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single-cell transcriptomics data from immune cells

Smart-seq2 protocol was used to perform single cell RNA-sequencing on 465 immune cells. The immune cells analysed include 215 HLA-DQ2: gluten-(DQ2.5-glia-α1, -α2, -ω1, and -ω2) tetramer-sorted T cells, 247 transglutaminase 2 (TG2)-positive plasma cells from intestinal biopsy or peripheral blood from celiac disease patients, and 3 unassigned cells in 3 batches.

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DATA ACCESS AGREEMENT (EGAS00001002911)

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 Shuo Wang Qiao 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: Shuo Wang Qiao and the collaborators listed in Appendix I responsible for the development, organisation, 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, 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. XXXXX: Your Institution details here 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 agrees to preserve, at all times, the confidentiality of these Data. 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. 3. 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. 4. 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. 5. 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. 6. 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. 7. 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. 8. 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. 9. 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. 10. 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 ). 11. 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. 12. The User Institution will notify Shuo Wang Qiao within 30 days of any changes or departures of Authorised Personnel. 13. The User Institution will notify Shuo Wang Qiao prior to any significant changes to the protocol for the Project. 14. The User Institution will notify Shuo Wang Qiao as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. Shuo Wang Qiao 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. 16. 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 Shuo Wang Qiao. 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. 17. 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. 18. 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. 19. 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 Norway and shall be subject to the exclusive jurisdiction of the Norwegian courts. Agreed for User Institution Signature: Name: Title: Date: Principal Investigator I confirm that I have read and understood this Agreement. Signature: Name: Title: Date: Agreed for University of Oslo Signature: Name: Title: Date: APPENDIX I – DATASET DETAILS APPENDIX II ––PROJECT DETAILS APPENDIX III –– PUBLICATION POLICY APPENDIX I – DATASET DETAILS Dataset reference EGA Study ID: EGAS00001002911 Dataset Details: The immune cells including 215 HLA-DQ2: gluten-(DQ2.5-glia-α1, -α2, -ω1, and -ω2) tetramer-sorted T cells, 247 transglutaminase 2 (TG2)-positive plasma cells, and 3 unassigned cells in 3 batches were sampled from intestinal biopsy or peripheral blood from celiac disease patients. We used the Smart-seq2 protocol to perform single cell RNA-sequencing. The data is provided as fastq files. Name of project that created the dataset Exploiting immune cell receptor information to quantify index switching in single cell transcriptome sequencing experiment Names of other data producers/collaborators Shuo-Wang Qiao Ying Yao Specific limitations on areas of research Should not be used to query for disease-associated genotype. Should not be used for person identification of any kind. Minimum protection measures required File access: Data can be held in encrypted files on an institutional compute system, with Unix user group read/write access for one or more appropriate groups but not Unix world read/write access behind a secure firewall. Laptops holding these data should only be used for temperary transfer of data and data should be deleted from the laptops after the transfer is complete. If held on USB keys or other portable hard drives, the data must be encrypted. APPENDIX II – PROJECT DETAILS (to be completed by the Requestor) Details of dataset requested i.e., EGA Study and Dataset Accession Number Brief abstract of the Project in which the Data will be used (500 words max) All Individuals who 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 Shuo Wang Qiao 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. Shuo Wang Qiao 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 12 months after these data were first made available on the relevant hosting database, unless Shuo Wang Qiao 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 (The European Genome-phenome Archive at the European Bioinformatics Institute) and its accession numbers (EGAS00001002911), and acknowledge its use in a form agreed by the User Institution with Shuo Wang Qiao.

