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RNAseq of NSCLC and melanoma tumor xenografts treated with ADC

RNAseq of tumours derived from NSCLC (n=3 PDX; n=1 CDX) and melanoma (n=1 CDX) xenograft models treated with ADC or controls (64 samples; 189 FASTQ files).

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Genmab B/V data access 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 Authorised Personnel: The individuals at the User Institution to whom Genmab B/V 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: Genmab B/V (Genmab B/V, Uppsalalaan 15, 3584 CT Utrecht, The Netherlands) 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. XXXXX: 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. The User Institution must at all times assess and observe any relevant and applicable data protection requirements. 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. The User Institution agrees and acknowledges that the Data Producers own all intellectual property rights, title and interest to the Data. Except for any licenses granted herein, User Institution will not as a result of this Data Access Agreement acquire any intellectual property rights, title, or interest to the 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 Genmab B/V within 30 days of any changes or departures of Authorised Personnel. 13. The User Institution will notify Genmab B/V prior to any significant changes to the protocol for the Project. 14. The User Institution will notify Genmab B/V as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. Genmab B/V 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 Genmab B/V. 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 the Netherlands and shall be subject to the exclusive jurisdiction of the Dutch 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 Genmab B/V Signature: Name: Title: 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) EGAS00001004562 • RNASeq data of PDX and CDX tumours treated with ADC Name of project that created the dataset Cooperative targeting of immunotherapy-resistant melanoma and lung cancer by an AXL-targeting antibody-drug conjugate and immune checkpoint blockade Names of other data producers/collaborators Prof. Daniel S. Peeper, Division of Molecular Oncology at the Netherlands Cancer Institute, Amsterdam, the Netherlands Specific limitations on areas of research Research by the User and User Institutions shall be limited to not-for-profit research only and must not pertain commercial development of pharmaceuticals or therapeutic or diagnostic procedures. 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 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 Genmab B/V intend 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. Genmab B/V 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 12 months after these data were first made available on the relevant hosting database, unless Genmab B/V 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., EGAS00001004562), and acknowledge its use in a form agreed by the User Institution with Genmab B/V.

