aligned.out.sam file), normal standard output will go into Log.std.out + |SAM + ///alignments in BAM format, unsorted. Requires --outSAMtype BAM Unsorted + |BAMUnsorted + ///alignments in BAM format, unsorted. Requires --outSAMtype BAM SortedByCoordinate + |BAMSortedByCoordinate + ///alignments to transcriptome in BAM format, unsorted. Requires --quantMode TranscriptomeSAM + |BAMQuant + + static member make = function + |Log -> "Log" + |SAM -> "SAM" + |BAMUnsorted -> "BAM_Unsorted" + |BAMSortedByCoordinate -> "BAM_SortedByCoordinate" + |BAMQuant -> "BAM_Quant" + + type AlignmentOrder = + ///quasi-random order used before 2.5.0 + |Old24 + ///random order of alignments for each multi-mapper. Read mates (pairs) are always adjacent, all alignment for each read stay together. This option will become default in the future releases. + |Random + + static member make = function + |Old24 -> "Old_2.4" + |Random -> "Random" + + type SAMSortingOptions = + ///standard unsorted + |Unsorted + ///sorted by coordinate. This option will allocate extra memory for sorting which can be specified by --limitBAMsortRAM. + |SortedByCoordinate + + static member make = function + |Unsorted -> "Unsorted" + |SortedByCoordinate -> "SortedByCoordinate" + + ///type of SAM/BAM output + type OutputTypeOptions = + ///no SAM/BAM output + |NoOutput + ///output BAM + |BAM of SAMSortingOptions + ///output SAM + |SAM of SAMSortingOptions + + static member make = function + |NoOutput -> sprintf "None" + |BAM s -> sprintf "BAM %s" (SAMSortingOptions.make s) + |SAM s -> sprintf "SAM %s" (SAMSortingOptions.make s) + + ///mode of SAM output + type OutputModeOptions = + ///no SAM output + | NoOutput + ///full SAM output + | Full + ///full SAM but without quality scores + | NoQS + + static member make = function + |NoOutput -> "NoOutput" + |Full -> "Full" + |NoQS -> "NoQS" + + ///Cufflinks-like strand field flag + type StrandFieldOptions = + |NotUsed + ///strand derived from the intron motif. Reads with inconsistent and/or non-canonical introns are filtered out. + |IntronMotif + + static member make = function + |NotUsed -> "None" + |IntronMotif -> "intronMotif" + + ///desired SAM attributes, in the order desired for the output SAM + type AttributeOptions = + ///NH HI AS nM NM MD jM jI XS MC ch ... any combination in any order + |Custom of string list + ///no attributes + |NoAttributes + ///NH HI AS nM + |Standard + ///NH HI AS nM NM MD jM jI MC ch + |All + ///variant allele + |VA + ///genomic coordiante of the variant overlapped by the read + |VG + ///0/1 - alignment does not pass / passes WASP filtering. Requires --waspOutputMode SAMtag + |VW + ///CR CY UR UY ... sequences and quality scores of cell barcodes and UMIs for the solo* demultiplexing + /// + ///CB UB ... error-corrected cell barcodes and UMIs for solo* demultiplexing. Requires --outSAMtype BAM SortedByCoordinate. + |SoloCustom of string list + ///assessment of CB and UMI + |SM + ///sequence of the entire barcode (CB,UMI,adapter...) + |SS + ///quality of the entire barcode + |SQ + ///alignment block read/genomic coordinates + |RB + ///read coordinate of the variant + |VR + + static member make = function + |Custom c -> c |> String.concat " " + |SoloCustom c -> c |> String.concat " " + |NoAttributes -> "None" + |Standard -> "Standard" + |All -> "All" + |VA -> "vA" + |VG -> "vG" + |VW -> "vW" + |SM -> "sM" + |SS -> "sS" + |SQ -> "sQ" + |RB -> "rB" + |VR -> "vR" + + ///output of unmapped reads in the SAM format + type UnmappedReadOptions = + ///no output + | Discard + ///output unmapped reads within the main SAM file (i.e. Aligned.out.sam) + | Within + ///record unmapped mate for each alignment, and, in case of unsorted output, keep it adjacent to its mapped mate. Only affects multi-mapping reads. + | WithinKeepPairs + + static member make = function + |Discard -> "None" + |Within -> "Within" + |WithinKeepPairs -> "Within KeepPairs" + + ///type of sorting for the SAM output + type OutputSortingOptions = + ///one mate after the other for all paired alignments + |Paired + ///one mate after the other for all paired alignments, the order is kept the same as in the input FASTQ files + |PairedKeepInputOrder + + static member make = function + |Paired -> "Paired" + |PairedKeepInputOrder -> "PairedKeepInputOrder" + + ///which alignments are considered primary - all others will be marked with 0x100 bit in the FLAG + type PrimaryFlagOptions = + ///only one alignment with the best score is primary + |OneBestScore + ///all alignments with the best score are primary + |AllBestScore + + static member make = function + |OneBestScore -> "OneBestScore" + |AllBestScore -> "AllBestScore" + + ///read ID record type + type ReadIDOptions = + ///first word (until space) from the FASTx read ID line, removing /1,/2 from the end + |Standard + ///read number (index) in the FASTx file + |Number + + static member make = function + |Standard -> "Standard" + |Number -> "Number" + + ///filter the output into main SAM/BAM files + type OutputFilterOptions = + ///only keep the reads for which all alignments are to the extra reference sequences added with --genomeFastaFiles at the mapping stage. + |KeepOnlyAddedReferences + ///keep all alignments to the extra reference sequences added with --genomeFastaFiles at the mapping stage. + |KeepAllAddedReferences + + static member make = function + |KeepOnlyAddedReferences -> "KeepOnlyAddedReferences" + |KeepAllAddedReferences -> "KeepAllAddedReferences" + + type OutputFormattingOptions = + ///mode of SAM output + |OutputMode of OutputModeOptions + ///Cufflinks-like strand field flag + |StrandField of StrandFieldOptions + ///desired SAM attributes, in the order desired for the output SAM + |Attributes of AttributeOptions list + ///start value for the IH attribute. 0 may be required by some downstream software, such as Cufflinks or StringTie. + |AttributeIHSTart of int + ///output of unmapped reads in the SAM format + |UnmappedReads of UnmappedReadOptions + ///type of sorting for the SAM output + |Sorting of OutputSortingOptions + ///which alignments are considered primary - all others will be marked with 0x100 bit in the FLAG + |PrimaryFlag of PrimaryFlagOptions + ///read ID record type + |ReadID of ReadIDOptions + ///0 to 255: the MAPQ value for unique mappers + |MAPQUinque of int + ///0 to 65535: sam FLAG will be bitwise OR'd with this value, i.e. FLAG=FLAG | outSAMflagOR. This is applied after all flags have been set by STAR, and after outSAMflagAND. Can be used to set specific bits that are not set otherwise. + |FlagOR of int + ///0 to 65535: sam FLAG will be bitwise AND'd with this value, i.e. FLAG=FLAG & outSAMflagOR. This is applied after all flags have been set by STAR, but before outSAMflagOR. Can be used to unset specific bits that are not set otherwise. + |FlagAND of int + ///SAM/BAM read group line. The first word contains the read group identifier and must start with "ID:", e.g. --outSAMattrRGline ID:xxx CN:yy "DS:z z z".xxx will be added as RG tag to each output alignment. Any spaces in the tag values have to be double quoted. Comma separated RG lines correspons to different (comma separated) input files in --readFilesIn. Commas have to be surrounded by spaces, e.g. --outSAMattrRGline ID:xxx , ID:zzz "DS:z z" , ID:yyy DS:yyyy + |ReadGroupLine of string + ///@HD (header) line of the SAM header + |HeaderLine of string + ///extra @PG (software) line of the SAM header (in addition to STAR) + |PGLine of string + ///path to the file with @CO (comment) lines of the SAM header + |CommentLineFile of string + ///filter the output into main SAM/BAM files + |Filter of OutputFilterOptions + ///max number of multiple alignments for a read that will be output to the SAM/BAM files. + |MaxMultipleAlignments of int + ///calculation method for the TLEN field in the SAM/BAM files. 