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De novo modeling of chromoplectic Ewing sarcoma tumors from patient-derived mesenchymal stem cells

Ewing sarcoma is characterized by pathognomonic translocations fusing most frequently EWSR1 with FLI1 (EF1). In addition, Ewing sarcoma can also display alterations in STAG2, TP53 and CDKN2A (SPC). Starting from Ewing sarcoma derived human mesenchymal stem cells (MSCpat), we recapitulated this translocation and SPC alterations using a CRISPR/cas9 approach and generated a bona fide Ewing sarcoma model (EWIma1) displaying transcriptomic (RNA-seq) and epigenetic (ChIP-seq) hallmarks of EwS.

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Standard policy of the Data Access Committee for Institut Curie

DATA ACCESS AGREEMENT – Institut Curie 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 Institut Curie 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: Institut Curie 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. Institut du Radium: 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 Institut Curie within 30 days of any changes or departures of Authorised Personnel. 13. The User Institution will notify Institut Curie prior to any significant changes to the protocol for the Project. 14. The User Institution will notify Institut Curie as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. Institut Curie 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 Institut Curie. 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 France and shall be subject to the exclusive jurisdiction of the French 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 XXXXX 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 and Dataset Details) EGAS00001002761 Name of project that created the dataset Names of other data producers/collaborators Rodriguez et al. Specific limitations on areas of research Minimum protection measures required 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. APPENDIX II – PROJECT DETAILS (to be completed by the Requestor) Details of dataset requested i.e., EGA Study and Dataset Accession Number EGA**** 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 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) and its accession numbers (i.e. EGAS00001002505), and acknowledge its use in a form agreed by the User Institution with Institut Curie.

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
EGAS50000001172 Epigenetics
EGAS50000001173 RNASeq

