About file location

As the EGA is co-managed by the EMBL-EBI and CRG, files could be located in the UK and/or Spain, as indicated by their respective flags.

Alternatively, files could be located in one of the international Federated EGA nodes, as indicated next to the node's flag.
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Multi-omics profiling identifies two epithelioid sarcoma molecular subtypes with distinct signaling and immune characteristics

Bulk RNA Sequencing of 33 epithelioid sarcomas (EpS) and 3 extracranial extra-renal rhabdoid tumors (EERT) Whole-exome sequencing of 30 EpS and 3 EERT Single-cell RNA Sequencing of 8 EpS Visium Spatial Transcriptomics of 3 EpS

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SWISARC 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 Authorized Personnel: The individuals at the User Institution to whom the Data Access Committee 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 Producers: The individuals, 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, 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(s) that has requested access to the Data (detailed in Appendix II). Data Producers Institution(s): The Institution(s) that has produced the Data (detailed in Appendix I). Data Access Committee: The committee responsible for authorizing access to the data. Committee members are listed in Appendix I. 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 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. 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://www.sanger.ac.uk/wp-content/uploads/fortlauderdalereport.pdf) and the Toronto Statement (http://www.nature.com/nature/journal/v461/n7261/full/461168a.html). This includes but is not limited to recognizing the contribution of the Data Producers and including a proper acknowledgment 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 analyzing 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.ott.nih.gov/sites/default/files/documents/pdfs/70fr18413.pdf) in conformity with the Organization 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 Data Access Committee within 30 days of any changes or departures of Authorized Personnel. 13. The User Institution will notify the Data Access Committee prior to any significant changes to the protocol for the Project. 14. The User Institution will notify the Data Access Committee as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. The Data Access Committee 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. 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 Authorized Personnel. The User Institution will procure that the Authorized 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 France and shall be subject to the exclusive jurisdiction of the France courts. Agreed for User Institution (Name, Title, Date, Signature): Principal Investigator (Name, Title, Date, Signature): I confirm that I have read and understood this Agreement. Agreed for the Data Access Committee (Name, Title, Date, Signature): APPENDIX I – DATASET DETAILS & DATA ACCESS COMMITTEE APPENDIX II – PROJECT DETAILS APPENDIX III – PUBLICATION POLICY APPENDIX I – DATASET DETAILS & DATA ACCESS COMMITTEE Dataset reference (EGA Study ID, Dataset Accession Numbers and Dataset Details): Study: Multi-omics bulk and single-cell profiling of epithelioid sarcoma ID: 1899 Name of the project that created the dataset : Multi-omics profiling identifies two epithelioid sarcoma molecular subtypes with distinct signaling and immune characteristics Data Producers Institution(s): Gustave Roussy, 114, rue Edouard Vaillant – 94805 VILLEJUIF Cedex, FRANCE Names of other data producers/collaborators (Name, Email, Job Title): Specific limitations on areas of research: 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. Name of the Data Access Committee: Multi-omics profiling identifies two epithelioid sarcoma molecular subtypes with distinct signaling and immune characteristics Data Access Committee Members (Name, Email, Job Title): Principal Investigator PhD Dr Sophie POSTEL-VINAY (sophie.postel-vinay@gustaveroussy.fr) PhD Dr Carine NGO (carine.ngo@gustaveroussy.fr) Head of Bioinformatics platform Marc Deloger (Marc.DELOGER@gustaveroussy.fr) Bio-informatician Léo COLMET-DAAGE (leo.colmet-daage@gustaveroussy.fr) Data Manager Data Protection Officer Clara BECHET (Clara.BECHET@gustaveroussy.fr) 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): User Institution(s): All Individuals who the User Institution to be named as registered users (Name, Email, Job Title, Supervisor): All Individuals that should have an account created at the EGA (Name, Email, Job Title): APPENDIX III – PUBLICATION POLICY The Data Access Committee anticipates 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 the Data Access Committee have published their own global analysis or twelve (12) months after these data were first made available on the relevant hosting database, unless the Data Access Committee 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., EGAS00000000029), and acknowledge its use in a form agreed by the User Institution with the Data Access Committee.