1 ... leftmost base of the (+)strand mate to rightmost base of the (-)mate. (+)sign for the (+)strand mate 2 ... leftmost base of any mate to rightmost base of any mate. (+)sign for the mate with the leftmost base. This is different from 1 for overlapping mates with protruding ends + |TLenCalculation of int + + static member makeCmd = function + |OutputMode m ->["--outSAMmode" ; m |> OutputModeOptions.make] + |StrandField s ->["--outSAMstrandField" ; s |> StrandFieldOptions.make] + |Attributes a ->["--outSAMattributes" ; a |> List.map AttributeOptions.make |> String.concat " "] + |AttributeIHSTart s ->["--outSAMattrIHstart" ; s |> string] + |UnmappedReads u ->["--outSAMunmapped" ; u |> UnmappedReadOptions.make] + |Sorting s ->["--outSAMorder" ; s |> OutputSortingOptions.make] + |PrimaryFlag p ->["--outSAMprimaryFlag" ; p |> PrimaryFlagOptions.make] + |ReadID r ->["--outSAMreadID" ; r |> ReadIDOptions.make] + |MAPQUinque i ->["--outSAMmapqUnique" ; i |> string] + |FlagOR i ->["--outSAMflagOR" ; i |> string] + |FlagAND i ->["--outSAMflagAND" ; i |> string] + |ReadGroupLine l ->["--outSAMattrRGline" ; l] + |HeaderLine l ->["--outSAMheaderHD" ; l] + |PGLine l ->["--outSAMheaderPG" ; l] + |CommentLineFile p ->["--outSAMheaderCommentFile" ; p] + |Filter f ->["--outSAMfilter" ; f |> OutputFilterOptions.make] + |MaxMultipleAlignments i ->["--outSAMmultNmax" ; i |> string] + |TLenCalculation i ->["--outSAMtlen" ; i |> string] + + static member makeCmdWith (m:MountInfo) = function + |OutputMode m ->["--outSAMmode" ; m |> OutputModeOptions.make] + |StrandField s ->["--outSAMstrandField" ; s |> StrandFieldOptions.make] + |Attributes a ->["--outSAMattributes" ; a |> List.map AttributeOptions.make |> String.concat " "] + |AttributeIHSTart s ->["--outSAMattrIHstart" ; s |> string] + |UnmappedReads u ->["--outSAMunmapped" ; u |> UnmappedReadOptions.make] + |Sorting s ->["--outSAMorder" ; s |> OutputSortingOptions.make] + |PrimaryFlag p ->["--outSAMprimaryFlag" ; p |> PrimaryFlagOptions.make] + |ReadID r ->["--outSAMreadID" ; r |> ReadIDOptions.make] + |MAPQUinque i ->["--outSAMmapqUnique" ; i |> string] + |FlagOR i ->["--outSAMflagOR" ; i |> string] + |FlagAND i ->["--outSAMflagAND" ; i |> string] + |ReadGroupLine l ->["--outSAMattrRGline" ; l] + |HeaderLine l ->["--outSAMheaderHD" ; l] + |PGLine l ->["--outSAMheaderPG" ; l] + |CommentLineFile p ->["--outSAMheaderCommentFile" ; p |> MountInfo.containerPathOf m] + |Filter f ->["--outSAMfilter" ; f |> OutputFilterOptions.make] + |MaxMultipleAlignments i ->["--outSAMmultNmax" ; i |> string] + |TLenCalculation i ->["--outSAMtlen" ; i |> string] + + ///mark duplicates in the BAM file, for now only works with (i) sorted BAM fed with inputBAMfile, and (ii) for paired-end alignments only + type RemoveDuplicatesTypeOptions = + ///no duplicate removal/marking + |NoRemoval + ///mark all multimappers, and duplicate unique mappers. The coordinates, FLAG, CIGAR must be identical + |UniqueIdentical + ///mark duplicate unique mappers but not multimappers + |UniqueIdenticalNotMulti + + static member make = function + |NoRemoval -> "-" + |UniqueIdentical -> "UniqueIdentical" + |UniqueIdenticalNotMulti -> "UniqueIdenticalNotMulti" + + type BAMHandlingOptions = + ///BAM compression level, -1=default compression (6?), 0=no compression, 10=maximum compression + |Compression of int + ///number of threads for BAM sorting. 0 will default to min(6,--runThreadN). + |SortingThreadNumber of int + ///number of genome bins fo coordinate-sorting + |SortingBinsNumber of int + ///mark duplicates in the BAM file, for now only works with (i) sorted BAM fed with inputBAMfile, and (ii) for paired-end alignments only + |RemoveDuplicatesType of RemoveDuplicatesTypeOptions + ///number of bases from the 5' of mate 2 to use in collapsing (e.g. for RAMPAGE) + |DuplicatesMate2basesN of int + + static member makeCmd = function + |Compression i -> ["outBAMcompression" ; i |> string] + |SortingThreadNumber i -> ["outBAMsortingThreadN" ; i |> string] + |SortingBinsNumber i -> ["outBAMsortingBinsN" ; i |> string] + |RemoveDuplicatesType r -> ["bamRemoveDuplicatesType" ; r |> RemoveDuplicatesTypeOptions.make] + |DuplicatesMate2basesN i -> ["bamRemoveDuplicatesMate2basesN"; i |> string] + + type OutputParams = + ///type of SAM/BAM output + |Type of OutputTypeOptions + ///output files name prefix (including full or relative path). Can only be defined on the command line. + |FileNamePrefix of string + ///path to a directory that will be used as temporary by STAR. All contents of this directory will be removed! the temp directory will default to outFileNamePrefix_STARtmp + |TmpDir of string + ///whether to keep the temporary files after STAR runs is finished + |TmpKeep of bool (*true -> All false -> None*) + ///which output will be directed to stdout (standard out) + |Std of OutputSTDOptions + ///output of unmapped and partially mapped (i.e. mapped only one mate of a paired end read) reads in separate file(s). either no output or output in separate fasta/fastq files, Unmapped.out.mate1/2 + |KeepUnmappedReads of bool (*true -> Fastx false -> None*) + ///int: add this number to the quality score (e.g. to convert from Illumina to Sanger, use -31) + |QSconversionAdd of int + ///string: order of multimapping alignments in the output files + |MultimapperOrder of AlignmentOrder + ///various SAM/BAM formatting options + |Formatting of OutputFormattingOptions list + ///various BAM specific options + |BAMHandling of BAMHandlingOptions list + + static member makeCmd = function + |FileNamePrefix p -> ["--outFileNamePrefix" ; p] + |TmpDir p -> ["--outTmpDir" ; p] + |TmpKeep b -> ["--outTmpKeep" ; (if b then "All" else "None")] + |Std s -> ["--outStd" ; s |> OutputSTDOptions.make] + |KeepUnmappedReads b -> ["--outReadsUnmapped" ; (if b then "Fastx" else "None")] + |QSconversionAdd i -> ["--outQSconversionAdd" ; i |> string] + |MultimapperOrder m -> ["--outMultimapperOrder" ; m |> AlignmentOrder.make] + |Type s -> ["--outSAMtype" ; s |> OutputTypeOptions.make] + |Formatting f -> f |> List.map OutputFormattingOptions.makeCmd |> List.concat + |BAMHandling f -> f |> List.map BAMHandlingOptions.makeCmd |> List.concat + + static member makeCmdWith (m:MountInfo) = function + |FileNamePrefix p -> ["--outFileNamePrefix" ; p] + |TmpDir p -> ["--outTmpDir" ; p |> MountInfo.containerPathOf m] + |TmpKeep b -> ["--outTmpKeep" ; (if b then "All" else "None")] + |Std s -> ["--outStd" ; s |> OutputSTDOptions.make] + |KeepUnmappedReads b -> ["--outReadsUnmapped" ; (if b then "Fastx" else "None")] + |QSconversionAdd i -> ["--outQSconversionAdd" ; i |> string] + |MultimapperOrder m -> ["--outMultimapperOrder" ; m |> AlignmentOrder.make] + |Type s -> ["--outSAMtype" ; s |> OutputTypeOptions.make] + |Formatting f -> f |> List.map (OutputFormattingOptions.makeCmdWith m) |> List.concat + |BAMHandling f -> f |> List.map BAMHandlingOptions.makeCmd |> List.concat + + type WiggleSignal = + ///Do not specify Wiggle signal + |All + ///signal from only 5' of the 1st read, useful for CAGE/RAMPAGE etc + |Read1_5p + ///signal from only 2nd read + |Read2 + + static member make = function + |All + |Read1_5p -> "read1_5p" + |Read2 -> "read2" + + ///type of signal output, e.g. "bedGraph" OR "bedGraph read1_5p". Requires sorted BAM: --outSAMtype BAM SortedByCoordinate . + type WiggleTypeOptions = + ///no signal output + |NoSignal + ///bedGraph format + |BedGraph of WiggleSignal + ///wiggle format + |Wiggle of WiggleSignal + + static member make = function + |NoSignal -> "None" + |BedGraph w -> match w with | All -> "bedGraph" | Read1_5p | Read2 -> sprintf "bedGraph %s" (w |> WiggleSignal.make) + |Wiggle w -> match w with | All -> "wiggle" | Read1_5p | Read2 -> sprintf "wiggle %s" (w |> WiggleSignal.make) + + type WiggleStrandOptions = + ///separate strands, str1 and str2 + | Stranded + ///collapsed strands + | Unstranded + + static member make = function + | Stranded -> "Stranded" + | Unstranded -> "Unstranded" + + type WiggleNormalizationOptions = + ///no normalization, "raw" counts + |NoNorm + ///reads per million of mapped reads + |RPM + + static member make = function + |NoNorm -> "NoNorm" + |RPM -> "RPM" + + type OutputWiggleParams = + ///type of signal output, e.g. "bedGraph" OR "bedGraph read1_5p". Requires sorted BAM: --outSAMtype BAM SortedByCoordinate . + |WiggleType of WiggleTypeOptions + ///strandedness of wiggle/bedGraph output + |WiggleStrand of WiggleStrandOptions + ///prefix matching reference names to include in the output wiggle file, e.g. "chr", default "-" - include all references + |ReferencesPrefix of string + ///type of normalization for the signal + |Normalization of WiggleNormalizationOptions + + static member makeCmd = function + |WiggleType w -> ["--outWigType" ; w |> WiggleTypeOptions.make] + |WiggleStrand w -> ["--outWigStrand" ; w |> WiggleStrandOptions.make] + |ReferencesPrefix w -> ["--outWigReferencesPrefix" ; w ] + |Normalization w -> ["--outWigNorm" ; w |> WiggleNormalizationOptions.make] + + type