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Clear cell sarcoma dataset

This deposit consists of DNA and RNA sequencing data from 67 CCS samples. 55 samples had tumor DNA sequencing data. 6 had matched normal sequencing data. 34 samples had tumor RNA sequencing data.

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Data access policy

DATA ACCESS AGREEMENT These terms and conditions govern access to the managed access datasets 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 Children’s Cancer Therapy Development Institute (cc-TDI) grants access to the Data. This includes the User and any other individuals for whom the User Institution subsequently requests access to the Data. Data: The managed access datasets to which the User Institution has requested access. Data Producers: cc-TDI and collaborators 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. 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. 1. The User Institution agrees to only use these Data for the purpose of the Project 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 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. 9. 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 ). 10. 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. 11. The User Institution will notify cc-TDI within 30 days of any changes or departures of Authorised Personnel. 12. The User Institution will notify cc-TDI prior to any significant changes to the protocol for the Project. 13. The User Institution will notify cc-TDI as soon as it becomes aware of a breach of the terms or conditions of this agreement. 14. cc-TDI 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. 15. 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 cc-TDI. 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. 16. 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. 17. 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. 18. 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 Specific limitations on areas of research No limitations for use of data so long as no attempt is made to identify the original subjects associated with the de-identified patient samples Minimum protection measures required Data should not be shared to other research groups or research institutions. Data access by new requesters should be made through EGA . 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. Laptops holding these data should have password protected logins and screenlocks (set to lock after 5 min of inactivity). If held on USB keys or other portable hard drives, the data must be encrypted.

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
EGAF00006040547 1646187238778 3.9 GB
EGAF00006040548 1646187238778 4.1 GB
EGAF00006040549 1646187238778 3.7 GB
EGAF00006040550 1646187238778 3.7 GB
EGAF00006040551 1646187238778 3.8 GB
EGAF00006040552 1646187238778 3.9 GB
EGAF00006040553 1646187238778 5.9 GB
EGAF00006040554 1646187238778 5.7 GB
EGAF00006040555 1646187238778 3.4 GB
EGAF00006040556 1646187238778 3.5 GB
EGAF00006040557 1646187238778 2.3 GB
EGAF00006040558 1646187238778 2.2 GB
EGAF00006040559 1646187238778 4.0 GB
EGAF00006040560 1646187238778 4.0 GB
EGAF00006040561 1646187238778 3.7 GB
EGAF00006040562 1646187238778 3.7 GB