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
EGAS50000000973 Cancer Genomics

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 Quality Report
Located in
i
EGAF50000354395 fastq.gz 3.2 GB
EGAF50000354396 fastq.gz 8.8 GB
EGAF50000354397 fastq.gz 2.0 GB
EGAF50000354398 fastq.gz 3.1 GB
EGAF50000354399 fastq.gz 4.4 GB
EGAF50000354400 fastq.gz 3.3 GB
EGAF50000354401 fastq.gz 4.2 GB
EGAF50000354402 fastq.gz 5.7 GB
EGAF50000354403 fastq.gz 5.2 GB
EGAF50000354404 fastq.gz 10.0 GB
EGAF50000354405 fastq.gz 3.9 GB
EGAF50000354406 fastq.gz 10.7 GB
EGAF50000354407 fastq.gz 2.8 GB
EGAF50000354408 fastq.gz 2.9 GB
EGAF50000354409 fastq.gz 3.3 GB
EGAF50000354410 fastq.gz 3.4 GB
EGAF50000354411 fastq.gz 1.5 GB
EGAF50000354412 fastq.gz 4.8 GB
EGAF50000354413 fastq.gz 9.4 GB
EGAF50000354414 fastq.gz 4.2 GB
EGAF50000354415 fastq.gz 4.3 GB
EGAF50000354416 fastq.gz 3.2 GB
EGAF50000354417 fastq.gz 5.2 GB
EGAF50000354418 fastq.gz 5.6 GB
EGAF50000354419 fastq.gz 2.6 GB
EGAF50000354420 fastq.gz 2.7 GB
EGAF50000354421 fastq.gz 6.5 GB
EGAF50000354422 fastq.gz 5.4 GB
EGAF50000354423 fastq.gz 4.6 GB
EGAF50000354424 fastq.gz 5.4 GB
EGAF50000354425 fastq.gz 5.5 GB
EGAF50000354426 fastq.gz 8.6 GB
EGAF50000354427 fastq.gz 4.3 GB
EGAF50000354428 fastq.gz 2.3 GB
EGAF50000354429 fastq.gz 2.4 GB
EGAF50000354430 fastq.gz 3.8 GB
EGAF50000354431 fastq.gz 4.0 GB
EGAF50000354432 fastq.gz 2.6 GB
EGAF50000354433 fastq.gz 2.8 GB
EGAF50000354434 fastq.gz 7.0 GB
EGAF50000354435 fastq.gz 7.5 GB
EGAF50000354436 fastq.gz 4.6 GB
EGAF50000354437 fastq.gz 4.8 GB
EGAF50000354438 fastq.gz 7.7 GB
EGAF50000354439 fastq.gz 3.8 GB
EGAF50000354440 fastq.gz 3.9 GB
EGAF50000354441 fastq.gz 4.8 GB
EGAF50000354442 fastq.gz 4.5 GB
EGAF50000354443 fastq.gz 5.5 GB
EGAF50000354444 fastq.gz 5.7 GB
EGAF50000354445 fastq.gz 3.1 GB
EGAF50000354446 fastq.gz 3.1 GB
EGAF50000354447 fastq.gz 4.5 GB
EGAF50000354448 fastq.gz 5.2 GB
EGAF50000354449 fastq.gz 6.3 GB
EGAF50000354450 fastq.gz 6.6 GB
EGAF50000354451 fastq.gz 2.0 GB
EGAF50000354452 fastq.gz 9.7 GB
EGAF50000354453 fastq.gz 10.0 GB
EGAF50000354454 fastq.gz 1.5 GB
EGAF50000354455 fastq.gz 4.6 GB
EGAF50000354456 fastq.gz 4.4 GB
EGAF50000354457 fastq.gz 5.2 GB
EGAF50000354458 fastq.gz 5.2 GB
EGAF50000354459 fastq.gz 4.3 GB
EGAF50000354460 fastq.gz 4.0 GB
EGAF50000354461 fastq.gz 3.8 GB
EGAF50000354462 fastq.gz 3.5 GB