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
EGAS00001002911 Other

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
EGAF00001963222 fastq.gz 31.4 MB
EGAF00001963223 fastq.gz 35.6 MB
EGAF00001963224 fastq.gz 35.9 MB
EGAF00001963225 fastq.gz 39.5 MB
EGAF00001963226 fastq.gz 54.0 MB
EGAF00001963227 fastq.gz 68.8 MB
EGAF00001963228 fastq.gz 10.4 MB
EGAF00001963229 fastq.gz 11.9 MB
EGAF00001963230 fastq.gz 15.2 MB
EGAF00001963231 fastq.gz 16.8 MB
EGAF00001963232 fastq.gz 154.5 MB
EGAF00001963233 fastq.gz 176.0 MB
EGAF00001963234 fastq.gz 217.2 MB
EGAF00001963235 fastq.gz 245.4 MB
EGAF00001963236 fastq.gz 23.4 MB
EGAF00001963237 fastq.gz 26.0 MB
EGAF00001963268 fastq.gz 8.0 MB
EGAF00001963269 fastq.gz 8.8 MB
EGAF00001963270 fastq.gz 16.7 MB
EGAF00001963271 fastq.gz 18.1 MB
EGAF00001963272 fastq.gz 37.0 MB
EGAF00001963273 fastq.gz 41.5 MB
EGAF00001963274 fastq.gz 160.2 MB
EGAF00001963275 fastq.gz 182.3 MB
EGAF00001963276 fastq.gz 223.9 MB
EGAF00001963277 fastq.gz 264.8 MB
EGAF00001963278 fastq.gz 163.7 MB
EGAF00001963279 fastq.gz 194.6 MB
EGAF00001963280 fastq.gz 54.6 MB
EGAF00001963281 fastq.gz 60.4 MB
EGAF00001963282 fastq.gz 141.6 MB
EGAF00001963283 fastq.gz 158.5 MB
EGAF00001963284 fastq.gz 113.7 MB
EGAF00001963285 fastq.gz 126.5 MB
EGAF00001963286 fastq.gz 361.4 MB
EGAF00001963287 fastq.gz 415.2 MB
EGAF00001963288 fastq.gz 978.3 MB
EGAF00001963289 fastq.gz 1.2 GB
EGAF00001963290 fastq.gz 9.9 MB
EGAF00001963291 fastq.gz 11.1 MB
EGAF00001963292 fastq.gz 116.4 MB
EGAF00001963293 fastq.gz 130.8 MB
EGAF00001963294 fastq.gz 154.9 MB
EGAF00001963295 fastq.gz 188.5 MB
EGAF00001963296 fastq.gz 8.7 MB
EGAF00001963297 fastq.gz 9.7 MB
EGAF00001963298 fastq.gz 482.6 MB
EGAF00001963299 fastq.gz 584.2 MB
EGAF00001963330 fastq.gz 374.3 MB
EGAF00001963331 fastq.gz 444.7 MB
EGAF00001963332 fastq.gz 201.5 MB
EGAF00001963333 fastq.gz 232.2 MB
EGAF00001963334 fastq.gz 530.9 MB
EGAF00001963335 fastq.gz 669.6 MB
EGAF00001963336 fastq.gz 250.8 MB
EGAF00001963337 fastq.gz 301.6 MB
EGAF00001963338 fastq.gz 117.3 MB
EGAF00001963339 fastq.gz 133.6 MB
EGAF00001963340 fastq.gz 444.0 MB
EGAF00001963341 fastq.gz 584.2 MB
EGAF00001963342 fastq.gz 6.2 MB
EGAF00001963343 fastq.gz 6.9 MB
EGAF00001963344 fastq.gz 7.3 MB
EGAF00001963345 fastq.gz 8.5 MB
EGAF00001963346 fastq.gz 123.6 MB
EGAF00001963347 fastq.gz 139.8 MB
EGAF00001963348 fastq.gz 111.9 MB
EGAF00001963349 fastq.gz 129.8 MB
EGAF00001963350 fastq.gz 47.6 MB
EGAF00001963351 fastq.gz 52.9 MB
EGAF00001963352 fastq.gz 131.2 MB
EGAF00001963353 fastq.gz 148.1 MB
EGAF00001963354 fastq.gz 314.5 MB
EGAF00001963355 fastq.gz 397.9 MB
EGAF00001963356 fastq.gz 145.8 MB
EGAF00001963357 fastq.gz 165.8 MB
EGAF00001963358 fastq.gz 56.3 MB
EGAF00001963359 fastq.gz 63.0 MB
EGAF00001963360 fastq.gz 443.2 MB
EGAF00001963361 fastq.gz 549.9 MB
EGAF00001963392 fastq.gz 256.7 MB
EGAF00001963393 fastq.gz 302.6 MB
EGAF00001963394 fastq.gz 61.0 MB
EGAF00001963395 fastq.gz 68.0 MB
EGAF00001963396 fastq.gz 584.3 MB
EGAF00001963397 fastq.gz 741.4 MB
EGAF00001963398 fastq.gz 76.4 MB
EGAF00001963399 fastq.gz 85.2 MB
EGAF00001963400 fastq.gz 40.0 MB
EGAF00001963401 fastq.gz 43.9 MB
EGAF00001963402 fastq.gz 2.2 MB
EGAF00001963403 fastq.gz 2.4 MB
EGAF00001963404 fastq.gz 7.7 MB
EGAF00001963405 fastq.gz 8.7 MB
EGAF00001963406 fastq.gz 5.4 MB
EGAF00001963407 fastq.gz 5.9 MB
EGAF00001963408 fastq.gz 101.8 MB
EGAF00001963409 fastq.gz 116.8 MB
