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10x Genomics raw data of intestinal plasma cells

The dataset contains raw fastq files (fastq.gz) for Chromium Single Cell 5’ gene expression (GEX), human B cell VDJ and feature barcode (CSP) sequencing from transglutaminase 2-specific and other small intestinal plasma cells isolated from four untreated celiac disease patients. Single cell 5’ gene expression, V(D)J-enriched and cell surface protein libraries were generated using Chromium single cell kits, and barcoded cDNA from a total of 5,000-10,000 cells per sample was generated using the 10x Genomics Chromium Controller. The libraries were pooled prior to sequencing on a NovaSeq 6000 instrument (Illumina) using the following configuration: read 1: 26 cycles, read 2: 89 cycles, index read 1: 8 cycles.

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scRNA-seq policy

DATA ACCESS AGREEMENT These terms and conditions govern access to the managed access datasets (details of which are set out in Appendix I) to which the User Institution has requested access. The User Institution agrees to be bound by these terms and conditions. Definitions Authorised Personnel: The individuals at the User Institution to whom the B-lineage cells in coeliac disease (BLCICD) Data Access Committee (DAC) for the datasets, hereafter termed BLCICD DAC, grants access to the Data. This includes the User, the individuals listed in Appendix II and any other individuals for whom the User Institution subsequently requests access to the Data. Details of the initial Authorised Personnel are set out in Appendix II. Data: The managed access datasets to which the User Institution has requested access. Data Producers: BLCICD DAC and the collaborators listed in Appendix I responsible for the development, organization, and oversight of these Data. External Collaborator: A collaborator of the User, working for an institution other than the User Institution. Project: The project for which the User Institution has requested access to these Data. A description of the Project is set out in Appendix II. Publications: Includes, without limitation, articles published in print journals, electronic journals, reviews, books, posters and other written and verbal presentations of research. Research Participant: An individual whose data form part of these Data. Research Purposes: Shall mean research that is seeking to advance the understanding of genetics and genomics in immunological mechanisms for celiac disease, including the treatment of disorders, and work on statistical methods that may be applied to such research. User: The principal investigator for the Project. User Institution(s): The Institution that has requested access to the Data. 1. The User Institution agrees to only use these Data for the purpose of the Project (described in Appendix II) and only for Research Purposes. The User Institution further agrees that it will only use these Data for Research Purposes which are within the limitations (if any) set out in Appendix I. 2. The User Institution is responsible for obtaining all necessary approvals in according to own national legislation before request for access to the data, including provide documentation for such approvals. 3. The User Institution agrees to preserve, at all times, the confidentiality of these Data in accordance to applicable legislation concerning protection of personal data protection. In particular, it undertakes not to use, or attempt to use these Data to compromise or otherwise infringe the confidentiality of information on Research Participants. Without prejudice to the generality of the foregoing, the User Institution agrees to use at least the measures set out in Appendix I to protect these Data. 4. The User Institution agrees to protect the confidentiality of Research Participants in any research papers or publications that they prepare by taking all reasonable care to limit the possibility of identification. 5. The User Institution agrees not to link or combine these Data to other information or archived data available in a way that could re-identify the Research Participants, even if access to that data has been formally granted to the User Institution or is freely available without restriction. 6. The User Institution agrees only to transfer or disclose these Data, in whole or part, or any material derived from these Data, to the Authorised Personnel. Should the User Institution wish to share these Data with an External Collaborator, the External Collaborator must complete a separate application for access to these Data. 7. The User Institution agrees that the Data Producers, and all other parties involved in the creation, funding or protection of these Data: a) make no warranty or representation, express or implied as to the accuracy, quality or comprehensiveness of these Data; b) exclude to the fullest extent permitted by law all liability for actions, claims, proceedings, demands, losses (including but not limited to loss of profit), costs, awards damages and payments made by the Recipient that may arise (whether directly or indirectly) in any way whatsoever from the Recipient’s use of these Data or from the unavailability of, or break in access to, these Data for whatever reason and; c) bear no responsibility for the further analysis or interpretation of these Data. 8. The User Institution agrees to follow the Fort Lauderdale Guidelines (http://www.wellcome.ac.uk/stellent/groups/corporatesite/@policy_communications/documents/web_document/wtd003207.pdf ) and the Toronto Statement (http://www.nature.com/nature/journal/v461/n7261/full/461168a.html). This includes but is not limited to recognising the contribution of the Data Producers and including a proper acknowledgement in all reports or publications resulting from the use of these Data. 9. The User