OutputFilterTypeOptions = + ///standard filtering using only current alignment + | Normal + ///BySJout ... keep only those reads that contain junctions that passed filtering into SJ.out.tab + | BySJout + + static member make = function + | Normal -> "Normal" + | BySJout -> "BySJout" + + ///filter alignment using their motifs + type OutputFilterIntronMotifsOptions = + ///no filtering + |NoFilter + ///filter out alignments that contain non-canonical junctions + |RemoveNoncanonical + ///filter out alignments that contain non-canonical unannotated junctions when using annotated splice junctions database. The annotated non-canonical junctions will be kept. + |RemoveNoncanonicalUnannotated + + static member make = function + |NoFilter -> "None" + |RemoveNoncanonical -> "RemoveNoncanonical" + |RemoveNoncanonicalUnannotated -> "RemoveNoncanonicalUnannotated" + + ///which reads to consider for collapsed splice junctions output + type SpliceJunctionsFilterReadOptions = + ///all reads, unique- and multi-mappers + |All + ///Unique: uniquely mapping reads only + |Unique + + static member make = function + |All -> "All" + |Unique -> "Unique" + + type OutputFilteringSpliceJunctionsOptions = + ///which reads to consider for collapsed splice junctions output + |FilterRead of SpliceJunctionsFilterReadOptions + ///minimum overhang length for splice junctions on both sides for: (1) non-canonical motifs, (2) GT/AG and CT/AC motif, (3) GC/AG and CT/GC motif, (4) AT/AC and GT/AT motif. -1 means no output for that motif does not apply to annotated junctions + |OverhangMin of (int*int*int*int) + ///minimum uniquely mapping read count per junction for: (1) non-canonical motifs, (2) GT/AG and CT/AC motif, (3) GC/AG and CT/GC motif, (4) AT/AC and GT/AT motif. -1 means no output for that motif Junctions are output if one of outSJfilterCountUniqueMin OR outSJfilterCountTotalMin conditions are satisfied does not apply to annotated junctions + |CountUniqueMin of (int*int*int*int) + ///minimum total (multi-mapping+unique) read count per junction for: (1) non-canonical motifs, (2) GT/AG and CT/AC motif, (3) GC/AG and CT/GC motif, (4) AT/AC and GT/AT motif. -1 means no output for that motif Junctions are output if one of outSJfilterCountUniqueMin OR outSJfilterCountTotalMin conditions are satisfied does not apply to annotated junctions + |CountTotalMin of (int*int*int*int) + ///minimum allowed distance to other junctions' donor/acceptor does not apply to annotated junctions + |DistToOtherSJmin of (int*int*int*int) + ///maximum gap allowed for junctions supported by 1,2,3,,,N reads i.e. by default junctions supported by 1 read can have gaps <=50000b, by 2 reads: <=100000b, by 3 reads: <=200000. by >=4 reads any gap <=alignIntronMax does not apply to annotated junctions + |IntronMaxVsReadN of int list + + static member makeCmd = function + |FilterRead f -> ["--outSJfilterReads" ; f |> SpliceJunctionsFilterReadOptions.make] + |OverhangMin f -> ["--outSJfilterOverhangMin" ; f |> handleQuadruples ] + |CountUniqueMin f -> ["--outSJfilterCountUniqueMin" ; f |> handleQuadruples ] + |CountTotalMin f -> ["--outSJfilterCountTotalMin" ; f |> handleQuadruples ] + |DistToOtherSJmin f -> ["--outSJfilterDistToOtherSJmin" ; f |> handleQuadruples ] + |IntronMaxVsReadN f -> ["--outSJfilterIntronMaxVsReadN" ; f |> List.map string |> String.concat " "] + + type OutputFilteringParams = + ///type of filtering + |FilterType of OutputFilterTypeOptions + ///the score range below the maximum score for multimapping alignments + |MultimapScoreRange of int + ///maximum number of loci the read is allowed to map to. Alignments (all of them) will be output only if the read maps to no more loci than this value. Otherwise no alignments will be output, and the read will be counted as "mapped to too many loci" in the Log.final.out . + |MultimapNmax of int + ///alignment will be output only if it has no more mismatches than this value. + |MismatchNmax of int + ///alignment will be output only if its ratio of mismatches to *mapped* length is less than or equal to this value. + |MismatchNoverLmax of float + ///alignment will be output only if its ratio of mismatches to *read* length is less than or equal to this value. + |MismatchNoverReadLmax of float + ///alignment will be output only if its score is higher than or equal to this value. + |ScoreMin of int + ///same as outFilterScoreMin, but normalized to read length (sum of mates' lengths for paired-end reads) + |ScoreMinOverLread of float + ///alignment will be output only if the number of matched bases is higher than or equal to this value. + |MatchNmin of int + ///same as outFilterMatchNmin, but normalized to the read length (sum of mates' lengths for paired-end reads). + |MatchNminOverLread of float + ///filter alignment using their motifs + |IntronMotifs of OutputFilterIntronMotifsOptions + ///filter alignments: remove alignments that have junctions with inconsistent strands or no filtering + |RemoveInconsistentIntronStrands of bool //(true -> RemoveInconsistentStrands false -> None) + ///various splice junction filtering options + |SpliceJunctionsFiltering of OutputFilteringSpliceJunctionsOptions list + + static member makeCmd = function + |FilterType f -> ["--outFilterType" ; f |> OutputFilterTypeOptions.make ] + |MultimapScoreRange i -> ["--outFilterMultimapScoreRange" ; i |> string] + |MultimapNmax i -> ["--outFilterMultimapNmax" ; i |> string] + |MismatchNmax i -> ["--outFilterMismatchNmax" ; i |> string] + |MismatchNoverLmax f -> ["--outFilterMismatchNoverLmax" ; f |> string] + |MismatchNoverReadLmax f -> ["--outFilterMismatchNoverReadLmax" ; f |> string] + |ScoreMin i -> ["--outFilterScoreMin" ; i |> string] + |ScoreMinOverLread f -> ["--outFilterScoreMinOverLread" ; f |> string] + |MatchNmin i -> ["--outFilterMatchNmin" ; i |> string] + |MatchNminOverLread f -> ["--outFilterMatchNminOverLread" ; f |> string] + |IntronMotifs m -> ["--outFilterIntronMotifs" ; m |> OutputFilterIntronMotifsOptions.make] + |RemoveInconsistentIntronStrands b -> ["--outFilterIntronStrands" ; if b then "RemoveInconsistentStrands" else "None"] + |SpliceJunctionsFiltering s -> s |> List.map OutputFilteringSpliceJunctionsOptions.makeCmd |> List.concat + type AlignmentScoringOptions = + ///splice junction penalty (independent on intron motif) + |Gap of int + ///non-canonical junction penalty (in addition to scoreGap) + |GapNoncan of int + ///GC/AG and CT/GC junction penalty (in addition to scoreGap) + |GapGCAG of int + ///AT/AC and GT/AT junction penalty (in addition to scoreGap) + |GapATAC of int + ///extra score logarithmically scaled with genomic length of the alignment: scoreGenomicLengthLog2scale*log2(genomicLength) + |GenomicLengthLog2scal of int + ///deletion open penalty + |DelOpen of int + ///deletion extension penalty per base (in addition to scoreDelOpen) + |DelBase of int + ///insertion open penalty + |InsOpen of int + ///insertion extension penalty per base (in addition to scoreInsOpen) + |InsBase of int + ///maximum score reduction while searching for SJ boundaries inthe stitching step + |StitchSJshift of int + + static member makeCmd = function + |Gap i -> ["--scoreGap" ; i |> string ] + |GapNoncan i -> ["--scoreGapNoncan" ; i |> string ] + |GapGCAG i -> ["--scoreGapGCAG" ; i |> string ] + |GapATAC i -> ["--scoreGapATAC" ; i |> string ] + |GenomicLengthLog2scal f -> ["--scoreGenomicLengthLog2scale" ; f |> string ] + |DelOpen i -> ["--scoreDelOpen" ; i |> string ] + |DelBase i -> ["--scoreDelBase" ; i |> string ] + |InsOpen i -> ["--scoreInsOpen" ; i |> string ] + |InsBase i -> ["--scoreInsBase" ; i |> string ] + |StitchSJshift i -> ["--scoreStitchSJshift" ; i |> string ] + + type AlignmentSeedOptions = + /// defines the search start point through the read - the read is split into pieces no longer than this value + |SearchStartLmax of int + /// seedSearchStartLmax normalized to read length (sum of mates' lengths for paired-end reads) + |SearchStartLmaxOverLread of float + /// defines the maximum length of the seeds, if =0 max seed lengthis infinite + |SearchLmax of int + /// only pieces that map fewer than this value are utilized in the stitching procedure + |MultimapNmax of int + /// max number of seeds per read + |PerReadNmax of int + /// max number of seeds per window + |PerWindowNmax of int + /// max number of one seed loci per window + |NoneLociPerWindow of int + /// min