EGAF00001963410 fastq.gz 96.5 MB
EGAF00001963411 fastq.gz 109.9 MB
EGAF00001963412 fastq.gz 5.6 MB
EGAF00001963413 fastq.gz 6.3 MB
EGAF00001963414 fastq.gz 355.4 MB
EGAF00001963415 fastq.gz 443.9 MB
EGAF00001963416 fastq.gz 134.1 MB
EGAF00001963417 fastq.gz 149.1 MB
EGAF00001963418 fastq.gz 29.5 MB
EGAF00001963419 fastq.gz 32.7 MB
EGAF00001963420 fastq.gz 9.5 MB
EGAF00001963421 fastq.gz 11.3 MB
EGAF00001963422 fastq.gz 791.1 MB
EGAF00001963423 fastq.gz 959.3 MB
EGAF00001963454 fastq.gz 50.3 MB
EGAF00001963455 fastq.gz 53.5 MB
EGAF00001963456 fastq.gz 43.5 MB
EGAF00001963457 fastq.gz 49.2 MB
EGAF00001963458 fastq.gz 1.3 MB
EGAF00001963459 fastq.gz 1.6 MB
EGAF00001963460 fastq.gz 48.2 MB
EGAF00001963461 fastq.gz 56.8 MB
EGAF00001963462 fastq.gz 721.5 MB
EGAF00001963463 fastq.gz 867.9 MB
EGAF00001963464 fastq.gz 178.9 MB
EGAF00001963465 fastq.gz 207.5 MB
EGAF00001963466 fastq.gz 43.4 MB
EGAF00001963467 fastq.gz 49.9 MB
EGAF00001963468 fastq.gz 291.6 MB
EGAF00001963469 fastq.gz 345.5 MB
EGAF00001963470 fastq.gz 301.4 MB
EGAF00001963471 fastq.gz 339.7 MB
EGAF00001963472 fastq.gz 663.8 MB
EGAF00001963473 fastq.gz 784.0 MB
EGAF00001963474 fastq.gz 289.3 MB
EGAF00001963475 fastq.gz 326.6 MB
EGAF00001963476 fastq.gz 18.0 MB
EGAF00001963477 fastq.gz 19.8 MB
EGAF00001963478 fastq.gz 355.2 MB
EGAF00001963479 fastq.gz 424.4 MB
EGAF00001963480 fastq.gz 21.1 MB
EGAF00001963481 fastq.gz 23.6 MB
EGAF00001963482 fastq.gz 1.6 MB
EGAF00001963483 fastq.gz 1.8 MB
EGAF00001963484 fastq.gz 8.0 MB
EGAF00001963485 fastq.gz 8.8 MB
EGAF00001963516 fastq.gz 130.9 MB
EGAF00001963517 fastq.gz 149.5 MB
EGAF00001963518 fastq.gz 54.3 MB
EGAF00001963519 fastq.gz 61.1 MB
EGAF00001963520 fastq.gz 576.5 MB
EGAF00001963521 fastq.gz 743.9 MB
EGAF00001963522 fastq.gz 95.3 MB
EGAF00001963523 fastq.gz 105.7 MB
EGAF00001963524 fastq.gz 243.6 MB
EGAF00001963525 fastq.gz 276.0 MB
EGAF00001963526 fastq.gz 78.6 MB
EGAF00001963527 fastq.gz 87.2 MB
EGAF00001963528 fastq.gz 690.5 MB
EGAF00001963529 fastq.gz 781.7 MB
EGAF00001963530 fastq.gz 163.7 MB
EGAF00001963531 fastq.gz 179.5 MB
EGAF00001963532 fastq.gz 166.0 MB
EGAF00001963533 fastq.gz 192.3 MB
EGAF00001963534 fastq.gz 19.5 MB
EGAF00001963535 fastq.gz 21.5 MB
EGAF00001963536 fastq.gz 887.2 kB
EGAF00001963537 fastq.gz 996.2 kB
EGAF00001963538 fastq.gz 105.4 MB
EGAF00001963539 fastq.gz 138.2 MB
EGAF00001963540 fastq.gz 195.8 MB
EGAF00001963541 fastq.gz 225.7 MB
EGAF00001963542 fastq.gz 159.3 MB
EGAF00001963543 fastq.gz 182.3 MB
EGAF00001963544 fastq.gz 202.5 MB
EGAF00001963545 fastq.gz 230.4 MB
EGAF00001963546 fastq.gz 126.3 MB
EGAF00001963547 fastq.gz 143.7 MB
EGAF00001963578 fastq.gz 111.3 MB
EGAF00001963579 fastq.gz 122.3 MB
EGAF00001963580 fastq.gz 7.7 MB
EGAF00001963581 fastq.gz 8.0 MB
EGAF00001963582 fastq.gz 152.4 MB
EGAF00001963583 fastq.gz 164.6 MB
EGAF00001963584 fastq.gz 128.0 MB
EGAF00001963585 fastq.gz 145.8 MB
EGAF00001963586 fastq.gz 1.8 MB
EGAF00001963587 fastq.gz 2.1 MB
EGAF00001963588 fastq.gz 15.3 MB
EGAF00001963589 fastq.gz 16.8 MB
EGAF00001963590 fastq.gz 4.3 MB
EGAF00001963591 fastq.gz 4.8 MB
EGAF00001963592 fastq.gz 37.6 MB
EGAF00001963593 fastq.gz 42.4 MB
EGAF00001963594 fastq.gz 38.9 MB
EGAF00001963595 fastq.gz 42.3 MB
EGAF00001963596 fastq.gz 90.8 MB
EGAF00001963597 fastq.gz 102.8 MB
EGAF00001963598 fastq.gz 133.6 MB
EGAF00001963599 fastq.gz 150.8 MB
EGAF00001963600 fastq.gz 188.7 MB
EGAF00001963601 fastq.gz 222.7 MB
200 Files (35.8 GB)