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Transcriptome analysis of CD8 T-cells from blood, fat, liver and skin

CD8 Tcells were FACS sorted and processed with 10x Genomics Chromium Next GEM SingleCell V(D)J Reagents Kits v1.1 sequencing. In total 6 samples were processed. Fastq files are supplied.

Request Access

DATA Access Agreement between LIT and data user. Based on GDPR and informed consent by the donor.

DATA ACCESS AGREEMENT Between : LIT Leibniz-Institute for Immunotherapy, represented by the Director Prof. Dr. Philipp Beckhove, Project Leader: Prof. Dr. Markus Feuerer, LIT c/o University Hospital Regensburg, Franz-Josef-Strauß-Allee 11, D-93053 Regensburg, Germany -Data Producers/LIT Leibniz-Institute for Immunotherapy- and -USER- 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 LIT Leibniz-Institute for Immunotherapy 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: LIT Leibniz-Institute for Immunotherapy (further referred to as LIT) 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. Data Producers Details: LIT Leibniz-Institute for Immunotherapy c/o University Hospital Regensburg Franz-Josef-Strauß-Allee 11 D-93053 Regensburg Germany Phone: +49 941 944-38100 Fax: +49 941 944-38103 Email: info(at)LIT.de LIT NextGenerationSequencing-Core (NGS-Core) Phone: +49 941 944-18188 email: genomics-core@rcii.de 1. The User Institution agrees to comply with all applicable regulations, especially the General Data Protection Regulation (GDPR), 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 ( https://commonfund.nih.gov/sites/default/files/WellcomeReport0303.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 OECD’s (Organisation for Economic Co-operation and Development) Guidelines for the Licensing of the Genetic Inventions (2006) (https://www.oecd.org/sti/emerging-tech/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 the LIT within 30 days of any changes or departures of Authorised Personnel. 13. The User Institution will notify the LIT prior to any significant changes to the protocol for the Project. 14. The User Institution will notify the LIT as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. Either party may terminate this agreement by 30 days 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. 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 via a written amendment to this agreement signed by an authorized representative of the parties. As an example, this may include specific provisions relating to the Data required by Data Producers other than LIT. 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 Germany and shall be subject to the exclusive jurisdiction of the courts of Regensburg, Germany. 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 the Data Producers / LIT: Signature:   Name:  Prof. Dr. Philipp Beckhove Title:   Director of the LIT Date:   Acknowledged and agreed: Signature:   Name: Title: Project Leader Date:   APPENDIX I – DATASET DETAILS APPENDIX II ––PROJECT DETAILS APPENDIX III –– PUBLICATION POLICY APPENDIX I – DATASET DETAILS (to be completed by the data producer before passing to applicant) Dataset reference (EGA Study ID and Dataset Details) EGA StudyID: EGA DatasetID: EGAD0 Name of project that created the dataset : Names of other data producers/collaborators: Specific limitations on areas of research Health/Medical/Biomedical Research Use (DUO:0000006) Research Ethics Approval Required (DUO:0000021) user specific restriction (DUO:0000026) non-commercial use only (DUO:0000046) not for profit, non-commercial use only (DUO:0000018) research specific restrictions (DUO:0000012) data use permission (DUO:0000001) Legal basis for Data sharing: The User and User institution shall be responsible for the acquired