Institution agrees to follow the Publication Policy in Appendix III. This includes respecting the moratorium period for the Data Producers to publish the first peer-reviewed report describing and analysing these Data. 10. The User Institution agrees not to make intellectual property claims on these Data and not to use intellectual property protection in ways that would prevent or block access to, or use of, any element of these Data, or conclusion drawn directly from these Data. 11. The User Institution can elect to perform further research that would add intellectual and resource capital to these data and decide to obtain intellectual property rights on these downstream discoveries. In this case, the User Institution agrees to implement licensing policies that will not obstruct further research and to follow the U.S. National Institutes of Health Best Practices for the Licensing of Genomic Inventions (2005) (https://www.icgc.org/files/daco/NIH_BestPracticesLicensingGenomicInventions_2005_en.pdf ) in conformity with the Organisation for Economic Co-operation and Development Guidelines for the Licensing of the Genetic Inventions (2006) (http://www.oecd.org/science/biotech/36198812.pdf ). 12. The User Institution agrees to destroy/discard the Data held, once it is no longer used for the Project, unless obliged to retain the data for archival purposes in conformity with audit or legal requirements. 13. The User Institution will notify BLCICD DAC within 30 days of any changes or departures of Authorised Personnel. 14. The User Institution will notify BLCICD DAC prior to any significant changes to the protocol for the Project. 15. The User Institution will notify BLCICD DAC as soon as it becomes aware of a breach of the terms or conditions of this agreement. 16. BLCICD DAC may terminate this agreement by written notice to the User Institution. If this agreement terminates for any reason, the User Institution will be required to destroy any Data held, including copies and backup copies. This clause does not prevent the User Institution from retaining these data for archival purpose in conformity with audit or legal requirements. 17. The User Institution accepts that it may be necessary for the Data Producers to alter the terms of this agreement from time to time. As an example, this may include specific provisions relating to the Data required by Data Producers other than BLCICD DAC. In the event that changes are required, the Data Producers or their appointed agent will contact the User Institution to inform it of the changes and the User Institution may elect to accept the changes or terminate the agreement. 18. If requested, the User Institution will allow data security and management documentation to be inspected to verify that it is complying with the terms of this agreement. 19. The User Institution agrees to distribute a copy of these terms to the Authorised Personnel. The User Institution will procure that the Authorised Personnel comply with the terms of this agreement. 20. This agreement (and any dispute, controversy, proceedings or claim of whatever nature arising out of this agreement or its formation) shall be construed, interpreted and governed by the laws of England and Wales and shall be subject to the exclusive jurisdiction of the English courts. APPENDIX I – DATASET DETAILS Dataset reference (EGA Study ID and Dataset Details) Name of project that created the dataset “Immunologisk basis for cøliaki (gluten indusert enteropati)” approved by The Regional Committee for Medical and Health Research Ethics South-East Norway (6544). Specific limitations on areas of research Usage of the data is limited to research that is seeking to advance the understanding of immunological mechanisms for autoimmune diseases. Minimum protection measures required File access: Data must be stored and analyzed on a secured institutional compute system with a minimum of two-factor authentication and without internet access. Furthermore, the data must at a minimum be secured with Unix user group read/write access for one or more appropriate groups but not Unix world read/write access. APPENDIX II – PROJECT DETAILS (to be completed by the Requestor) Details of dataset requested i.e., EGA Study and Dataset Accession Number Study: Datasets: Brief abstract of the Project in which the Data will be used (500 words max) All Individuals from the User Institution to be named as registered users Name of Registered User Email Job Title Supervisor* All Individuals that should have an account created at the EGA Name of Registered User Email Job Title   APPENDIX III – PUBLICATION POLICY BLCICD DAC intend to publish the results of their analysis of this dataset and do not consider its deposition into public databases to be the equivalent of such publications. DAC anticipate that the dataset could be useful to other qualified researchers for a variety of purposes. However, some areas of work are subject to a publication moratorium. The publication moratorium covers any publications (including oral communications) that describe the use of the dataset. For research papers, submission for publication should not occur until 3 months after these data were first made available on the relevant hosting database, unless BLCICD DAC has provided written consent to earlier submission. In any publications based on these data, please describe how the data can be accessed, including the name of the hosting database (e.g., The European Genome-phenome Archive at the European Bioinformatics Institute) and its accession number, and acknowledge its use in a form agreed by the User Institution with BLCICD DAC.

Studies are experimental investigations of a particular phenomenon, e.g., case-control studies on a particular trait or cancer research projects reporting matching cancer normal genomes from patients.

