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CODE_OF_CONDUCT.md

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+---
+title: "Contributor Code of Conduct"
+---
+
+As contributors and maintainers of this project,
+we pledge to follow the [The Carpentries Code of Conduct][coc].
+
+Instances of abusive, harassing, or otherwise unacceptable behavior
+may be reported by following our [reporting guidelines][coc-reporting].
+
+
+[coc-reporting]: https://docs.carpentries.org/topic_folders/policies/incident-reporting.html
+[coc]: https://docs.carpentries.org/topic_folders/policies/code-of-conduct.html

LICENSE.md

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+---
+title: "Licenses"
+---
+
+## Instructional Material
+
+All Carpentries (Software Carpentry, Data Carpentry, and Library Carpentry)
+instructional material is made available under the [Creative Commons
+Attribution license][cc-by-human]. The following is a human-readable summary of
+(and not a substitute for) the [full legal text of the CC BY 4.0
+license][cc-by-legal].
+
+You are free:
+
+- to **Share**---copy and redistribute the material in any medium or format
+- to **Adapt**---remix, transform, and build upon the material
+
+for any purpose, even commercially.
+
+The licensor cannot revoke these freedoms as long as you follow the license
+terms.
+
+Under the following terms:
+
+- **Attribution**---You must give appropriate credit (mentioning that your work
+  is derived from work that is Copyright (c) The Carpentries and, where
+  practical, linking to <https://carpentries.org/>), provide a [link to the
+  license][cc-by-human], and indicate if changes were made. You may do so in
+  any reasonable manner, but not in any way that suggests the licensor endorses
+  you or your use.
+
+- **No additional restrictions**---You may not apply legal terms or
+  technological measures that legally restrict others from doing anything the
+  license permits.  With the understanding that:
+
+Notices:
+
+* You do not have to comply with the license for elements of the material in
+  the public domain or where your use is permitted by an applicable exception
+  or limitation.
+* No warranties are given. The license may not give you all of the permissions
+  necessary for your intended use. For example, other rights such as publicity,
+  privacy, or moral rights may limit how you use the material.
+
+## Software
+
+Except where otherwise noted, the example programs and other software provided
+by The Carpentries are made available under the [OSI][osi]-approved [MIT
+license][mit-license].
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of
+this software and associated documentation files (the "Software"), to deal in
+the Software without restriction, including without limitation the rights to
+use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies
+of the Software, and to permit persons to whom the Software is furnished to do
+so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+
+## Trademark
+
+"The Carpentries", "Software Carpentry", "Data Carpentry", and "Library
+Carpentry" and their respective logos are registered trademarks of [Community
+Initiatives][ci].
+
+[cc-by-human]: https://creativecommons.org/licenses/by/4.0/
+[cc-by-legal]: https://creativecommons.org/licenses/by/4.0/legalcode
+[mit-license]: https://opensource.org/licenses/mit-license.html
+[ci]: https://communityin.org/
+[osi]: https://opensource.org

data/E-MTAB-11349.idf.txt

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+MAGE-TAB Version	1.1
+Investigation Title	Whole blood expression profiling of patients with inflammatory bowel diseases in IBD-Character cohort
+
+Experimental Design	case control design
+Experimental Design Term Source REF	EFO
+Experimental Design Term Accession Number	EFO:0001427
+
+Experimental Factor Name	disease
+Experimental Factor Type	disease
+Experimental Factor Term Source REF	EFO
+Experimental Factor Term Accession Number	EFO_0000408
+
+Person Last Name	Halfvarson	Kalla	Adams	Satsangi	Nowak
+Person First Name	Jonas	Rahul	Alex	Jack	Jan
+Person Mid Initials			T		K
+Person Email	jonas.halfvarsson@regionorebrolan.se	Rahul.Kalla@ed.ac.uk	alex.adams@ndm.ox.ac.uk	jack.satsangi@ndm.ox.ac.uk	jan.nowak@ump.edu.pl
+Person Phone
+Person Fax
+Person Affiliation	Department of Gastroenterology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden	MRC Centre for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom	Translational Gastroenterology Unit, Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom	Translational Gastroenterology Unit, Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom - and - Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom	Translational Gastroenterology Unit, Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom - and - Department of Pediatric Gastroenterology and Metabolic Diseases, Poznan University of Medical Sciences, Poznan, Poland
+Person Address	Örebro University, SE-701 82, Örebro, Sweden	47 Little France Crescent, Edinburgh, EH16 4TJ, UK	Experimental Medicine Division, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DU, UK	Experimental Medicine Division, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DU, UK	Experimental Medicine Division, John Radcliffe Hospital, Headley Way, Headington, Oxford, OX3 9DU, UK
+Person Roles	investigator	investigator	investigator	investigator	submitter
+Person Roles Term Source REF
+Person Roles Term Accession Number
+
+Quality Control Type
+Quality Control Term Source REF
+Quality Control Term Accession Number
+
+Replicate Type
+Replicate Term Source REF
+Replicate Term Accession Number
+
+Normalization Type
+Normalization Term Source REF
+Normalization Term Accession Number
+
+Date of Experiment	2017-01-01
+Public Release Date	2022-03-01
+
+PubMed ID
+Publication DOI
+Publication Author List
+Publication Title
+Publication Status
+Publication Status Term Source REF
+Publication Status Term Accession Number
+
+Experiment Description	The IBD-Character cohort (Edinburgh, Oslo, Örebro, Linköping, Zaragoza, Maastricht) included patients with inflammatory bowel diseases (IBD: Crohn's disease, ulcerative colitis) recruited at diagnosis and non-IBD controls. Paired-end RNA sequencing was used for whole blood expression profiling. Raw and normalized counts tables are provided.
+
+Protocol Name	P-MTAB-117949	P-MTAB-117946	P-MTAB-117948	P-MTAB-117947	P-MTAB-117950
+Protocol Type	normalization data transformation protocol	sample collection protocol	nucleic acid library construction protocol	nucleic acid extraction protocol	nucleic acid sequencing protocol
+Protocol Term Source REF	EFO	EFO	EFO	EFO	EFO
+Protocol Term Accession Number	EFO_0003816	EFO_0005518	EFO_0004184	EFO_0002944	EFO_0004170
+Protocol Description	Normalization: DESeq2, only includes transcripts with mean raw expression > 10.	Blood collection: PAXgene tubes.	AmpliSeq Library Kit Plus, Ion AmpliSeq Human Gene Expression Core Panel. Libraries were combined for template preparation: equimolar pools of 8 samples. Quality check: Ion Library TaqmanTM Quantitation kit.	Quantification: Qubit 2.0.	Alignment to hg19: Torrent Software v. 4.6, ampliSeqRNA plugin v. 4.6.0.1.
+Protocol Parameters
+Protocol Hardware					unspecified
+Protocol Software
+Protocol Contact
+
+Term Source Name	EFO	ArrayExpress
+Term Source File	http://www.ebi.ac.uk/efo/	http://www.ebi.ac.uk/arrayexpress/
+Term Source Version	http://www.ebi.ac.uk/efo/
+
+SDRF File	E-MTAB-11349.sdrf.txt
+Comment [Submitted Name]	Whole blood expression profiling of patients with inflammatory bowel diseases in IBD-Character cohort
+Comment [TemplateType]	Human - High-throughput sequencing
+Comment [AEExperimentType]	RNA-seq of coding RNA
+Comment[ArrayExpressAccession]	E-MTAB-11349