personal data as defined in the General Data Protection Regulation (GDPR) (https://eur-lex.europa.eu/legal-content/EN/TXT/?uri=CELEX:02016R0679-20160504). The GDPR is a binding law, which is publicly available. The wording and content of the law cannot be changed via an agreement. We ask the user and user institution to especially consider Article 24 and 25 GDPR in particular in conjunction with Article 5 Paragraph 1, and Paragraph 2 GDPR. The measures to be taken are state of the art measures of data security and measures that guarantee a protection level appropriate to the risk concerning confidentiality, integrity, availability and resilience of the systems. The state of the art, implementation costs, the nature, scope and purposes of processing as well as the probability of occurrence and the severity of the risk to the rights and freedoms of natural persons within the meaning of Article 32 Paragraph 1 GDPR must be taken into account. The Technical and Organisational Measures are subject to technical progress and further development. In this respect, it is permissible for the Supplier to implement alternative adequate measures. In so doing, the security level of the defined measures must not be reduced. Substantial changes must be documented. For user institutions outside the EU in the absence of a decision pursuant to Article 45(3) GDPR standard data protection clauses adopted by the Commission in accordance with the examination procedure referred to in Article 93(2) GDPR should be concluded preferably. Minimum technical and organisational measures required: Measures suitable for preventing unauthorised persons from gaining access to data processing equipment with which personal data are processed or used. Access control measures for building and room security include automatic access control systems, the use of chip cards and transponders, access control by gatekeepers and alarm systems. Servers, telecommunications equipment, network technology and similar equipment must be protected in lockable server cabinets. In addition, access control should be supported by organisational measures (e.g. service instructions which provide for the locking of the offices during absence). Measures suitable to prevent data processing systems (computers) from being used by unauthorised persons. User identification with password for operating systems and software products used, screen saver with password. Up-to-date Anti-Virus-Software and firewalls on client computers and servers. Server hardening, intrusion detection systems and encryption of data media or data files. Use of VPN for remote accesses. Ssh-based client-server communication. Central management of user rights and permissions. File access: Data can be held in unencrypted 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, for a limited period of time (up to 3 month) for primary analysis. They can be again decrypted if primary analysis has to be repeated. The hard drives of Laptops holding these data must be encrypted. If held on USB keys or other portable hard drives, the data must be encrypted. Measures to ensure that those authorised to use a data processing system can only access the data subject to their access authorisation and that personal data cannot be read, copied, altered or removed without authorisation during processing, use and after storage. Access control can be ensured, among other things, by means of suitable user authorization concepts that enable differentiated control of access to data. In doing so, it is important to differentiate both the content of the data and the possible access functions to the data. Furthermore, suitable control mechanisms and responsibilities must be defined to document the granting and