EGAF50000354463 fastq.gz 3.5 GB
EGAF50000354464 fastq.gz 6.3 GB
EGAF50000354465 fastq.gz 5.0 GB
EGAF50000354466 fastq.gz 3.9 GB
EGAF50000354467 fastq.gz 4.0 GB
EGAF50000354468 fastq.gz 3.5 GB
EGAF50000354469 fastq.gz 3.7 GB
EGAF50000354470 fastq.gz 3.4 GB
EGAF50000354471 fastq.gz 3.5 GB
EGAF50000354472 fastq.gz 2.6 GB
EGAF50000354473 fastq.gz 2.7 GB
EGAF50000354474 fastq.gz 3.4 GB
EGAF50000354475 fastq.gz 3.4 GB
EGAF50000354476 fastq.gz 3.0 GB
EGAF50000354477 fastq.gz 3.1 GB
EGAF50000354478 fastq.gz 7.9 GB
EGAF50000354479 fastq.gz 8.6 GB
EGAF50000354480 fastq.gz 9.0 GB
EGAF50000354481 fastq.gz 8.8 GB
EGAF50000354482 fastq.gz 9.1 GB
EGAF50000354483 fastq.gz 9.7 GB
EGAF50000354484 fastq.gz 10.1 GB
EGAF50000354485 fastq.gz 11.1 GB
EGAF50000354486 fastq.gz 9.2 GB
EGAF50000354487 fastq.gz 9.5 GB
EGAF50000354488 fastq.gz 8.9 GB
EGAF50000354489 fastq.gz 9.5 GB
EGAF50000354490 fastq.gz 9.8 GB
EGAF50000354491 fastq.gz 10.2 GB
EGAF50000354492 fastq.gz 7.0 GB
EGAF50000354493 fastq.gz 7.0 GB
EGAF50000354494 fastq.gz 5.9 GB
EGAF50000354495 fastq.gz 6.1 GB
EGAF50000354496 fastq.gz 5.4 GB
EGAF50000354497 fastq.gz 5.4 GB
EGAF50000354498 fastq.gz 1.1 GB
EGAF50000354499 fastq.gz 1.1 GB
EGAF50000354500 fastq.gz 1.1 GB
EGAF50000354501 fastq.gz 1.1 GB
EGAF50000354502 fastq.gz 1.1 GB
EGAF50000354503 fastq.gz 706.8 MB
EGAF50000354504 fastq.gz 725.8 MB
EGAF50000354505 fastq.gz 1.1 GB
EGAF50000354506 fastq.gz 1.1 GB
EGAF50000354507 fastq.gz 2.2 GB
EGAF50000354508 fastq.gz 692.8 MB
EGAF50000354509 fastq.gz 694.5 MB
EGAF50000354510 fastq.gz 1.8 GB
EGAF50000354511 fastq.gz 2.0 GB
EGAF50000354512 fastq.gz 1.9 GB
EGAF50000354513 fastq.gz 685.0 MB
EGAF50000354514 fastq.gz 711.4 MB
EGAF50000354515 fastq.gz 2.2 GB
EGAF50000354516 fastq.gz 1.7 GB
EGAF50000354517 fastq.gz 1.7 GB
EGAF50000354518 fastq.gz 2.0 GB
EGAF50000354519 fastq.gz 1.0 GB
EGAF50000354520 fastq.gz 1.0 GB
EGAF50000354521 fastq.gz 1.3 GB
EGAF50000354522 fastq.gz 1.3 GB
EGAF50000354523 fastq.gz 1.4 GB
EGAF50000354524 fastq.gz 4.2 GB
EGAF50000354525 fastq.gz 700.5 MB
EGAF50000354526 fastq.gz 714.5 MB
EGAF50000354527 fastq.gz 1.1 GB
EGAF50000354528 fastq.gz 1.1 GB
EGAF50000354529 fastq.gz 1.1 GB
EGAF50000354530 fastq.gz 1.1 GB
EGAF50000354531 fastq.gz 1.1 GB
EGAF50000354532 fastq.gz 886.7 MB
EGAF50000354533 fastq.gz 2.1 GB
EGAF50000354534 fastq.gz 910.3 MB