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
EGAF50000411519 fastq.gz 5.0 GB
EGAF50000411520 fastq.gz 1.6 GB
EGAF50000411521 fastq.gz 1.7 GB
EGAF50000411522 fastq.gz 1.8 GB
EGAF50000411523 fastq.gz 3.0 GB
EGAF50000411524 fastq.gz 3.2 GB
EGAF50000411525 fastq.gz 7.7 GB
EGAF50000411526 fastq.gz 7.9 GB
EGAF50000411527 fastq.gz 7.1 GB
EGAF50000411528 fastq.gz 6.3 GB
EGAF50000411529 fastq.gz 2.9 GB
EGAF50000411530 fastq.gz 5.1 GB
EGAF50000411531 fastq.gz 8.5 GB
EGAF50000411532 fastq.gz 8.9 GB
EGAF50000411533 fastq.gz 6.2 GB
EGAF50000411534 fastq.gz 6.4 GB
EGAF50000411535 fastq.gz 5.6 GB
EGAF50000411536 fastq.gz 8.7 GB
EGAF50000411537 fastq.gz 9.0 GB
EGAF50000411538 fastq.gz 5.0 GB
EGAF50000411539 fastq.gz 4.0 GB
EGAF50000411540 fastq.gz 4.2 GB
EGAF50000411541 fastq.gz 4.5 GB
EGAF50000411542 fastq.gz 4.7 GB
EGAF50000411543 fastq.gz 6.0 GB
EGAF50000411544 fastq.gz 6.2 GB
EGAF50000411545 fastq.gz 6.7 GB
EGAF50000411546 fastq.gz 6.8 GB
EGAF50000411547 fastq.gz 5.1 GB
EGAF50000411548 fastq.gz 5.3 GB
EGAF50000411549 fastq.gz 3.7 GB
EGAF50000411550 fastq.gz 3.8 GB
EGAF50000411551 fastq.gz 3.1 GB
EGAF50000411552 fastq.gz 3.1 GB
EGAF50000411553 fastq.gz 10.9 GB
EGAF50000411554 fastq.gz 4.1 GB
EGAF50000411555 fastq.gz 4.3 GB
EGAF50000411556 fastq.gz 5.1 GB
EGAF50000411557 fastq.gz 5.3 GB
EGAF50000411558 fastq.gz 6.2 GB
EGAF50000411559 fastq.gz 6.5 GB
EGAF50000411560 fastq.gz 3.6 GB
EGAF50000411561 fastq.gz 3.7 GB
EGAF50000411562 fastq.gz 6.9 GB
EGAF50000411563 fastq.gz 7.1 GB
EGAF50000411564 fastq.gz 3.0 GB
EGAF50000411565 fastq.gz 1.7 GB
EGAF50000411566 fastq.gz 1.8 GB
EGAF50000411567 fastq.gz 3.4 GB
EGAF50000411568 fastq.gz 4.2 GB
EGAF50000411569 fastq.gz 4.1 GB
EGAF50000411570 fastq.gz 3.0 GB
EGAF50000411571 fastq.gz 2.3 GB
EGAF50000411572 fastq.gz 3.0 GB
EGAF50000411573 fastq.gz 3.2 GB
EGAF50000411574 fastq.gz 3.7 GB
EGAF50000411575 fastq.gz 3.9 GB
EGAF50000411576 fastq.gz 2.5 GB
EGAF50000411577 fastq.gz 2.6 GB
EGAF50000411578 fastq.gz 4.0 GB
EGAF50000411579 fastq.gz 1.8 GB
EGAF50000411580 fastq.gz 1.8 GB
EGAF50000411581 fastq.gz 3.3 GB
EGAF50000411582 fastq.gz 3.5 GB
EGAF50000411583 fastq.gz 3.0 GB
EGAF50000411584 fastq.gz 2.3 GB
EGAF50000411585 fastq.gz 1.6 GB
EGAF50000411586 fastq.gz 1.7 GB
EGAF50000411587 fastq.gz 3.7 GB
EGAF50000411588 fastq.gz 3.9 GB
EGAF50000411589 fastq.gz 1.8 GB
EGAF50000411590 fastq.gz 1.7 GB
EGAF50000411591 fastq.gz 1.9 GB
EGAF50000411592 fastq.gz 1.8 GB
EGAF50000411593 fastq.gz 5.5 GB
EGAF50000411594 fastq.gz 1.8 GB
EGAF50000411595 fastq.gz 2.0 GB
EGAF50000411596 fastq.gz 5.7 GB
EGAF50000411597 fastq.gz 2.1 GB
EGAF50000411598 fastq.gz 2.2 GB
EGAF50000411599 fastq.gz 2.9 GB
EGAF50000411600 fastq.gz 3.0 GB
EGAF50000411601 fastq.gz 1.6 GB
EGAF50000411602 fastq.gz 6.1 GB
EGAF50000411603 fastq.gz 6.4 GB
EGAF50000411604 fastq.gz 2.8 GB
EGAF50000411605 fastq.gz 1.8 GB
EGAF50000411606 fastq.gz 4.8 GB
EGAF50000411607 fastq.gz 10.6 GB
EGAF50000411608 fastq.gz 3.9 GB
EGAF50000411609 fastq.gz 2.8 GB
EGAF50000411610 fastq.gz 1.6 GB
EGAF50000411611 fastq.gz 1.6 GB
EGAF50000411612 fastq.gz 4.8 GB
EGAF50000411613 fastq.gz 5.0 GB
EGAF50000411614 fastq.gz 3.7 GB
EGAF50000411615 fastq.gz 3.3 GB
EGAF50000411616 fastq.gz 2.4 GB
EGAF50000411617 fastq.gz 1.7 GB
EGAF50000411618 fastq.gz 2.9 GB
EGAF50000411619 fastq.gz 1.9 GB
EGAF50000411620 fastq.gz 3.3 GB
EGAF50000411621 fastq.gz 2.0 GB
EGAF50000411622 fastq.gz 3.3 GB
EGAF50000411623 fastq.gz 2.0 GB
EGAF50000411624 fastq.gz 4.7 GB
EGAF50000411625 fastq.gz 2.2 GB
EGAF50000411626 fastq.gz 3.9 GB
EGAF50000411627 fastq.gz 3.9 GB
EGAF50000411628 fastq.gz 2.9 GB
EGAF50000411629 fastq.gz 7.3 GB
EGAF50000411630 fastq.gz 6.4 GB
EGAF50000411631 fastq.gz 5.4 GB
EGAF50000411632 fastq.gz 2.2 GB
EGAF50000411633 fastq.gz 2.3 GB
EGAF50000411634 fastq.gz 3.5 GB
EGAF50000411635 fastq.gz 1.6 GB
EGAF50000411636 fastq.gz 1.7 GB
EGAF50000411637 fastq.gz 3.5 GB
EGAF50000411638 fastq.gz 3.6 GB
EGAF50000411639 fastq.gz 3.8 GB
EGAF50000411640 fastq.gz 1.8 GB
EGAF50000411641 fastq.gz 4.0 GB
EGAF50000411642 fastq.gz 3.7 GB
EGAF50000411643 fastq.gz 1.8 GB
EGAF50000411644 fastq.gz 1.9 GB
126 Files (501.1 GB)