length of the seed sequences split by Ns or mate gap + |SplitMin of int + + static member makeCmd = function + |SearchStartLmax i -> ["--seedSearchStartLmax" ; i |> string] + |SearchStartLmaxOverLread f -> ["--seedSearchStartLmaxOverLread"; f |> string] + |SearchLmax i -> ["--seedSearchLmax" ; i |> string] + |MultimapNmax i -> ["--seedMultimapNmax" ; i |> string] + |PerReadNmax i -> ["--seedPerReadNmax" ; i |> string] + |PerWindowNmax i -> ["--seedPerWindowNmax" ; i |> string] + |NoneLociPerWindow i -> ["--seedNoneLociPerWindow" ; i |> string] + |SplitMin i -> ["--seedSplitMin" ; i |> string] + + ///type of read ends alignment + type AlignmentEndsTypeOptions = + ///standard local alignment with soft-clipping allowed + |Local + ///force end-to-end read alignment, do not soft-clip + |EndToEnd + ///fully extend only the 5p of the read1, all other ends: local alignment + |Extend5pOfRead1 + ///fully extend only the 5p of the both read1 and read2, all other ends: local alignment + |Extend5pOfReads12 + + static member make = function + |Local -> "Local" + |EndToEnd -> "EndToEnd" + |Extend5pOfRead1 -> "Extend5pOfRead1" + |Extend5pOfReads12 -> "Extend5pOfReads12" + + ///maximum and type of allowed allow protrusion of alignment ends, i.e. start (end) of the +strand mate downstream of the start (end) of the -strand mate + type AlignmentEndsProtrusionOptions = + ///report aligments with non-zero protrusion as concordant pairs + |ConcordantPair of int + ///report alignments with non-zero protrusion as discordant pairs + |DiscordantPair of int + + static member make = function + |ConcordantPair i -> sprintf "%i ConcordantPair" i + |DiscordantPair i -> sprintf "%i DiscordantPair" i + + ///how to flush ambiguous insertion positions + type AlignmentInsertionFlushOptions = + |DoNotFlush + |Right + + static member make = function + |DoNotFlush -> "None" + |Right -> "Right" + + type AligmentPairedEndReadOptions = + ///minimum number of overlap bases to trigger mates merging and realignment + |OverlapNbasesMin of int + ///maximum proportion of mismatched bases in the overlap area + |OverlapMMp of float + + static member makeCmd = function + |OverlapNbasesMin i -> ["--peOverlapNbasesMin" ; i |> string] + |OverlapMMp f -> ["--peOverlapMMp" ; f |> string] + + type AlignmentGeneralOptions = + ///minimum intron size: genomic gap is considered intron if its length>=alignIntronMin, otherwise it is considered Deletion + |IntronMin of int + ///maximum intron size, if 0, max intron size will be determined by (2^winBinNbits)*winAnchorDistNbins + |IntronMax of int + ///maximum gap between two mates, if 0, max intron gap will be determined by (2^winBinNbits)*winAnchorDistNbins + |MatesGapMax of int + ///minimum overhang (i.e. block size) for spliced alignments + |SJoverhangMin of int + ///maximum number of mismatches for stitching of the splice junctions (-1: no limit). (1) non-canonical motifs, (2) GT/AG and CT/AC motif, (3) GC/AG and CT/GC motif, (4) AT/AC and GT/AT motif. + |SJstitchMismatchNmax of (int*int*int*int) + ///minimum overhang (i.e. block size) for annotated (sjdb) spliced alignments + |SJDBoverhangMin of int + ///minimum mapped length for a read mate that is spliced + |SplicedMateMapLmin of int + ///alignSplicedMateMapLmin normalized to mate length + |SplicedMateMapLminOverLmate of float + ///max number of windows per read + |WindowsPerReadNmax of int + ///max number of transcripts per window + |TranscriptsPerWindowNmax of int + ///max number of different alignments per read to consider + |TranscriptsPerReadNmax of int + ///type of read ends alignment + |EndsType of AlignmentEndsTypeOptions + ///maximum and type of allowed allow protrusion of alignment ends, i.e. start (end) of the +strand mate downstream of the start (end) of the -strand mate + |EndsProtrusion of AlignmentEndsProtrusionOptions + ///allow the soft-clipping of the alignments past the end of the chromosomes: allow, or prohibit(useful for compatibility with Cufflinks) + |SoftClipAtReferenceEnds of bool //true -> Yes false -> No + ///string: how to flush ambiguous insertion positions + |InsertionFlush of AlignmentInsertionFlushOptions + ///options how to handle paired end reads + |PairedEndReadOptions of AligmentPairedEndReadOptions list + + static member makeCmd = function + |IntronMin p -> ["--alignIntronMin" ; p |> string] + |IntronMax p -> ["--alignIntronMax" ; p |> string] + |MatesGapMax p -> ["--alignMatesGapMax" ; p |> string] + |SJoverhangMin p -> ["--alignSJoverhangMin" ; p |> string] + |SJstitchMismatchNmax p -> ["--alignSJstitchMismatchNmax" ; p |> handleQuadruples] + |SJDBoverhangMin p -> ["--alignSJDBoverhangMin" ; p |> string] + |SplicedMateMapLmin p -> ["--alignSplicedMateMapLmin" ; p |> string] + |SplicedMateMapLminOverLmate p -> ["--alignSplicedMateMapLminOverLmate" ; p |> string] + |WindowsPerReadNmax p -> ["--alignWindowsPerReadNmax" ; p |> string] + |TranscriptsPerWindowNmax p -> ["--alignTranscriptsPerWindowNmax" ; p |> string] + |TranscriptsPerReadNmax p -> ["--alignTranscriptsPerReadNmax" ; p |> string] + |EndsType p -> ["--alignEndsType" ; p |> AlignmentEndsTypeOptions.make] + |EndsProtrusion p -> ["--alignEndsProtrude" ; p |> AlignmentEndsProtrusionOptions.make] + |SoftClipAtReferenceEnds p -> ["--alignSoftClipAtReferenceEnds" ; if p then "Yes" else "No"] + |InsertionFlush p -> ["--alignInsertionFlush" ; p |> AlignmentInsertionFlushOptions.make] + |PairedEndReadOptions p -> p |> List.map AligmentPairedEndReadOptions.makeCmd |> List.concat + + ///Windows, Anchors, Binning Options + type AlignmentWindowOptions = + ///max number of loci anchors are allowed to map to + |AnchorMultimapNmax of int + ///=log2(winBin), where winBin is the size of the bin for the windows/clustering, each window will occupy an integer number of bins. + |BinNbits of int + ///max number of bins between two anchors that allows aggregation of anchors into one window + |AnchorDistNbins of int + ///log2(winFlank), where win Flank is the size of the left and right flanking regions for each window + |FlankNbins of int + ///minimum relative coverage of the read sequence by the seeds in a window, for STARlong algorithm only. + |ReadCoverageRelativeMin of float + ///minimum number of bases covered by the seeds in a window , for STARlong algorithm only. + |ReadCoverageBasesMin of int + + static member makeCmd = function + |AnchorMultimapNmax i -> ["--winAnchorMultimapNmax" ; i |> string ] + |BinNbits i -> ["--winBinNbits" ; i |> string ] + |AnchorDistNbins i -> ["--winAnchorDistNbins" ; i |> string ] + |FlankNbins i -> ["--winFlankNbins" ; i |> string ] + |ReadCoverageRelativeMin f -> ["--winReadCoverageRelativeMin" ; f |> string ] + |ReadCoverageBasesMin i -> ["--winReadCoverageBasesMin" ; i |> string ] + + ///type of chimeric output + type ChimericAlignmentOutputTypeOptions = + ///Chimeric.out.junction + ///output old SAM into separate Chimeric.out.sam file + ///output into main aligned BAM files (Aligned.*.bam) + ///(default) hard-clipping in the CIGAR for supplemental chimeric alignments (defaultif no 2nd word is present) + ///soft-clipping in the CIGAR for supplemental chimeric alignments + |Junctions + |SeparateSAMold + |WithinBAM + |WithinBAMHardClip + |WithinBAMSoftClip + + static member make = function + |Junctions -> "Junctions" + |SeparateSAMold -> "SeparateSAMold" + |WithinBAM -> "WithinBAM" + |WithinBAMHardClip -> "WithinBAM HardClip" + |WithinBAMSoftClip -> "WithinBAM SoftClip" + ///different filters for chimeric alignments + type ChimericAlignmentFilterOptions = + ///no filtering + |NoFiltering + ///Ns are not allowed in the genome sequence around the chimeric junction + |BanGenomicN + + static member make = function + |NoFiltering -> "None" + |BanGenomicN -> "banGenomicN" + + ///formatting type for the Chimeric.out.junction file + type ChimericOutJunctionFormatOptions = + ///no comment lines/headers + |NoComments + ///comment lines at the end of the file: command line and Nreads: total, unique, multi + |CommentLines + + static member make = function + |NoComments -> "0" + |CommentLines -> "1" + + type AlignmentChimericOptions = + ///type of chimeric output + |ChimericAlignmentOutputType of ChimericAlignmentOutputTypeOptions + ///minimum length of chimeric segment length, if ==0, no chimeric output + |SegmentMin of int + ///minimum total (summed) score of the chimeric segments + |ScoreMin of int + ///max drop (difference) of