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
EGAF00004858381 fastq.gz 632.9 MB
EGAF00004858382 fastq.gz 594.8 MB
EGAF00004858383 fastq.gz 619.1 MB
EGAF00004858384 fastq.gz 649.9 MB
EGAF00004858385 fastq.gz 731.7 MB
EGAF00004858386 fastq.gz 614.1 MB
EGAF00004858387 fastq.gz 691.4 MB
EGAF00004858388 fastq.gz 1.0 GB
EGAF00004858389 fastq.gz 794.6 MB
EGAF00004858390 fastq.gz 1.3 GB
EGAF00004858391 fastq.gz 1.5 GB
EGAF00004858392 fastq.gz 822.3 MB
EGAF00004858393 fastq.gz 660.6 MB
EGAF00004858394 fastq.gz 611.4 MB
EGAF00004858395 fastq.gz 1.2 GB
EGAF00004858396 fastq.gz 1.1 GB
EGAF00004858397 fastq.gz 579.2 MB
EGAF00004858398 fastq.gz 788.7 MB
EGAF00004858399 fastq.gz 9.1 GB
EGAF00004858400 fastq.gz 9.5 GB
EGAF00004858401 fastq.gz 9.4 GB
EGAF00004858402 fastq.gz 9.9 GB
EGAF00004858403 fastq.gz 7.3 GB
EGAF00004858404 fastq.gz 7.6 GB
EGAF00004858405 fastq.gz 9.6 GB
EGAF00004858406 fastq.gz 10.0 GB
EGAF00004858407 fastq.gz 8.5 GB
EGAF00004858408 fastq.gz 9.0 GB
EGAF00004858409 fastq.gz 1.7 GB
EGAF00004858410 fastq.gz 1.7 GB
EGAF00004858411 fastq.gz 3.9 GB
EGAF00004858412 fastq.gz 4.1 GB
EGAF00004858413 fastq.gz 1.9 GB
EGAF00004858414 fastq.gz 2.0 GB
EGAF00004858415 fastq.gz 4.5 GB
EGAF00004858416 fastq.gz 4.7 GB
EGAF00004858417 fastq.gz 9.3 GB
EGAF00004858418 fastq.gz 9.7 GB
EGAF00004858419 fastq.gz 1.8 GB
EGAF00004858420 fastq.gz 1.9 GB
EGAF00004858421 fastq.gz 4.4 GB
EGAF00004858422 fastq.gz 4.5 GB
EGAF00004858423 fastq.gz 1.9 GB
EGAF00004858424 fastq.gz 2.0 GB
EGAF00004858425 fastq.gz 4.5 GB
EGAF00004858426 fastq.gz 4.7 GB
EGAF00004858427 fastq.gz 2.1 GB
EGAF00004858428 fastq.gz 2.2 GB
EGAF00004858429 fastq.gz 5.1 GB
EGAF00004858430 fastq.gz 5.4 GB
EGAF00004858431 fastq.gz 1.8 GB
EGAF00004858432 fastq.gz 1.9 GB
EGAF00004858433 fastq.gz 4.3 GB
EGAF00004858434 fastq.gz 4.6 GB
EGAF00004858435 fastq.gz 2.3 GB
EGAF00004858436 fastq.gz 2.5 GB
EGAF00004858437 fastq.gz 5.6 GB
EGAF00004858438 fastq.gz 5.9 GB
EGAF00004858439 fastq.gz 1.9 GB
EGAF00004858440 fastq.gz 2.0 GB
EGAF00004858441 fastq.gz 4.6 GB
EGAF00004858442 fastq.gz 4.8 GB
EGAF00004858443 fastq.gz 1.9 GB
EGAF00004858444 fastq.gz 2.0 GB
EGAF00004858445 fastq.gz 4.5 GB
EGAF00004858446 fastq.gz 4.7 GB
EGAF00004858447 fastq.gz 1.9 GB
EGAF00004858448 fastq.gz 2.0 GB
EGAF00004858449 fastq.gz 4.6 GB
EGAF00004858450 fastq.gz 4.8 GB
EGAF00004858451 fastq.gz 1.8 GB
EGAF00004858452 fastq.gz 1.9 GB
EGAF00004858453 fastq.gz 4.3 GB
EGAF00004858454 fastq.gz 4.5 GB
EGAF00004858455 fastq.gz 2.3 GB
EGAF00004858456 fastq.gz 2.4 GB
EGAF00004858457 fastq.gz 5.6 GB
EGAF00004858458 fastq.gz 5.9 GB
EGAF00004858459 fastq.gz 1.2 GB
EGAF00004858460 fastq.gz 1.3 GB
EGAF00004858461 fastq.gz 2.9 GB
EGAF00004858462 fastq.gz 3.1 GB
EGAF00004858463 fastq.gz 2.6 GB