EGAF50000354535 fastq.gz 1.7 GB
EGAF50000354536 fastq.gz 1.3 GB
EGAF50000354537 fastq.gz 1.4 GB
EGAF50000354538 fastq.gz 1.2 GB
EGAF50000354539 fastq.gz 1.2 GB
EGAF50000354540 fastq.gz 1.8 GB
EGAF50000354541 fastq.gz 1.8 GB
EGAF50000354542 fastq.gz 1.6 GB
EGAF50000354543 fastq.gz 712.6 MB
EGAF50000354544 fastq.gz 739.0 MB
EGAF50000354545 fastq.gz 1.7 GB
EGAF50000354546 fastq.gz 738.1 MB
EGAF50000354547 fastq.gz 723.6 MB
EGAF50000354548 fastq.gz 745.6 MB
EGAF50000354549 fastq.gz 2.1 GB
EGAF50000354550 fastq.gz 1.1 GB
EGAF50000354551 fastq.gz 1.1 GB
EGAF50000354552 fastq.gz 1.9 GB
EGAF50000354553 fastq.gz 1.3 GB
EGAF50000354554 fastq.gz 1.3 GB
EGAF50000354555 fastq.gz 1.4 GB
EGAF50000354556 fastq.gz 1.4 GB
EGAF50000354557 fastq.gz 2.2 GB
EGAF50000354558 fastq.gz 2.0 GB
EGAF50000354559 fastq.gz 1.0 GB
EGAF50000354560 fastq.gz 1.0 GB
EGAF50000354561 fastq.gz 2.2 GB
EGAF50000354562 fastq.gz 1.6 GB
EGAF50000354563 fastq.gz 1.6 GB
EGAF50000354564 fastq.gz 1.0 GB
EGAF50000354565 fastq.gz 635.7 MB
EGAF50000354566 fastq.gz 1.5 GB
EGAF50000354567 fastq.gz 991.5 MB
EGAF50000354568 fastq.gz 656.1 MB
EGAF50000354569 fastq.gz 762.7 MB
EGAF50000354570 fastq.gz 1.9 GB
EGAF50000354571 h5 13.3 MB
EGAF50000354572 png 441.1 kB
EGAF50000354573 csv 184.8 kB
EGAF50000354574 jpg 1.5 MB
EGAF50000354575 jpg 778.1 kB
EGAF50000354576 json 315 Bytes
EGAF50000354577 csv 2.0 MB
EGAF50000354578 png 4.8 MB
EGAF50000354579 jpg 2.4 MB
EGAF50000354580 jpg 904.0 kB
EGAF50000354581 json 316 Bytes
EGAF50000354582 png 7.7 MB
EGAF50000354583 png 611.6 kB
EGAF50000354584 h5 17.6 MB
EGAF50000354585 csv 2.2 MB
EGAF50000354586 csv 184.8 kB
EGAF50000354587 txt 11.0 MB
EGAF50000354588 mtx 163.0 MB
EGAF50000354589 txt 17.1 MB
EGAF50000354590 mtx 395.0 MB
EGAF50000354591 txt 12.5 MB
EGAF50000354592 mtx 280.5 MB
EGAF50000354593 mtx 415.2 MB
EGAF50000354594 txt 8.8 MB
EGAF50000354595 txt 8.5 MB
EGAF50000354596 mtx 286.8 MB
EGAF50000354597 jpg 1.5 MB
EGAF50000354598 jpg 795.0 kB
EGAF50000354599 h5 10.1 MB
EGAF50000354600 json 317 Bytes
EGAF50000354601 png 4.6 MB
EGAF50000354602 png 450.3 kB
EGAF50000354603 csv 184.9 kB
EGAF50000354604 csv 2.1 MB
EGAF50000354605 txt 10.1 MB
EGAF50000354606 mtx 603.5 MB
EGAF50000354607 txt 9.6 MB
EGAF50000354608 mtx 428.1 MB
EGAF50000354609 txt 5.0 MB
EGAF50000354610 mtx 76.3 MB
EGAF50000354611 txt 1.1 MB
217 Files (648.1 GB)