withdrawal of authorizations and to keep them up to date (e.g. upon hiring, change of job, termination of employment). Special attention should always be paid to the role and possibilities of administrators. Logging of user and administrator access and retrieval of the data should be supported. Further measures should include data protection management by an internal / external data protection officer and incident response management should be in place to prevent the uncontrolled distribution of data during the period when data has to be store unencrypted for analysis. APPENDIX II – PROJECT DETAILS (to be completed by the Requestor) Details of dataset requested i.e., EGA Study and Dataset Accession Number EGA StudyID: EGA DatasetID: 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 The LIT intends 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. The LIT 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 24 months after these data were first made available on the relevant hosting database, unless the LIT 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 numbers (e.g., EGAS00001004900), and acknowledge its use in a form agreed by the User Institution with the Data Producers/LIT.

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
EGAS00001006960 Transcriptome Analysis

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
EGAF00007909560 fastq.gz 813.9 MB
EGAF00007909561 fastq.gz 1.5 GB
EGAF00007909562 fastq.gz 808.5 MB
EGAF00007909563 fastq.gz 1.4 GB
EGAF00007909564 fastq.gz 828.4 MB
EGAF00007909565 fastq.gz 1.5 GB
EGAF00007909566 fastq.gz 826.5 MB
EGAF00007909567 fastq.gz 1.5 GB
EGAF00007909568 fastq.gz 818.2 MB
EGAF00007909569 fastq.gz 1.4 GB
EGAF00007909570 fastq.gz 812.3 MB
EGAF00007909571 fastq.gz 1.4 GB
EGAF00007909572 fastq.gz 831.6 MB
EGAF00007909573 fastq.gz 1.5 GB
EGAF00007909574 fastq.gz 830.2 MB
EGAF00007909575 fastq.gz 1.5 GB
EGAF00007909576 fastq.gz 479.0 MB
EGAF00007909577 fastq.gz 853.2 MB
EGAF00007909578 fastq.gz 470.4 MB
EGAF00007909579 fastq.gz 835.5 MB
EGAF00007909580 fastq.gz 485.4 MB
EGAF00007909581 fastq.gz 864.7 MB
EGAF00007909582 fastq.gz 482.5 MB
EGAF00007909583 fastq.gz 858.2 MB
EGAF00007909584 fastq.gz 697.6 MB
EGAF00007909585 fastq.gz 1.2 GB
EGAF00007909586 fastq.gz 684.6 MB
EGAF00007909587 fastq.gz 1.2 GB
EGAF00007909588 fastq.gz 707.1 MB
EGAF00007909589 fastq.gz 1.2 GB
EGAF00007909590 fastq.gz 702.2 MB
EGAF00007909591 fastq.gz 1.2 GB
EGAF00007909592 fastq.gz 319.1 MB
EGAF00007909593 fastq.gz 564.9 MB
EGAF00007909594 fastq.gz 311.4 MB
EGAF00007909595 fastq.gz 551.3 MB
EGAF00007909596 fastq.gz 322.2 MB
EGAF00007909597 fastq.gz 569.9 MB
EGAF00007909598 fastq.gz 320.5 MB
EGAF00007909599 fastq.gz 566.8 MB
EGAF00007909600 fastq.gz 1.0 GB
EGAF00007909601 fastq.gz 1.8 GB
EGAF00007909602 fastq.gz 996.2 MB
EGAF00007909603 fastq.gz 1.8 GB
EGAF00007909604 fastq.gz 1.0 GB
EGAF00007909605 fastq.gz 1.8 GB
EGAF00007909606 fastq.gz 1.0 GB
EGAF00007909607 fastq.gz 1.8 GB
EGAF00007909608 fastq.gz 104.0 MB
EGAF00007909609 fastq.gz 181.3 MB
EGAF00007909610 fastq.gz 102.5 MB
EGAF00007909611 fastq.gz 178.5 MB
EGAF00007909612 fastq.gz 105.4 MB
EGAF00007909613 fastq.gz 183.7 MB
EGAF00007909614 fastq.gz 105.1 MB
EGAF00007909615 fastq.gz 183.1 MB
EGAF00007909616 fastq.gz 19.8 MB
EGAF00007909617 fastq.gz 34.6 MB
EGAF00007909618 fastq.gz 19.7 MB
EGAF00007909619 fastq.gz 34.3 MB
EGAF00007909620 fastq.gz 19.7 MB
EGAF00007909621 fastq.gz 34.4 MB
EGAF00007909622 fastq.gz 19.7 MB
EGAF00007909623 fastq.gz 34.2 MB
EGAF00007909624 fastq.gz 526.1 MB
EGAF00007909625 fastq.gz 921.5 MB
EGAF00007909626 fastq.gz 523.5 MB
EGAF00007909627 fastq.gz 916.1 MB
EGAF00007909628 fastq.gz 524.7 MB
EGAF00007909629 fastq.gz 917.1 MB
EGAF00007909630 fastq.gz 522.8 MB
EGAF00007909631 fastq.gz 914.6 MB