Study ID Study Title Study Type
EGAS50000000229 RNASeq

This table displays only public information pertaining to the files in the dataset. If you wish to access this dataset, please submit a request. If you already have access to these data files, please consult the download documentation.

ID File Type Size Located in
EGAF50000088925 fastq.gz 1.6 GB
EGAF50000088926 fastq.gz 450.9 MB
EGAF50000088927 fastq.gz 3.7 GB
EGAF50000088928 fastq.gz 57.3 MB
EGAF50000088929 fastq.gz 307.3 MB
EGAF50000088930 fastq.gz 156.1 MB
EGAF50000088931 fastq.gz 503.3 MB
EGAF50000088932 fastq.gz 85.4 MB
EGAF50000088933 fastq.gz 245.3 MB
EGAF50000088934 fastq.gz 156.4 MB
EGAF50000088935 fastq.gz 501.0 MB
EGAF50000088936 fastq.gz 1.1 GB
EGAF50000088937 fastq.gz 2.2 GB
EGAF50000088938 fastq.gz 5.3 GB
EGAF50000088939 fastq.gz 652.5 MB
EGAF50000088940 fastq.gz 2.3 GB
EGAF50000088941 fastq.gz 671.5 MB
EGAF50000088942 fastq.gz 5.4 GB
EGAF50000088943 fastq.gz 979.5 MB
EGAF50000088944 fastq.gz 163.0 MB
EGAF50000088945 fastq.gz 487.5 MB
EGAF50000088946 fastq.gz 162.7 MB
EGAF50000088947 fastq.gz 489.2 MB
EGAF50000088948 fastq.gz 963.7 MB
EGAF50000088949 fastq.gz 255.0 MB
EGAF50000088950 fastq.gz 514.3 MB
EGAF50000088951 fastq.gz 94.3 MB
EGAF50000088952 fastq.gz 1.1 GB
EGAF50000088953 fastq.gz 519.6 MB
EGAF50000088954 fastq.gz 166.3 MB
EGAF50000088989 fastq.gz 456.3 MB
EGAF50000088990 fastq.gz 3.7 GB
EGAF50000088991 fastq.gz 1.6 GB
EGAF50000088992 fastq.gz 154.8 MB
EGAF50000088993 fastq.gz 1.1 GB
EGAF50000088994 fastq.gz 491.9 MB
EGAF50000088995 fastq.gz 100.4 MB
EGAF50000088996 fastq.gz 294.8 MB
EGAF50000088997 fastq.gz 640.0 MB
EGAF50000088998 fastq.gz 1.7 GB
EGAF50000088999 fastq.gz 708.5 MB
EGAF50000089000 fastq.gz 231.9 MB
EGAF50000089001 fastq.gz 235.5 MB
EGAF50000089002 fastq.gz 722.0 MB
EGAF50000089003 fastq.gz 1.7 GB
EGAF50000089004 fastq.gz 5.2 GB
EGAF50000089005 fastq.gz 645.0 MB
EGAF50000089006 fastq.gz 2.2 GB
EGAF50000089007 fastq.gz 663.9 MB
EGAF50000089008 fastq.gz 5.3 GB
EGAF50000089009 fastq.gz 2.2 GB
EGAF50000089010 fastq.gz 155.4 MB
EGAF50000089011 fastq.gz 312.1 MB
EGAF50000089012 fastq.gz 57.3 MB
EGAF50000089013 fastq.gz 85.2 MB
EGAF50000089014 fastq.gz 244.6 MB
EGAF50000089015 fastq.gz 510.9 MB
EGAF50000089016 fastq.gz 94.2 MB
EGAF50000089017 fastq.gz 505.0 MB
EGAF50000089018 fastq.gz 255.6 MB
EGAF50000089531 fastq.gz 621.4 MB
EGAF50000089532 fastq.gz 286.9 MB
EGAF50000089533 fastq.gz 98.2 MB
EGAF50000089534 fastq.gz 772.7 MB
EGAF50000089535 fastq.gz 116.0 MB
EGAF50000089536 fastq.gz 357.0 MB
EGAF50000089537 fastq.gz 366.1 MB
EGAF50000089538 fastq.gz 794.2 MB
EGAF50000089539 fastq.gz 118.1 MB
EGAF50000089540 fastq.gz 168.1 MB
EGAF50000089541 fastq.gz 529.4 MB
EGAF50000089542 fastq.gz 1.2 GB
EGAF50000089599 csv 306.6 kB
73 Files (68.9 GB)