EGAF00006040563 1646187238778 4.1 GB
EGAF00006040564 1646187238778 4.2 GB
EGAF00006040565 1646187238778 3.8 GB
EGAF00006040566 1646187238778 3.9 GB
EGAF00006040567 1646187238778 3.5 GB
EGAF00006040568 1646187238778 3.6 GB
EGAF00006040569 1646187238778 3.7 GB
EGAF00006040570 1646187238778 3.8 GB
EGAF00006040571 1646187238778 1.7 GB
EGAF00006040572 1646187238778 1.7 GB
EGAF00006040573 1646187238778 6.4 GB
EGAF00006040574 1646187238778 6.5 GB
EGAF00006040575 1646187238778 1.4 GB
EGAF00006040576 1646187238778 1.3 GB
EGAF00006040577 1646187238778 6.4 GB
EGAF00006040578 1646187238778 6.6 GB
EGAF00006040579 1646187238778 2.3 GB
EGAF00006040580 1646187238778 2.2 GB
EGAF00006040581 1646187238778 4.2 GB
EGAF00006040582 1646187238778 4.2 GB
EGAF00006040583 1646187238778 4.0 GB
EGAF00006040584 1646187238778 3.8 GB
EGAF00006040585 1646187238778 5.8 GB
EGAF00006040586 1646187238778 5.9 GB
EGAF00006040587 1646187238778 6.2 GB
EGAF00006040588 1646187238778 6.3 GB
EGAF00006040589 1646187238778 5.6 GB
EGAF00006040590 1646187238778 5.7 GB
EGAF00006040591 1646187238778 2.5 GB
EGAF00006040592 1646187238778 2.5 GB
EGAF00006040593 1646187238778 3.8 GB
EGAF00006040594 1646187238778 3.8 GB
EGAF00006040595 1646187238778 3.3 GB
EGAF00006040596 1646187238778 3.4 GB
EGAF00006040597 1646187238778 3.5 GB
EGAF00006040598 1646187238778 3.4 GB
EGAF00006040599 1646187238778 2.8 GB
EGAF00006040600 1646187238778 2.9 GB
EGAF00006040601 1646187238778 6.4 GB
EGAF00006040602 1646187238778 6.5 GB
EGAF00006040603 1646187238778 3.9 GB
EGAF00006040604 1646187238778 3.9 GB
EGAF00006040605 1646187238778 1.9 GB
EGAF00006040606 1646187238778 1.8 GB
EGAF00006040607 1646187238778 3.4 GB
EGAF00006040608 1646187238778 3.5 GB
EGAF00006040609 1646187238778 5.2 GB
EGAF00006040610 1646187238778 5.3 GB
EGAF00006040611 1646187238778 3.4 GB
EGAF00006040612 1646187238778 3.5 GB
EGAF00006040613 1646187238778 3.5 GB
EGAF00006040614 1646187238778 3.5 GB
EGAF00006040615 1646187238778 2.2 GB
EGAF00006040616 1646187238778 2.2 GB
EGAF00006040617 1646187238778 5.5 GB
EGAF00006040618 1646187238778 5.6 GB
EGAF00006040619 1646187238778 4.6 GB
EGAF00006040620 1646187238778 4.5 GB
EGAF00006040621 1646187238778 5.5 GB
EGAF00006040622 1646187238778 5.6 GB
EGAF00006040623 1646187238778 3.8 GB
EGAF00006040624 1646187238778 3.8 GB
EGAF00006040625 1646187238778 4.1 GB
EGAF00006040626 1646187238778 4.2 GB
EGAF00006040627 1646187238778 4.1 GB
EGAF00006040628 1646187238778 4.2 GB
EGAF00006040629 1646187238778 3.2 GB
EGAF00006040630 1646187238778 3.3 GB
EGAF00006040631 1646187238778 3.0 GB
EGAF00006040632 1646187238778 3.0 GB
EGAF00006040633 1646187238778 3.7 GB
EGAF00006040634 1646187238778 3.7 GB
EGAF00006040635 1646187238778 6.2 GB
EGAF00006040636 1646187238778 6.2 GB
EGAF00006040637 1646187238778 6.3 GB
EGAF00006040638 1646187238778 6.5 GB
EGAF00006040639 1646187238778 4.4 GB
EGAF00006040640 1646187238778 4.6 GB
EGAF00006040641 1646187238778 3.4 GB
EGAF00006040642 1646187238778 3.5 GB
EGAF00006040643 1646187238778 526.3 MB
EGAF00006040644 1646187238778 526.0 MB
EGAF00006040645 1646187238778 6.4 GB
EGAF00006040646 1646187238778 6.3 GB
EGAF00006040647 1646187238778 3.1 GB
EGAF00006040648 1646187238778 3.1 GB
EGAF00006040649 1646187238778 4.4 GB
