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mRNA and T cell receptor sequencing of patients with Pandemrix-associated narcolepsy type 1

PBMCs isolated from 27 individuals (11 narcolepsy type 1 patients, 16 healthy controls) were stimulated with the peptide Neuroaminidase 175-189 or Protein-O-mannosyl transferase 1 (POMT1) 675-689 or media as control. FACS sorted CD4+ and CD8+ lymphocytes from one patient were subjected to the same stimulation. Transcriptome profiling was done with a 3' tagging protocol. T cell receptor repertoires were profiled with amplicon sequencing (Rep-seq). The dataset contains FASTQ files with sequencing reads, transcript count matrices and TCR clonotypes.

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NARPANord Pandemrix-induced narcolepsy study

DATA ACCESS AGREEMENT [TEMPLATE] (“Agreement”) This Agreement is made by and between the following parties: University of Helsinki (“UH”), Faculty of Medicine, Research Programs Unit Business ID: FI0313471-7 Address: Yliopistonkatu 3 (P.O. Box 4) 00014 University of Helsinki, Finland and [NAME OF RECIPIENT] (“User Institution”) Business ID / similar: [ADD NUMBER] Address: [ADD ADDRESS] 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. 1. Definitions Authorized Personnel: The individuals at the User Institution to whom UH 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 Authorized Personnel are set out in Appendix II. Data: The managed access datasets to which the User Institution has requested access. Data may include personal data as defined in the EU General Data Protection Regulation (2016/679) (“GDPR”). Data Producers: UH 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: non-commercial 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 at the User Institution 2. Terms and Conditions 2.1. 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. 2.2. The User Institution agrees to use all reasonable efforts 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. 2.3. The User Institution agrees to use reasonable efforts to protect the confidentiality of Research Participants in any research papers or publications that they prepare by taking reasonable care to limit the possibility of identification. 2.4. 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. 2.5. The User Institution agrees only to transfer or disclose these Data, in whole or part, or any material derived from these Data, to the Authorized 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. 2.6. 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. Notwithstanding the above, the User Institution will not be responsible for claims arising from or related to the negligence or willful misconduct of the Data Producers, other parties involved in the creation, funding or protection of these Data, or their officers, agents or employees, or any person or entity not subject to User Institution’s supervision or control. 2.7. The User Institution agrees to follow the Fort Lauderdale Guidelines (attached as Appendix IV) and the Toronto Statement (as attached in Appendix III). This includes but is not limited to recognizing the contribution of the Data Producers and including a proper acknowledgement in all reports or publications resulting from the use of these Data. 2.8. 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 analyzing these Data. 2.9. 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. 2.10. 