chimeric score (the sum of scores of all chimeric segments) from the read length + |ScoreDropMax of int + ///minimum difference (separation) between the best chimeric score and the next one + |ScoreSeparation of int + ///penalty for a non-GT/AG chimeric junction + |ScoreJunctionNonGTAG of int + ///minimum overhang for a chimeric junction + |JunctionOverhangMin of int + ///maximum gap in the read sequence between chimeric segments + |SegmentReadGapMax of int + ///different filters for chimeric alignments + |ChimericAlignmentFilter of ChimericAlignmentFilterOptions + ///maximum number of multi-alignments for the main chimeric segment. =1 will prohibit multimapping main segments. + |MainSegmentMultNmax of int + ///maximum number of chimeric multi-alignments use the old scheme for chimeric detection which only considered unique alignments + |MultimapNmax of int + ///the score range for multi-mapping chimeras below the best chimeric score. Only works with --chimMultimapNmax > 1 + |MultimapScoreRange of int + ///to trigger chimeric detection, the drop in the best non-chimeric alignment score with respect to the read length has to be greater than this value + |NonchimScoreDropMin of int + ///formatting type for the Chimeric.out.junction file + |OutJunctionFormat of ChimericOutJunctionFormatOptions + + static member makeCmd = function + |ChimericAlignmentOutputType c -> ["--chimOutType" ; c |> ChimericAlignmentOutputTypeOptions.make] + |SegmentMin c -> ["--chimSegmentMin" ; c |> string] + |ScoreMin c -> ["--chimScoreMin" ; c |> string] + |ScoreDropMax c -> ["--chimScoreDropMax" ; c |> string] + |ScoreSeparation c -> ["--chimScoreSeparation" ; c |> string] + |ScoreJunctionNonGTAG c -> ["--chimScoreJunctionNonGTAG" ; c |> string] + |JunctionOverhangMin c -> ["--chimJunctionOverhangMin" ; c |> string] + |SegmentReadGapMax c -> ["--chimSegmentReadGapMax" ; c |> string] + |ChimericAlignmentFilter c -> ["--chimFilter" ; c |> ChimericAlignmentFilterOptions.make] + |MainSegmentMultNmax c -> ["--chimMainSegmentMultNmax" ; c |> string] + |MultimapNmax c -> ["--chimMultimapNmax" ; c |> string] + |MultimapScoreRange c -> ["--chimMultimapScoreRange" ; c |> string] + |NonchimScoreDropMin c -> ["--chimNonchimScoreDropMin" ; c |> string] + |OutJunctionFormat c -> ["--chimOutJunctionFormat" ; c |> ChimericOutJunctionFormatOptions.make] + + type AlignmentParams = + ///various options regarding alignment scoring + |ScoringOptions of AlignmentScoringOptions list + ///various options regarding alignment seeds + |SeedOptions of AlignmentSeedOptions list + ///various general alignment options + |AlignmentOptions of AlignmentGeneralOptions list + ///various options regarding alignment windows + |WindowOptions of AlignmentWindowOptions list + ///various options regarding chimeric alignments + |ChimericOptions of AlignmentChimericOptions list + + static member makeCmd = function + |ScoringOptions s -> s |> List.map AlignmentScoringOptions.makeCmd |> List.concat + |SeedOptions a -> a |> List.map AlignmentSeedOptions.makeCmd |> List.concat + |AlignmentOptions a -> a |> List.map AlignmentGeneralOptions.makeCmd |> List.concat + |WindowOptions w -> w |> List.map AlignmentWindowOptions.makeCmd |> List.concat + |ChimericOptions c -> c |> List.map AlignmentChimericOptions.makeCmd |> List.concat + +//### Quantification of Annotations + + ///types of quantification requested + type AnnotationQuantificationModeOptions = + ///none + | NoQuantification + ///output SAM/BAM alignments to transcriptome into a separate file + | TranscriptomeSAM + ///count reads per gene + | GeneCounts + + static member make = function + | NoQuantification -> "-" + | TranscriptomeSAM -> "TranscriptomeSAM" + | GeneCounts -> "GeneCounts" + + ///prohibit various alignment type + type TranscriptomeBanOptions = + ///prohibit indels, soft clipping and single-end alignments - compatible with RSEM + |IndelSoftclipSingleend + ///prohibit single-end alignments + |Singleend + + static member make = function + |IndelSoftclipSingleend -> "IndelSoftclipSingleend" + |Singleend -> "Singleend" + + type AnnotationQuantificationParams = + ///types of quantification requested + |QuantificationMode of AnnotationQuantificationModeOptions + ///-2 to 10 transcriptome BAM compression level + |TranscriptomeBAMcompression of int + ///prohibit various alignment type + |TranscriptomeBan of TranscriptomeBanOptions + + static member makeCmd = function + |QuantificationMode a -> ["--quantMode" ; a |> AnnotationQuantificationModeOptions.make] + |TranscriptomeBAMcompression i -> ["--quantTranscriptomeBAMcompression" ; i |> string] + |TranscriptomeBan a -> ["--quantTranscriptomeBan" ; a |> TranscriptomeBanOptions.make] + + ///type of filtering +//### 2-pass Mapping + + ///2-pass mapping mode. + type TwoPassModeOptions = + ///1-pass mapping + |NoTwoPassMapping + ///basic 2-pass mapping, with all 1st pass junctions inserted into the genome indices on the fly + |Basic + + static member make = function + |NoTwoPassMapping -> "None" + |Basic -> "Basic" + + type TwoPassMappingParams = + ///2-pass mapping mode. + |Mode of TwoPassModeOptions + ///number of reads to process for the 1st step. Use very large number (or default -1) to map all reads in the first step. + |FirstStepReadN of int + + static member makeCmd = function + |Mode m -> ["--twopassMode" ; m |> TwoPassModeOptions.make] + |FirstStepReadN i -> ["--twopass1readsN"; i |> string] + +//### WASP parameters + + ///WASP allele-specific output type. This is re-implemenation of the original WASP mappability filtering by Bryce van de Geijn, Graham McVicker, Yoav Gilad & Jonathan K Pritchard. Please cite the original WASP paper: Nature Methods 12, 10611063 (2015), https://www.nature.com/articles/nmeth.3582 . + type WASPOutputModeOptions = + |NoWASP + |SAMtag + + static member make = function + |NoWASP -> "None" + |SAMtag -> "SAMtag" + + type WASPParams = + ///WASP allele-specific output type. This is re-implemenation of the original WASP mappability filtering by Bryce van de Geijn, Graham McVicker, Yoav Gilad & Jonathan K Pritchard. Please cite the original WASP paper: Nature Methods 12, 10611063 (2015), https://www.nature.com/articles/nmeth.3582 . + |OutputMode of WASPOutputModeOptions + + static member makeCmd = function + |OutputMode o -> ["--waspOutputMode"; o |> WASPOutputModeOptions.make] + +//### STARsolo (single cell RNA-seq) parameters + + ///type of single-cell RNA-seq + type STARSoloTypeOptions = + ///None + |NoSoloType + ///(a.k.a. Droplet) one UMI and one Cell Barcode of fixed length in read2, e.g. Drop-seq and 10X Chromium + |CB_UMI_Simple + ///one UMI of fixed length, but multiple Cell Barcodes of varying length, as well as adapters sequences are allowed in read2 only, e.g. inDrop. + |CB_UMI_Complex + + static member make = function + |NoSoloType -> "None" + |CB_UMI_Simple -> "CB_UMI_Simple " + |CB_UMI_Complex -> "CB_UMI_Complex" + + ///length of the barcode read + type STARSoloBarcodeReadLengthOptions = + ///not defined, do not check + |NotDefined + ///equal to sum of soloCBlen+soloUMIlen + |Sum + + static member make = function + |NotDefined -> "0" + |Sum -> "1" + + ///matching the Cell Barcodes to the WhiteList + type STARSoloCellBarcodeWhiteListOptions = + ///only exact matches allowed + |Exact + ///only one match in whitelist with 1 mismatched base allowed. Allowed CBs have to have at least one read with exact match. + |OneMM + ///multiple matches in whitelist with 1 mismatched base allowed, posterior probability calculation is used choose one of the matches. Allowed CBs have to have at least one read with exact match. Similar to CellRanger 2.2.0 + |OneMM_multi + ///same as 1MM_Multi, but pseudocounts of 1 are added to all whitelist barcodes. Similar to CellRanger 3.x.x + |OneMM_multi_pseudocounts + + static member make = function + |Exact -> "Exact" + |OneMM -> "1MM" + |OneMM_multi -> "1MM_multi" + |OneMM_multi_pseudocounts -> "1MM_multi_pseudocounts" + + ///strandedness of the solo libraries: + type STARSoloStrandOptions = + ///no strand information + |Unstranded + ///read strand same as the original RNA molecule + |Forward + ///read strand opposite to the original RNA molecule + |Reverse + + static member make = function + |Unstranded -> "Unstranded" + |Forward -> "Forward" + |Reverse -> "Reverse" + + ///genomic features for which the UMI counts per Cell Barcode are collected + type STARSoloFeaturesOptions = + ///genes: reads match the gene transcript + |Gene + ///splice junctions: reported in SJ.out.tab + |SJ + ///full genes: count all reads overlapping genes' exons and introns + |GeneFull + ///quantification of transcript for 3' protocols + |Transcript3p + + static member make = function + |Gene -> "Gene" + |SJ -> "SJ" + |GeneFull -> "GeneFull" + |Transcript3p -> "Transcript3p" + + ///type of UMI deduplication (collapsing) algorithm + type STARSoloUMIDeDuplicationOptions = + ///all UMIs with 1 mismatch distance to each other are collapsed (i.e. counted once) + |OneMM_All + ///follows the "directional" method from the UMI-tools by Smith, Heger and Sudbery (Genome Research 2017). + |OneMM_Directional + ///only exactly matching UMIs are collapsed + |Exact + + static member make = function + |OneMM_All -> "1MM_All" + |OneMM_Directional -> "1MM_Directional" + |Exact -> "Exact" + + ///type of UMI filtering + type STARSoloUMIFilteringOptions = + ///basic filtering: remove UMIs with N and homopolymers (similar to CellRanger 2.2.0) + |Basic + ///remove lower-count UMIs that map to more than one gene (introduced in CellRanger 3.x.x) + |MultiGeneUMI + + static member make = function + |Basic -> "-" + |MultiGeneUMI -> "MultiGeneUMI" + + ///cell filtering type and parameters + type STARSoloCellFilterOptions = + ///do not output filtered cells + |NoCellFilter + ///simple filtering of CellRanger 2.2, followed by thre numbers: number of expected cells, robust maximum percentile for UMI count, maximum to minimum ratio for UMI count + |CellRanger2_2 + ///only report top cells by UMI count, followed by the excat number of cells + |TopCells + + static member make = function + |NoCellFilter -> "None" + |CellRanger2_2 -> "CellRanger2.2" + |TopCells -> "TopCells" + + type STARSoloParams = + ///type of single-cell RNA-seq + |SoloType of STARSoloTypeOptions + ///length of the barcode read + |BarcodeReadLengthOptions of STARSoloBarcodeReadLengthOptions + ///matching the Cell Barcodes to the WhiteList + |CBmatchWLtype of STARSoloCellBarcodeWhiteListOptions + ///strandedness of the solo libraries + |Strand of STARSoloStrandOptions + ///genomic features for which the UMI counts per Cell Barcode are collected + |Features of STARSoloFeaturesOptions list + ///type of UMI deduplication (collapsing) algorithm + |UMIdedup of STARSoloUMIDeDuplicationOptions list + ///type of UMI filtering + |UMIfiltering of STARSoloUMIFilteringOptions list + ///cell filtering type and parameters + |CellFilter of STARSoloCellFilterOptions list + ///file names for STARsolo output. default: file_name_prefix gene_names barcode_sequences cell_feature_count_matrix + |OutFileNames of string list + ///position of the UMI on the barcode read, same as soloCBposition Example: inDrop (Zilionis et al, Nat. Protocols, 2017): --soloCBposition 3_9_3_14 + |UMIposition of string + ///position of Cell Barcode(s) on the barcode read. Presently only works with --soloType CB_UMI_Complex, and barcodes are assumed to be on Read2. Format for each barcode: startAnchor_startDistance_endAnchor_endDistance start(end)Anchor defines the anchor base for the CB: 0: read start; 1: read end; 2: adapter start; 3: adapter end start(end)Distance is the distance from the CB start(end) to the Anchor base String for different barcodes are separated by space. Example: inDrop (Zilionis et al, Nat. Protocols, 2017): --soloCBposition 0_0_2_-1 3_1_3_8 + |CBposition of string + ///adapter sequence to anchor barcodes. + |AdapterSequence of string + ///file(s) with whitelist(s) of cell barcodes. Only one file allowed with + |CBwhitelist of string list + ///cell barcode start base + |CBstart of int + ///cell barcode length + |CBlen of int + ///UMI start base + |UMIstart of int + ///UMI length + |UMIlen of int + ///maximum number of mismatches allowed in adapter sequence. + |AdapterMismatchesNmax of int + + static member makeCmd = function + |SoloType s -> ["--soloType" ; s |> STARSoloTypeOptions.make] + |BarcodeReadLengthOptions s -> ["--soloBarcodeReadLength" ; s |> STARSoloBarcodeReadLengthOptions.make] + |CBmatchWLtype s -> ["--soloCBmatchWLtype" ; s |> STARSoloCellBarcodeWhiteListOptions.make] + |Strand s -> ["--soloStrand" ; s |> STARSoloStrandOptions.make] + |Features s -> ["--soloFeatures" ; s |> List.map STARSoloFeaturesOptions.make |> String.concat " "] + |UMIdedup s -> ["--soloUMIdedup" ; s |> List.map STARSoloUMIDeDuplicationOptions.make |> String.concat " "] + |UMIfiltering s -> ["--soloUMIfiltering" ; s |> List.map STARSoloUMIFilteringOptions.make |> String.concat " "] + |CellFilter s -> ["--soloCellFilter" ; s |> List.map STARSoloCellFilterOptions.make |> String.concat " "] + |OutFileNames s -> ["--soloOutFileNames" ; s |> String.concat " "] + |UMIposition s -> ["--soloUMIposition" ; s ] + |CBposition s -> ["--soloCBposition" ; s ] + |AdapterSequence s -> ["--soloAdapterSequence" ; s ] + |CBwhitelist s -> ["--soloCBwhitelist" ; s |> String.concat " "] + |CBstart s -> ["--soloCBstart" ; s |> string] + |CBlen s -> ["--soloCBlen" ; s |> string] + |UMIstart s -> ["--soloUMIstart" ; s |> string] + |UMIlen s -> ["--soloUMIlen" ; s |> string] + |AdapterMismatchesNmax s -> ["--soloAdapterMismatchesNmax" ; s |> string] + + static member makeCmdWith (m:MountInfo) = function + |SoloType s -> ["--soloType" ; s |> STARSoloTypeOptions.make] + |BarcodeReadLengthOptions s -> ["--soloBarcodeReadLength" ; s |> STARSoloBarcodeReadLengthOptions.make] + |CBmatchWLtype s -> ["--soloCBmatchWLtype" ; s |> STARSoloCellBarcodeWhiteListOptions.make] + |Strand s -> ["--soloStrand" ; s |> STARSoloStrandOptions.make] + |Features s -> ["--soloFeatures" ; s |> List.map STARSoloFeaturesOptions.make |> String.concat " "] + |UMIdedup s -> ["--soloUMIdedup" ; s |> List.map STARSoloUMIDeDuplicationOptions.make |> String.concat " "] + |UMIfiltering s -> ["--soloUMIfiltering" ; s |> List.map STARSoloUMIFilteringOptions.make |> String.concat " "] + |CellFilter s -> ["--soloCellFilter" ; s |> List.map STARSoloCellFilterOptions.make |> String.concat " "] + |OutFileNames s -> ["--soloOutFileNames" ; s |> String.concat " "] + |UMIposition s -> ["--soloUMIposition" ; s ] + |CBposition s -> ["--soloCBposition" ; s ] + |AdapterSequence s -> ["--soloAdapterSequence" ; s ] + |CBwhitelist s -> ["--soloCBwhitelist" ; s |> List.map (MountInfo.containerPathOf m) |> String.concat " "] + |CBstart s -> ["--soloCBstart" ; s |> string] + |CBlen s -> ["--soloCBlen" ; s |> string] + |UMIstart s -> ["--soloUMIstart" ; s |> string] + |UMIlen s -> ["--soloUMIlen" ; s |> string] + |AdapterMismatchesNmax s -> ["--soloAdapterMismatchesNmax" ; s |> string] + + type STARParams = + // string: name of a user-defined parameters file, "-": none. Can only be defined on the command line. + // string: path to the VCF file that contains variation data. + // string: path to BAM input file, to be used with --runMode inputAlignmentsFromBAM + |ParametersFilePath of string + |VariationDataFile of string + |InputBAMFile of string + |RunParameters of RunParams list + |GenomeParameters of GenomeParams list + |SpliceJunctionsDatabaseParameters of SpliceJunctionsDatabaseParams list + |LimitParameters of LimitParams list + |ReadParameters of ReadParams list + |OutputParameters of OutputParams list + |OutputWiggleParameters of OutputWiggleParams list + |OutputFilteringParameters of OutputFilteringParams list + |AlignmentParameters of AlignmentParams list + |AnnotationQuantificationParameters of AnnotationQuantificationParams list + |TwoPassMappingParameters of TwoPassMappingParams list + |WASPParameters of WASPParams list + |STARSoloParameters of STARSoloParams list + + static member makeCmd = function + |ParametersFilePath p -> ["--parametersFiles" ; p] + |VariationDataFile p -> ["--varVCFfile" ; p] + |InputBAMFile p -> ["--inputBAMfile" ; p] + |RunParameters p -> p |> List.map RunParams .makeCmd |> List.concat + |GenomeParameters p -> p |> List.map GenomeParams .makeCmd |> List.concat + |SpliceJunctionsDatabaseParameters p -> p |> List.map SpliceJunctionsDatabaseParams .makeCmd |> List.concat + |LimitParameters p -> p |> List.map LimitParams .makeCmd |> List.concat + |ReadParameters p -> p |> List.map ReadParams .makeCmd |> List.concat + |OutputParameters p -> p |> List.map OutputParams .makeCmd |> List.concat + |OutputWiggleParameters p -> p |> List.map OutputWiggleParams .makeCmd |> List.concat + |OutputFilteringParameters p -> p |> List.map OutputFilteringParams .makeCmd |> List.concat + |AlignmentParameters p -> p |> List.map AlignmentParams .makeCmd |> List.concat + |AnnotationQuantificationParameters p -> p |> List.map AnnotationQuantificationParams.makeCmd |> List.concat + |TwoPassMappingParameters p -> p |> List.map TwoPassMappingParams .makeCmd |> List.concat + |WASPParameters p -> p |> List.map WASPParams .makeCmd |> List.concat + |STARSoloParameters p -> p |> List.map STARSoloParams .makeCmd |> List.concat + + static member makeCmdWith (m:MountInfo) = function + |ParametersFilePath p -> ["--parametersFiles" ; p |> MountInfo.containerPathOf m] + |VariationDataFile p -> ["--varVCFfile" ; p |> MountInfo.containerPathOf m] + |InputBAMFile p -> ["--inputBAMfile" ; p |> MountInfo.containerPathOf m] + |RunParameters p -> p |> List.map (RunParams .makeCmd) |> List.concat + |GenomeParameters p -> p |> List.map (GenomeParams .makeCmdWith m) |> List.concat + |SpliceJunctionsDatabaseParameters p -> p |> List.map (SpliceJunctionsDatabaseParams .makeCmdWith m) |> List.concat + |LimitParameters p -> p |> List.map (LimitParams .makeCmd) |> List.concat + |ReadParameters p -> p |> List.map (ReadParams .makeCmdWith m) |> List.concat + |OutputParameters p -> p |> List.map (OutputParams .makeCmdWith m) |> List.concat + |OutputWiggleParameters p -> p |> List.map (OutputWiggleParams .makeCmd) |> List.concat + |OutputFilteringParameters p -> p |> List.map (OutputFilteringParams .makeCmd) |> List.concat + |AlignmentParameters p -> p |> List.map (AlignmentParams .makeCmd) |> List.concat + |AnnotationQuantificationParameters p -> p |> List.map (AnnotationQuantificationParams.makeCmd) |> List.concat + |TwoPassMappingParameters p -> p |> List.map (TwoPassMappingParams .makeCmd) |> List.concat + |WASPParameters p -> p |> List.map (WASPParams .makeCmd) |> List.concat + |STARSoloParameters p -> p |> List.map (STARSoloParams .makeCmdWith m) |> List.concat + + + let runSTARAsync (bcContext:BioContainer.BcContext) (opt:STARParams list)= + + let cmds = (opt |> List.map (STARParams.makeCmdWith bcContext.Mount)) + let tp = "STAR"::(cmds |> List.concat) + + printfn "Starting process STAR\r\nparameters:" + cmds |> List.iter (fun op -> printfn "\t%s" (String.concat " " op)) + + async { + let! res = BioContainer.execAsync bcContext tp + return res + } + + let runStar (bcContext:BioContainer.BcContext) (opt:STARParams list) = + runSTARAsync bcContext opt + |> Async.RunSynchronously + + module BasicWorkflows = + + let runBasicGenomeIndexingAsync threads directory genomesFastaPaths gtfPath (bcContext:BioContainer.BcContext) (additionalParameters:STARParams list) = + let presetOpts = + [ + STARParams.RunParameters [ + RunParams.Threads threads + RunParams.Mode RunMode.GenomeGenerate + ] + STARParams.GenomeParameters [ + GenomeParams.GenomeDirectory directory + GenomeParams.GenomeFastaFiles genomesFastaPaths + ] + SpliceJunctionsDatabaseParameters [ + SpliceJunctionsDatabaseParams.GTFfile gtfPath + ] + ] + runSTARAsync bcContext (presetOpts@additionalParameters) + + let runBasicGenomeIndexing threads directory genomesFastaPaths gtfPath (bcContext:BioContainer.BcContext) (additionalParameters:STARParams list) = + runBasicGenomeIndexingAsync threads directory genomesFastaPaths gtfPath bcContext additionalParameters + |> Async.RunSynchronously + From 0a0470b1ab4c38b3e216854ed296e599a5a11b4b Mon Sep 17 00:00:00 2001 From: kMutagene Date: Mon, 23 Mar 2020 09:22:12 +0100 Subject: [PATCH 09/11] parenthese an if else that travis does not like that way I hope this is not the start of 500 CIfix commits --- src/BioFSharp.BioContainers/STAR.fs | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/BioFSharp.BioContainers/STAR.fs b/src/BioFSharp.BioContainers/STAR.fs index 780c0653..f2e8360e 100644 --- a/src/BioFSharp.BioContainers/STAR.fs +++ b/src/BioFSharp.BioContainers/STAR.fs @@ -821,7 +821,7 @@ module STAR = |MatchNmin i -> ["--outFilterMatchNmin" ; i |> string] |MatchNminOverLread f -> ["--outFilterMatchNminOverLread" ; f |> string] |IntronMotifs m -> ["--outFilterIntronMotifs" ; m |> OutputFilterIntronMotifsOptions.make] - |RemoveInconsistentIntronStrands b -> ["--outFilterIntronStrands" ; if b then "RemoveInconsistentStrands" else "None"] + |RemoveInconsistentIntronStrands b -> ["--outFilterIntronStrands" ; (if b then "RemoveInconsistentStrands" else "None")] |SpliceJunctionsFiltering s -> s |> List.map OutputFilteringSpliceJunctionsOptions.makeCmd |> List.concat type AlignmentScoringOptions = ///splice junction penalty (independent on intron motif) @@ -980,7 +980,7 @@ module STAR = |TranscriptsPerReadNmax p -> ["--alignTranscriptsPerReadNmax" ; p |> string] |EndsType p -> ["--alignEndsType" ; p |> AlignmentEndsTypeOptions.make] |EndsProtrusion p -> ["--alignEndsProtrude" ; p |> AlignmentEndsProtrusionOptions.make] - |SoftClipAtReferenceEnds p -> ["--alignSoftClipAtReferenceEnds" ; if p then "Yes" else "No"] + |SoftClipAtReferenceEnds p -> ["--alignSoftClipAtReferenceEnds" ; (if p then "Yes" else "No")] |InsertionFlush p -> ["--alignInsertionFlush" ; p |> AlignmentInsertionFlushOptions.make] |PairedEndReadOptions p -> p |> List.map AligmentPairedEndReadOptions.makeCmd |> List.concat From 07c7c0101a904b7a1b1fc5bd97e76a6a699ee074 Mon Sep 17 00:00:00 2001 From: kMutagene Date: Mon, 23 Mar 2020 10:28:55 +0100 Subject: [PATCH 10/11] Fix comment lines: remove accidental tag starts --- src/BioFSharp.BioContainers/SRAToolkit.fs | 8 ++++---- src/BioFSharp.BioContainers/STAR.fs | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/src/BioFSharp.BioContainers/SRAToolkit.fs b/src/BioFSharp.BioContainers/SRAToolkit.fs index b32208b6..737dc039 100644 --- a/src/BioFSharp.BioContainers/SRAToolkit.fs +++ b/src/BioFSharp.BioContainers/SRAToolkit.fs @@ -48,15 +48,15 @@ module SRATools = |CheckAll ///Write file to FILE when downloading single file |OutputFile of string - ///Save files to path/ + ///Save files to path |OutputDirectory of string - /// to ngc file + ///path to ngc file |NGCFilePath of string - /// to permission file + ///path to permission file |PermissionFilePath of string ///location in cloud |CloudLocation of string - /// to cart file + ///path to cart file |CartPath of string ///disable multithreading |DisableMultiThreading diff --git a/src/BioFSharp.BioContainers/STAR.fs b/src/BioFSharp.BioContainers/STAR.fs index f2e8360e..ee1f7893 100644 --- a/src/BioFSharp.BioContainers/STAR.fs +++ b/src/BioFSharp.BioContainers/STAR.fs @@ -154,7 +154,7 @@ module STAR = |All -> "All" type SpliceJunctionsDatabaseParams = - ///path(s) to the files with genomic coordinates (chr start end strand) for the splice junction introns. Multiple files can be supplied wand will be concatenated. + ///path(s) to the files with genomic coordinates (chr tab start tab end tab strand) for the splice junction introns. Multiple files can be supplied wand will be concatenated. |FileChrStartEnd of string list ///string: path to the GTF file with annotations |GTFfile of string From 23c24353b711fafeca4e441dcf8c9e670a9591f3 Mon Sep 17 00:00:00 2001 From: kMutagene Date: Mon, 23 Mar 2020 10:59:24 +0100 Subject: [PATCH 11/11] Bump version to 1.1.0 --- RELEASE_NOTES.md | 14 ++++++++++++++ docsrc/content/release-notes.md | 14 ++++++++++++++ src/BioFSharp.BioContainers/AssemblyInfo.fs | 8 ++++---- src/BioFSharp.BioDB/AssemblyInfo.fs | 8 ++++---- src/BioFSharp.IO/AssemblyInfo.fs | 8 ++++---- src/BioFSharp.ImgP/AssemblyInfo.fs | 8 ++++---- src/BioFSharp.ML/AssemblyInfo.fs | 8 ++++---- src/BioFSharp.Parallel/AssemblyInfo.fs | 8 ++++---- src/BioFSharp.Stats/AssemblyInfo.fs | 8 ++++---- src/BioFSharp.Vis/AssemblyInfo.fs | 8 ++++---- src/BioFSharp/AssemblyInfo.fs | 8 ++++---- 11 files changed, 64 insertions(+), 36 deletions(-) diff --git a/RELEASE_NOTES.md b/RELEASE_NOTES.md index 14b86e6f..0bee5665 100644 --- a/RELEASE_NOTES.md +++ b/RELEASE_NOTES.md @@ -1,3 +1,17 @@ +#### 1.1.0 - Wednesday, March 23, 2020 +**Additions:** + * **BioFSharp.BioContainers:** + * Add [fasterq-dump](https://github.com/CSBiology/BioFSharp/commit/425fbb93b41700eeece8f8ab063c9c37b15124bd) and [prefetch](https://github.com/CSBiology/BioFSharp/commit/b08f307f203eea4c2a84cce10f1a72d05453806b) DSL for the SRATools biocontainer + * Add full [STAR](https://github.com/alexdobin/STAR) RNASeq aligner DSL for the respective BioContainer. [Commit details](https://github.com/CSBiology/BioFSharp/commit/d2cbc0a8691564a487d70d9825867e7eb261d03a) + * **BioFSharp.IO:** + * [Add