DPL-970 Import cDNA plates into Sequencescape

[KatyTaylor]

User story
As a member of the SSR team, who has received a plate from faculty containing cDNA, I would like to be able to import them into Sequencescape along with all the required data.

Who are the primary contacts for this story
Lesley, Katy

Who is the nominated tester for UAT
Lesley, Liz H?

Acceptance criteria
To be considered successful the solution must allow:

• I can upload the plate as a "LRC GEM-X 5p cDNA Input" plate in Sequencescape
• Record pools, with the following information:
  • TBC
• Update documentation - it currently has instructions from DPL-809 (linked below) - add similar instructions regarding this import.

References
This story has a non-blocking relationship with:

• DPL-809 Import fresh blood samples into Sequencescape #3849 - equivalent but for fresh blood
• DPL-823 Import PBMC pool plates into Sequencescape #3857 - equivalent but for PBMC pools

Additional information
This will use the normal manifest process - SSRs generate the manifest & barcode labels, send them to faculty, who use the barcodes on their plates and send the manifest back filled in.

[KatyTaylor]

Andrew and I just discussed this. We're putting it back into the backlog because it's not ready to be picked up. Reasons are:

• We may be able to re-use the manifest we have already developed for the previous entry point (DPL-823 Import PBMC pool plates into Sequencescape #3857 - manifest type is called "scRNA Core Pools Plate")
• Question (for Danni?) - do we need to import "retention instructions" for this plate (i.e. is it viewed as a 'stock plate'?)? The answer was "no" for the previous entry point (PBMC pools plate).
• We would like to import sample-level information (pool make-up) for the same reason as was decided for the previous entry point (PBMC pools plate). A few things to check here:
  • We discussed the equivalent decision for the previous entry point with HumGen Informatics - who are the people doing the data analysis for this entrypoing? CellGen Informatics?
  • Will the existing 10x pipelines work out of the box with sample-level information? (Existing 10x manifests import only pool-level information) If not, this will be a problem for plates coming through SeqOps from the previous entry points too.
• Discuss the contents of this manifest with the relevant SSR & faculty customers (CellGen?), to validate our assumptions and make sure they're happy to fill it out as designed.

Update: see answers / discussion in further comments below.

[KatyTaylor]

Retention instructions

Question (for Danni?) - do we need to import "retention instructions" for this plate (i.e. is it viewed as a 'stock plate'?)? The answer was "no" for the previous entry point (PBMC pools plate).

I looked back at my email thread with Danni, which was about the PBMC pool plates entrypoint earlier in the pipeline - related to #3857. Extracts below:

The policy covers stock and derivative samples. All stock samples must have retention information specified. A stock sample will have a stock barcode and is defined that way in SScape by plate or tube type.

Derivatives are anything other than a stock samples, this does included pooled and single samples. For any samples that are a derivative samples have a blanket 2 years then destroyed rule unless the sample custodian has requested long term storage/to be returned. This will be control at a labware level when we can decide a lifespan of a labware type in SScape. ( DPL-368 Set lifespan on labware [C=S] #363 not yet complete)

Thanks. So I assume these pool plates are treated as ‘derivative’ samples… even though they are coming into SeqOps in that state? I.e. we don’t hold the stock sample in SeqOps.

Yes I would agree with that.

I think it's clear that the same logic applies to this story - we're importing pooled samples from faculty. They're not the stock samples. So these count as 'derivative plates' and we don't need to specify 'retention instructions'.

[KatyTaylor]

Sample-level information

• We would like to import sample-level information (pool make-up) for the same reason as was decided for the previous entry point (PBMC pools plate). A few things to check here:
  • We discussed the equivalent decision for the previous entry point with HumGen Informatics - who are the people doing the data analysis for this entrypoing? CellGen Informatics?

I do think we should import the sample-level information, so that:
a) data product in MLWH is consistent for all routes through 007c pipeline - sample info available through compound sample table
b) plate purposes LRC GEM-X 5p Aggregate onwards have sample-level information, regardless of their origin

It's under discussion with Abby (R&D), and we will probably raise it with some relevant faculty contacts at the next working group.

• Will the existing 10x pipelines work out of the box with sample-level information? (Existing 10x manifests import only pool-level information) If not, this will be a problem for plates coming through SeqOps from the previous entry points too.

There was one thing we needed to tweak, but these have been discovered already when we tested the route coming through SeqOps. (MultiStamp page validation broke due to multiple aliquots in the well having a reference to the same request id.)

[KatyTaylor]

Existing manifest

We may be able to re-use the manifest we have already developed for the previous entry point (#3857 - manifest type is called "scRNA Core Pools Plate")

Tested this - it works - so should be fine as long as we agree that sample-level info will be imported, and as long as noone comes up with any additional metadata we need to import.

[KatyTaylor]

On hold - waiting for Camille to set up a meeting with R&D and relevant faculty contacts, to discuss the importing of sample-level information.

[KatyTaylor]

Putting back in 'to do' until this meeting happens.

[KatyTaylor]

Discussed today - still worth considering discussing this, but not urgent because a) there's a way to get the samples in (specifying sample-level info), and b) cDNA plates come in already using the existing pipelines, and not sure when they'll move over to using this.