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 non-commercial research and to follow the U.S. National Institutes of Health Best Practices for the Licensing of Genomic Inventions (2005) (attached as Appendix V ) in conformity with the Organisation for Economic Co-operation and Development Guidelines for the Licensing of the Genetic Inventions (2006) (attached as Appendix VI). 2.11. 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. 2.12. The User Institution will notify UH within 30 days of any changes or departures of Authorized Personnel. 2.13. The User Institution will notify UH prior to any significant changes to the protocol for the Project. 2.14. The User Institution will promptly notify UH should it become aware of a breach of the terms or conditions of this agreement. 2.15. Either Party may terminate this agreement for any reason by provided thirty (30) days prior written notice to the other Party. If this agreement terminates for any reason, the User Institution will be required to destroy any Data held, including copies and backup copies. The User Institution accepts that it may be necessary for the Data Producers to alter the terms of this agreement from time to time. 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. Any such changes shall be implemented upon execution of a dually signed amendment to this Agreement. 2.16. If requested, upon advance written notice, and to the extent necessary, during mutually agreeable normal administrative business hours 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. Any such visits shall be scheduled in coordination with User Institution, and shall be subject to compliance with User Institution’s reasonable measures for confidentiality, safety and security, and shall also be subject to compliance with generally applicable premises rules at User Institution. 2.17. The User Institution agrees to distribute a copy of these terms to the Authorized Personnel. The User Institution will require that the Authorized Personnel comply with the terms of this agreement. 2.18. The User Institution understands that upon receipt of the Data that includes or constitutes Personal Data, it will become a data controller as meant in the General Data Protection Regulation (2016/679) (“GDPR”). 2.19. IF THE USER INSTITUTION IS NOT LOCATED WITHIN THE EEA / A COUNTRY WITH AN ADEQUACY DECISION: As a data controller, the User Institution shall comply with, the terms and conditions set out in the Controller-Controller Standard Contractual Clauses appended to this Agreement as Appendix VII. In case of discrepancy between the provisions of Appendix VII and any other document included in this Agreement and/or its appendices, the provision included in Appendix VII shall prevail. 2.20 UH or its representative may at any moment inform the User Institution of a Research Participant withdrawing their consent or exercising their rights as a data subject under the GDPR. The User Institution shall perform all actions necessary in order to fulfil the rights of the Research Participant. 2.21 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 Finland and shall be subject to the exclusive jurisdiction of the Finnish courts. 2.22 This Agreement may be executed in counterparts, each and every one of which shall be deemed an original and all of which together shall constitute one and the same instrument. Each party may execute the Agreement in Adobe Portable Document Format (PDF) sent by electronic mail or as otherwise agreed between the parties. PDF signatures of authorised signatories of the parties shall be deemed to be original signatures, shall be valid and binding upon the parties, and, upon delivery, shall constitute due execution of this Agreement.

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