load script for referencing pretty printers](https://github.com/CSBiology/BioFSharp/commit/130e1c63264989978e54f114dbd04b6dfb9458d3), included in the nuget package + * [Add multiple new pretty printers for SOFT](https://github.com/CSBiology/BioFSharp/commit/97cca9bd06f63455ebafbf3cbb8029a0651137cb) + +**Bugfixes:** + * **BioFSharp.IO:** + * [Fix GFF3 pretty printer return type](https://github.com/CSBiology/BioFSharp/commit/bcec2cc719eef7e43827521bd281582a8b5ebe72) + + #### 1.0.03 - Wednesday, February 26, 2020 * **BioFSharp.Stats:** * Massively improved SAILENT characterization speed for [preprocessing of large datasets](https://github.com/CSBiology/BioFSharp/pull/82) diff --git a/docsrc/content/release-notes.md b/docsrc/content/release-notes.md index 14b86e6f..0bee5665 100644 --- a/docsrc/content/release-notes.md +++ b/docsrc/content/release-notes.md @@ -1,3 +1,17 @@ +#### 1.1.0 - Wednesday, March 23, 2020 +**Additions:** + * **BioFSharp.BioContainers:** + * Add [fasterq-dump](https://github.com/CSBiology/BioFSharp/commit/425fbb93b41700eeece8f8ab063c9c37b15124bd) and [prefetch](https://github.com/CSBiology/BioFSharp/commit/b08f307f203eea4c2a84cce10f1a72d05453806b) DSL for the SRATools biocontainer + * Add full [STAR](https://github.com/alexdobin/STAR) RNASeq aligner DSL for the respective BioContainer. [Commit details](https://github.com/CSBiology/BioFSharp/commit/d2cbc0a8691564a487d70d9825867e7eb261d03a) + * **BioFSharp.IO:** + * [Add load script for referencing pretty printers](https://github.com/CSBiology/BioFSharp/commit/130e1c63264989978e54f114dbd04b6dfb9458d3), included in the nuget package + * [Add multiple new pretty printers for SOFT](https://github.com/CSBiology/BioFSharp/commit/97cca9bd06f63455ebafbf3cbb8029a0651137cb) + +**Bugfixes:** + * **BioFSharp.IO:** + * [Fix GFF3 pretty printer return type](https://github.com/CSBiology/BioFSharp/commit/bcec2cc719eef7e43827521bd281582a8b5ebe72) + + #### 1.0.03 - Wednesday, February 26, 2020 * **BioFSharp.Stats:** * Massively improved SAILENT characterization speed for [preprocessing of large datasets](https://github.com/CSBiology/BioFSharp/pull/82) diff --git a/src/BioFSharp.BioContainers/AssemblyInfo.fs b/src/BioFSharp.BioContainers/AssemblyInfo.fs index 4b6309de..fad292a9 100644 --- a/src/BioFSharp.BioContainers/AssemblyInfo.fs +++ b/src/BioFSharp.BioContainers/AssemblyInfo.fs @@ -5,8 +5,8 @@ open System.Reflection [] [] [")>] -[] -[] +[] +[] [] do () @@ -14,6 +14,6 @@ module internal AssemblyVersionInformation = let [] AssemblyTitle = "BioFSharp.BioContainers" let [] AssemblyProduct = "BioFSharp" let [] AssemblyDescription = "An open source bioinformatics toolbox written in F#. " - let [] AssemblyVersion = "1.0.03" - let [] AssemblyFileVersion = "1.0.03" + let [] AssemblyVersion = "1.1.0" + let [] AssemblyFileVersion = "1.1.0" let [] AssemblyConfiguration = "Release" diff --git a/src/BioFSharp.BioDB/AssemblyInfo.fs b/src/BioFSharp.BioDB/AssemblyInfo.fs index c0777269..d3f51b2f 100644 --- a/src/BioFSharp.BioDB/AssemblyInfo.fs +++ b/src/BioFSharp.BioDB/AssemblyInfo.fs @@ -5,8 +5,8 @@ open System.Reflection [] [] [")>] -[] -[] +[] +[] [] do () @@ -14,6 +14,6 @@ module internal AssemblyVersionInformation = let [] AssemblyTitle = "BioFSharp.BioDB" let [] AssemblyProduct = "BioFSharp" let [] AssemblyDescription = "An open source bioinformatics toolbox written in F#. " - let [] AssemblyVersion = "1.0.03" - let [] AssemblyFileVersion = "1.0.03" + let [] AssemblyVersion = "1.1.0" + let [] AssemblyFileVersion = "1.1.0" let [] AssemblyConfiguration = "Release" diff --git a/src/BioFSharp.IO/AssemblyInfo.fs b/src/BioFSharp.IO/AssemblyInfo.fs index aa17b5a4..29c9f9ef 100644 --- a/src/BioFSharp.IO/AssemblyInfo.fs +++ b/src/BioFSharp.IO/AssemblyInfo.fs @@ -5,8 +5,8 @@ open System.Reflection [] [] [")>] -[] -[] +[] +[] [] do () @@ -14,6 +14,6 @@ module internal AssemblyVersionInformation = let [] AssemblyTitle = "BioFSharp.IO" let [] AssemblyProduct = "BioFSharp" let [] AssemblyDescription = "An open source bioinformatics toolbox written in F#. " - let [] AssemblyVersion = "1.0.03" - let [] AssemblyFileVersion = "1.0.03" + let [] AssemblyVersion = "1.1.0" + let [] AssemblyFileVersion = "1.1.0" let [] AssemblyConfiguration = "Release" diff --git a/src/BioFSharp.ImgP/AssemblyInfo.fs b/src/BioFSharp.ImgP/AssemblyInfo.fs index 368d703b..557c77a3 100644 --- a/src/BioFSharp.ImgP/AssemblyInfo.fs +++ b/src/BioFSharp.ImgP/AssemblyInfo.fs @@ -5,8 +5,8 @@ open System.Reflection [] [] [")>] -[] -[] +[] +[] [] do () @@ -14,6 +14,6 @@ module internal AssemblyVersionInformation = let [] AssemblyTitle = "BioFSharp.ImgP" let [] AssemblyProduct = "BioFSharp" let [] AssemblyDescription = "An open source bioinformatics toolbox written in F#. " - let [] AssemblyVersion = "1.0.03" - let [] AssemblyFileVersion = "1.0.03" + let [] AssemblyVersion = "1.1.0" + let [] AssemblyFileVersion = "1.1.0" let [] AssemblyConfiguration = "Release" diff --git a/src/BioFSharp.ML/AssemblyInfo.fs b/src/BioFSharp.ML/AssemblyInfo.fs index 0c35b8b7..bb4d8037 100644 --- a/src/BioFSharp.ML/AssemblyInfo.fs +++ b/src/BioFSharp.ML/AssemblyInfo.fs @@ -5,8 +5,8 @@ open System.Reflection [] [] [")>] -[] -[] +[] +[] [] do () @@ -14,6 +14,6 @@ module internal AssemblyVersionInformation = let [] AssemblyTitle = "BioFSharp.ML" let [] AssemblyProduct = "BioFSharp" let [] AssemblyDescription = "An open source bioinformatics toolbox written in F#. " - let [] AssemblyVersion = "1.0.03" - let [] AssemblyFileVersion = "1.0.03" + let [] AssemblyVersion = "1.1.0" + let [] AssemblyFileVersion = "1.1.0" let [] AssemblyConfiguration = "Release" diff --git a/src/BioFSharp.Parallel/AssemblyInfo.fs b/src/BioFSharp.Parallel/AssemblyInfo.fs index b13d51d4..0e7f53f8 100644 --- a/src/BioFSharp.Parallel/AssemblyInfo.fs +++ b/src/BioFSharp.Parallel/AssemblyInfo.fs @@ -5,8 +5,8 @@ open System.Reflection [] [] [")>] -[] -[] +[] +[] [] do () @@ -14,6 +14,6 @@ module internal AssemblyVersionInformation = let [] AssemblyTitle = "BioFSharp.Parallel" let [] AssemblyProduct = "BioFSharp" let [] AssemblyDescription = "An open source bioinformatics toolbox written in F#. " - let [] AssemblyVersion = "1.0.03" - let [] AssemblyFileVersion = "1.0.03" + let [] AssemblyVersion = "1.1.0" + let [] AssemblyFileVersion = "1.1.0" let [] AssemblyConfiguration = "Release" diff --git a/src/BioFSharp.Stats/AssemblyInfo.fs b/src/BioFSharp.Stats/AssemblyInfo.fs index fe0b5d1a..bf20f2d6 100644 --- a/src/BioFSharp.Stats/AssemblyInfo.fs +++ b/src/BioFSharp.Stats/AssemblyInfo.fs @@ -5,8 +5,8 @@ open System.Reflection [] [] [")>] -[] -[] +[] +[] [] do () @@ -14,6 +14,6 @@ module internal AssemblyVersionInformation = let [] AssemblyTitle = "BioFSharp.Stats" let [] AssemblyProduct = "BioFSharp" let [] AssemblyDescription = "An open source bioinformatics toolbox written in F#. " - let [] AssemblyVersion = "1.0.03" - let [] AssemblyFileVersion = "1.0.03" + let [] AssemblyVersion = "1.1.0" + let [] AssemblyFileVersion = "1.1.0" let [] AssemblyConfiguration = "Release" diff --git a/src/BioFSharp.Vis/AssemblyInfo.fs b/src/BioFSharp.Vis/AssemblyInfo.fs index 7fe8b05f..06d83f6e 100644 --- a/src/BioFSharp.Vis/AssemblyInfo.fs +++ b/src/BioFSharp.Vis/AssemblyInfo.fs @@ -5,8 +5,8 @@ open System.Reflection [] [] [")>] -[] -[] +[] +[] [] do () @@ -14,6 +14,6 @@ module internal AssemblyVersionInformation = let [] AssemblyTitle = "BioFSharp.Vis" let [] AssemblyProduct = "BioFSharp" let [] AssemblyDescription = "An open source bioinformatics toolbox written in F#. " - let [] AssemblyVersion = "1.0.03" - let [] AssemblyFileVersion = "1.0.03" + let [] AssemblyVersion = "1.1.0" + let [] AssemblyFileVersion = "1.1.0" let [] AssemblyConfiguration = "Release" diff --git a/src/BioFSharp/AssemblyInfo.fs b/src/BioFSharp/AssemblyInfo.fs index 1ae7d87b..4d663af8 100644 --- a/src/BioFSharp/AssemblyInfo.fs +++ b/src/BioFSharp/AssemblyInfo.fs @@ -5,8 +5,8 @@ open System.Reflection [] [] [")>] -[] -[] +[] +[] [] do () @@ -14,6 +14,6 @@ module internal AssemblyVersionInformation = let [] AssemblyTitle = "BioFSharp" let [] AssemblyProduct = "BioFSharp" let [] AssemblyDescription = "An open source bioinformatics toolbox written in F#. " - let [] AssemblyVersion = "1.0.03" - let [] AssemblyFileVersion = "1.0.03" + let [] AssemblyVersion = "1.1.0" + let [] AssemblyFileVersion = "1.1.0" let [] AssemblyConfiguration = "Release"