EGAF00006040650 1646187238778 4.2 GB
EGAF00006040651 1646187238778 4.0 GB
EGAF00006040652 1646187238778 4.1 GB
EGAF00006040653 1646187238778 5.9 GB
EGAF00006040654 1646187238778 5.5 GB
EGAF00006040655 1646187238778 5.4 GB
EGAF00006040656 1646187238778 5.5 GB
EGAF00006040657 1646187238778 3.3 GB
EGAF00006040658 1646187238778 3.4 GB
EGAF00006040659 1646187238778 1.6 GB
EGAF00006040660 1646187238778 1.5 GB
EGAF00006040661 1646187238778 1.6 GB
EGAF00006040662 1646187238778 1.5 GB
EGAF00006040663 1646187238778 6.2 GB
EGAF00006040664 1646187238778 6.3 GB
EGAF00006040665 1646187238778 3.4 GB
EGAF00006040666 1646187238778 3.4 GB
EGAF00006040667 1646187238778 1.9 GB
EGAF00006040668 1646187238778 1.8 GB
EGAF00006040669 1646187238778 3.0 GB
EGAF00006040670 1646187238778 3.0 GB
EGAF00006040671 1646187238778 9.0 GB
EGAF00006040672 1646187238778 9.3 GB
EGAF00006040673 1646187238778 3.2 GB
EGAF00006040674 1646187238778 3.2 GB
EGAF00006040675 1646187238778 3.3 GB
EGAF00006040676 1646187238778 3.5 GB
EGAF00006040677 1646187238778 1.1 GB
EGAF00006040678 1646187238778 1.0 GB
EGAF00006040679 1646187238778 6.0 GB
EGAF00006040680 1646187238778 6.1 GB
EGAF00006040681 1646187238778 3.6 GB
EGAF00006040682 1646187238778 3.6 GB
EGAF00006040683 1646187238778 3.7 GB
EGAF00006040684 1646187238778 3.7 GB
EGAF00006040685 1646187238778 3.8 GB
EGAF00006040686 1646187238778 3.8 GB
EGAF00006040687 1646187238778 5.5 GB
EGAF00006040688 1646187238778 5.5 GB
EGAF00006040689 1646187238778 3.7 GB
EGAF00006040690 1646187238778 3.6 GB
EGAF00006040691 1646187238778 3.0 GB
EGAF00006040692 1646187238778 3.0 GB
EGAF00006040693 1646187238778 2.8 GB
EGAF00006040694 1646187238778 2.7 GB
EGAF00006040695 1646187238778 2.2 GB
EGAF00006040696 1646187238778 2.1 GB
EGAF00006040697 1646187238778 3.6 GB
EGAF00006040698 1646187238778 3.7 GB
EGAF00006040699 1646187238778 3.6 GB
EGAF00006040700 1646187238778 3.7 GB
EGAF00006040701 1646187238778 5.9 GB
EGAF00006040702 1646187238778 5.9 GB
EGAF00006040703 1646187238778 5.9 GB
EGAF00006040704 1646187238778 5.9 GB
EGAF00006040705 1646187238778 5.8 GB
EGAF00006040706 1646187238778 5.6 GB
EGAF00006040707 1646187238778 3.9 GB
EGAF00006040708 1646187238778 3.9 GB
EGAF00006040709 1646187238778 4.2 GB
EGAF00006040710 1646187238778 4.2 GB
EGAF00006040711 1646187238778 3.3 GB
EGAF00006040712 1646187238778 3.3 GB
EGAF00006040713 1646187238778 2.9 GB
EGAF00006040714 1646187238778 2.9 GB
EGAF00006040715 1646187238778 3.6 GB
EGAF00006040716 1646187238778 3.7 GB
EGAF00006040717 1646187238778 1.8 GB
EGAF00006040718 1646187238778 1.8 GB
EGAF00006040719 1646187238778 4.8 GB
EGAF00006040720 1646187238778 4.9 GB
EGAF00006040721 1646187238778 5.5 GB
EGAF00006040722 1646187238778 5.6 GB
EGAF00006040723 1646187238778 6.3 GB
EGAF00006040724 1646187238778 6.3 GB
EGAF00006040725 1646187238778 6.2 GB
EGAF00006040726 1646187238778 6.4 GB
EGAF00006040727 1646187238778 6.0 GB
EGAF00006040728 1646187238778 5.9 GB
EGAF00006040729 1646187238778 3.9 GB
EGAF00006040730 1646187238778 4.0 GB
EGAF00006040731 1646187238778 5.9 GB
EGAF00006040732 1646187238778 5.9 GB
EGAF00006040733 1646187238778 3.9 GB
EGAF00006040734 1646187238778 3.9 GB
EGAF00006040735 1646187238778 3.9 GB
EGAF00006040736 1646187238778 3.7 GB
190 Files (774.2 GB)