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
EGAF00004953450 fastq.gz 3.4 MB
EGAF00004953451 fastq.gz 6.0 MB
EGAF00004953452 fastq.gz 18.9 MB
EGAF00004953453 fastq.gz 33.2 MB
EGAF00004953454 fastq.gz 6.2 MB
EGAF00004953455 fastq.gz 15.0 MB
EGAF00004953456 fastq.gz 852.6 kB
EGAF00004953457 fastq.gz 2.4 MB
EGAF00004953458 fastq.gz 11.1 MB
EGAF00004953459 fastq.gz 19.2 MB
EGAF00004953460 fastq.gz 8.6 MB
EGAF00004953461 fastq.gz 15.7 MB
EGAF00004953462 fastq.gz 38.9 MB
EGAF00004953463 fastq.gz 78.4 MB
EGAF00004953464 fastq.gz 10.0 MB
EGAF00004953465 fastq.gz 17.1 MB
EGAF00004953466 fastq.gz 54.3 MB
EGAF00004953467 fastq.gz 98.8 MB
EGAF00004953468 fastq.gz 9.4 MB
EGAF00004953469 fastq.gz 16.3 MB
EGAF00004953470 fastq.gz 165.2 MB
EGAF00004953471 fastq.gz 408.7 MB
EGAF00004953472 fastq.gz 97.3 MB
EGAF00004953473 fastq.gz 245.4 MB
EGAF00004953474 fastq.gz 1.1 GB
EGAF00004953475 fastq.gz 1.1 GB
EGAF00004953476 fastq.gz 709.4 kB
EGAF00004953477 fastq.gz 2.8 MB
EGAF00004953478 fastq.gz 117.0 kB
EGAF00004953479 fastq.gz 250.1 kB
EGAF00004953480 fastq.gz 2.1 MB
EGAF00004953481 fastq.gz 7.3 MB
EGAF00004953483 fastq.gz 6.8 MB
EGAF00004953484 fastq.gz 92.5 kB
EGAF00004953485 fastq.gz 688.4 kB
EGAF00004953486 fastq.gz 251.6 kB
EGAF00004953487 fastq.gz 1.4 MB
EGAF00004953488 fastq.gz 16.9 MB
EGAF00004953489 fastq.gz 30.5 MB
EGAF00004953491 fastq.gz 3.1 MB
EGAF00004953492 fastq.gz 15.8 MB
EGAF00004953493 fastq.gz 28.9 MB
EGAF00004953494 fastq.gz 19.1 MB
EGAF00004953495 fastq.gz 35.4 MB
EGAF00004953496 fastq.gz 29.8 MB
EGAF00004953497 fastq.gz 54.7 MB
EGAF00004953498 fastq.gz 18.8 MB
EGAF00004953499 fastq.gz 34.2 MB
EGAF00004953500 fastq.gz 2.2 MB
EGAF00004953501 fastq.gz 4.8 MB
EGAF00004953502 fastq.gz 9.8 MB
EGAF00004953503 fastq.gz 17.2 MB
EGAF00004953504 fastq.gz 42.2 MB
EGAF00004953505 fastq.gz 72.5 MB
EGAF00004953506 fastq.gz 5.2 MB
EGAF00004953507 fastq.gz 12.0 MB
EGAF00004953508 fastq.gz 81.1 MB
EGAF00004953509 fastq.gz 143.9 MB
EGAF00004953510 fastq.gz 51.3 MB
EGAF00004953511 fastq.gz 87.3 MB
EGAF00004953512 fastq.gz 6.0 MB
EGAF00004953513 fastq.gz 11.4 MB
EGAF00004953514 fastq.gz 6.8 MB
EGAF00004953529 fastq.gz 2.1 GB
EGAF00004953571 fastq.gz 26.6 MB
EGAF00004953572 fastq.gz 21.5 MB
EGAF00004953573 fastq.gz 40.1 MB
EGAF00004953574 fastq.gz 2.4 MB
EGAF00004953575 fastq.gz 4.5 MB
EGAF00004953576 fastq.gz 7.1 MB
EGAF00004953577 fastq.gz 12.7 MB
EGAF00004953578 fastq.gz 20.0 MB
EGAF00004953579 fastq.gz 38.8 MB
EGAF00004953580 fastq.gz 20.7 MB
EGAF00004953581 fastq.gz 38.5 MB
EGAF00004953582 fastq.gz 5.5 MB
EGAF00004953583 fastq.gz 13.5 MB
EGAF00004953584 fastq.gz 4.0 MB
EGAF00004953585 fastq.gz 7.0 MB
EGAF00004953586 fastq.gz 7.9 MB
EGAF00004953587 fastq.gz 14.2 MB
EGAF00004953588 fastq.gz 7.9 MB
EGAF00004953589 fastq.gz 13.4 MB
EGAF00004953590 fastq.gz 998.5 MB
EGAF00004953591 fastq.gz 2.6 GB
EGAF00004953592 fastq.gz 9.6 MB
EGAF00004953593 fastq.gz 16.1 MB
EGAF00004953594 fastq.gz 749.1 MB
EGAF00004953595 fastq.gz 1.9 GB
EGAF00004953596 fastq.gz 629.5 MB
EGAF00004953597 fastq.gz 1.6 GB
EGAF00004953598 fastq.gz 24.6 MB
EGAF00004953599 fastq.gz 45.2 MB
EGAF00004953600 fastq.gz 892.6 kB
EGAF00004953601 fastq.gz 3.4 MB
EGAF00004953602 fastq.gz 44.5 MB
EGAF00004953603 fastq.gz 84.2 MB
EGAF00004953604 fastq.gz 11.5 MB
EGAF00004953605 fastq.gz 27.1 MB
EGAF00004953606 fastq.gz 6.4 MB
EGAF00004953607 fastq.gz 15.6 MB
EGAF00004953608 fastq.gz 29.8 MB
EGAF00004953609 fastq.gz 50.0 MB
EGAF00004953610 fastq.gz 19.7 MB
EGAF00004953611 fastq.gz 35.8 MB
EGAF00004953616 txt 5.8 MB
EGAF00004953617 txt 562.2 kB
EGAF00004953618 csv 10.3 kB
EGAF00004953619 tar.gz 18.7 MB
109 Files (15.8 GB)