EGAF00007909632 fastq.gz 476.0 MB
EGAF00007909633 fastq.gz 831.2 MB
EGAF00007909634 fastq.gz 473.2 MB
EGAF00007909635 fastq.gz 825.0 MB
EGAF00007909636 fastq.gz 475.0 MB
EGAF00007909637 fastq.gz 827.6 MB
EGAF00007909638 fastq.gz 472.2 MB
EGAF00007909639 fastq.gz 822.6 MB
EGAF00007909640 fastq.gz 21.7 MB
EGAF00007909641 fastq.gz 37.4 MB
EGAF00007909642 fastq.gz 21.6 MB
EGAF00007909643 fastq.gz 37.4 MB
EGAF00007909644 fastq.gz 21.7 MB
EGAF00007909645 fastq.gz 37.4 MB
EGAF00007909646 fastq.gz 21.8 MB
EGAF00007909647 fastq.gz 37.6 MB
EGAF00007909648 fastq.gz 576.0 MB
EGAF00007909649 fastq.gz 994.4 MB
EGAF00007909650 fastq.gz 575.2 MB
EGAF00007909651 fastq.gz 994.6 MB
EGAF00007909652 fastq.gz 575.6 MB
EGAF00007909653 fastq.gz 994.2 MB
EGAF00007909654 fastq.gz 578.2 MB
EGAF00007909655 fastq.gz 999.2 MB
EGAF00007909656 fastq.gz 521.6 MB
EGAF00007909657 fastq.gz 901.2 MB
EGAF00007909658 fastq.gz 519.5 MB
EGAF00007909659 fastq.gz 898.2 MB
EGAF00007909660 fastq.gz 521.1 MB
EGAF00007909661 fastq.gz 900.7 MB
EGAF00007909662 fastq.gz 522.6 MB
EGAF00007909663 fastq.gz 902.8 MB
EGAF00007909664 fastq.gz 702.9 MB
EGAF00007909665 fastq.gz 1.2 GB
EGAF00007909666 fastq.gz 695.5 MB
EGAF00007909667 fastq.gz 1.2 GB
EGAF00007909668 fastq.gz 712.6 MB
EGAF00007909669 fastq.gz 1.3 GB
EGAF00007909670 fastq.gz 707.9 MB
EGAF00007909671 fastq.gz 1.2 GB
EGAF00007909672 fastq.gz 804.0 MB
EGAF00007909673 fastq.gz 1.4 GB
EGAF00007909674 fastq.gz 794.0 MB
EGAF00007909675 fastq.gz 1.4 GB
EGAF00007909676 fastq.gz 812.8 MB
EGAF00007909677 fastq.gz 1.4 GB
EGAF00007909678 fastq.gz 802.0 MB
EGAF00007909679 fastq.gz 1.4 GB
EGAF00007909680 fastq.gz 604.0 MB
EGAF00007909681 fastq.gz 1.0 GB
EGAF00007909682 fastq.gz 592.5 MB
EGAF00007909683 fastq.gz 1.0 GB
EGAF00007909684 fastq.gz 601.6 MB
EGAF00007909685 fastq.gz 1.0 GB
EGAF00007909686 fastq.gz 605.8 MB
EGAF00007909687 fastq.gz 1.0 GB
EGAF00007909688 fastq.gz 594.2 MB
EGAF00007909689 fastq.gz 1.0 GB
EGAF00007909690 fastq.gz 588.6 MB
EGAF00007909691 fastq.gz 1.0 GB
EGAF00007909692 fastq.gz 605.7 MB
EGAF00007909693 fastq.gz 1.0 GB
EGAF00007909694 fastq.gz 598.8 MB
EGAF00007909695 fastq.gz 1.0 GB
EGAF00007909696 fastq.gz 777.9 MB
EGAF00007909697 fastq.gz 1.4 GB
EGAF00007909698 fastq.gz 764.6 MB
EGAF00007909699 fastq.gz 1.3 GB
EGAF00007909700 fastq.gz 776.4 MB
EGAF00007909701 fastq.gz 1.4 GB
EGAF00007909702 fastq.gz 784.4 MB
EGAF00007909703 fastq.gz 1.4 GB
EGAF00007909704 fastq.gz 782.8 MB
EGAF00007909705 fastq.gz 1.4 GB
EGAF00007909706 fastq.gz 769.5 MB
EGAF00007909707 fastq.gz 1.4 GB
EGAF00007909708 fastq.gz 780.6 MB
EGAF00007909709 fastq.gz 1.4 GB
EGAF00007909710 fastq.gz 788.8 MB
EGAF00007909711 fastq.gz 1.4 GB
EGAF00007909712 fastq.gz 509.5 MB
EGAF00007909713 fastq.gz 889.9 MB
EGAF00007909714 fastq.gz 510.4 MB
EGAF00007909715 fastq.gz 892.5 MB
EGAF00007909716 fastq.gz 524.8 MB
EGAF00007909717 fastq.gz 916.2 MB
EGAF00007909718 fastq.gz 520.2 MB
EGAF00007909719 fastq.gz 909.3 MB
EGAF00007909720 fastq.gz 713.8 MB
EGAF00007909721 fastq.gz 1.3 GB
EGAF00007909722 fastq.gz 714.4 MB
EGAF00007909723 fastq.gz 1.3 GB
EGAF00007909724 fastq.gz 733.9 MB
EGAF00007909725 fastq.gz 1.3 GB
EGAF00007909726 fastq.gz 728.1 MB
EGAF00007909727 fastq.gz 1.3 GB
EGAF00007909728 fastq.gz 395.8 MB
EGAF00007909729 fastq.gz 689.8 MB
EGAF00007909730 fastq.gz 387.6 MB
EGAF00007909731 fastq.gz 676.3 MB
EGAF00007909732 fastq.gz 402.0 MB
EGAF00007909733 fastq.gz 700.7 MB
EGAF00007909734 fastq.gz 397.1 MB
EGAF00007909735 fastq.gz 692.1 MB
EGAF00007909736 fastq.gz 603.5 MB
EGAF00007909737 fastq.gz 1.1 GB
EGAF00007909738 fastq.gz 591.3 MB
EGAF00007909739 fastq.gz 1.0 GB
EGAF00007909740 fastq.gz 613.2 MB
EGAF00007909741 fastq.gz 1.1 GB
EGAF00007909742 fastq.gz 605.8 MB
EGAF00007909743 fastq.gz 1.1 GB
184 Files (142.1 GB)