EGAF00004858464 fastq.gz 2.6 GB
EGAF00004858465 fastq.gz 1.7 GB
EGAF00004858466 fastq.gz 1.8 GB
EGAF00004858467 fastq.gz 4.1 GB
EGAF00004858468 fastq.gz 4.3 GB
EGAF00004858469 fastq.gz 1.9 GB
EGAF00004858470 fastq.gz 2.0 GB
EGAF00004858471 fastq.gz 4.6 GB
EGAF00004858472 fastq.gz 4.9 GB
EGAF00004858473 fastq.gz 9.1 GB
EGAF00004858474 fastq.gz 9.4 GB
EGAF00004858475 fastq.gz 2.2 GB
EGAF00004858476 fastq.gz 2.3 GB
EGAF00004858477 fastq.gz 5.2 GB
EGAF00004858478 fastq.gz 5.4 GB
EGAF00004858479 fastq.gz 1.5 GB
EGAF00004858480 fastq.gz 1.6 GB
EGAF00004858481 fastq.gz 3.7 GB
EGAF00004858482 fastq.gz 3.9 GB
EGAF00004858483 fastq.gz 635.1 MB
EGAF00004858484 fastq.gz 630.9 MB
EGAF00004858485 fastq.gz 3.2 GB
EGAF00004858486 fastq.gz 3.2 GB
EGAF00004858487 fastq.gz 1.0 GB
EGAF00004858488 fastq.gz 1.1 GB
EGAF00004858489 fastq.gz 2.5 GB
EGAF00004858490 fastq.gz 2.6 GB
EGAF00004858491 fastq.gz 8.5 GB
EGAF00004858492 fastq.gz 8.9 GB
EGAF00004858493 fastq.gz 11.2 GB
EGAF00004858494 fastq.gz 11.7 GB
EGAF00004858495 fastq.gz 2.3 GB
EGAF00004858496 fastq.gz 2.4 GB
EGAF00004858497 fastq.gz 5.4 GB
EGAF00004858498 fastq.gz 5.7 GB
EGAF00004858499 fastq.gz 2.6 GB
EGAF00004858500 fastq.gz 2.7 GB
EGAF00004858501 fastq.gz 6.2 GB
EGAF00004858502 fastq.gz 6.5 GB
EGAF00004858503 fastq.gz 2.6 GB
EGAF00004858504 fastq.gz 2.8 GB
EGAF00004858505 fastq.gz 6.3 GB
EGAF00004858506 fastq.gz 6.6 GB
EGAF00004858507 fastq.gz 2.2 GB
EGAF00004858508 fastq.gz 2.2 GB
EGAF00004858509 fastq.gz 5.2 GB
EGAF00004858510 fastq.gz 5.4 GB
EGAF00004858511 fastq.gz 1.5 GB
EGAF00004858512 fastq.gz 1.6 GB
EGAF00004858513 fastq.gz 3.7 GB
EGAF00004858514 fastq.gz 3.9 GB
EGAF00004858515 fastq.gz 857.3 MB
EGAF00004858516 fastq.gz 857.6 MB
EGAF00004858517 fastq.gz 1.6 GB
EGAF00004858518 fastq.gz 1.7 GB
EGAF00004858519 fastq.gz 4.0 GB
EGAF00004858520 fastq.gz 4.2 GB
EGAF00004858521 fastq.gz 177.4 MB
EGAF00004858522 fastq.gz 174.3 MB
EGAF00004858523 fastq.gz 2.1 GB
EGAF00004858524 fastq.gz 2.2 GB
EGAF00004858525 fastq.gz 5.0 GB
EGAF00004858526 fastq.gz 5.2 GB
EGAF00004858527 fastq.gz 1.9 GB
EGAF00004858528 fastq.gz 2.0 GB
EGAF00004858529 fastq.gz 4.6 GB
EGAF00004858530 fastq.gz 4.8 GB
EGAF00004858531 fastq.gz 2.3 GB
EGAF00004858532 fastq.gz 2.4 GB
EGAF00004858533 fastq.gz 5.6 GB
EGAF00004858534 fastq.gz 5.8 GB
EGAF00004858535 fastq.gz 1.8 GB
EGAF00004858536 fastq.gz 1.8 GB
EGAF00004858537 fastq.gz 4.2 GB
EGAF00004858538 fastq.gz 4.4 GB
EGAF00004858539 fastq.gz 7.3 GB
EGAF00004858540 fastq.gz 7.6 GB
EGAF00004858541 fastq.gz 1.8 GB
EGAF00004858542 fastq.gz 1.9 GB
EGAF00004858543 fastq.gz 4.3 GB
EGAF00004858544 fastq.gz 4.5 GB
EGAF00004858545 fastq.gz 7.1 GB
EGAF00004858546 fastq.gz 7.7 GB
EGAF00004858547 fastq.gz 1.8 GB
EGAF00004858548 fastq.gz 1.8 GB
EGAF00004858549 fastq.gz 4.2 GB
EGAF00004858550 fastq.gz 4.4 GB
EGAF00004858551 fastq.gz 1.7 GB
EGAF00004858552 fastq.gz 1.7 GB
EGAF00004858553 fastq.gz 4.0 GB
EGAF00004858554 fastq.gz 4.2 GB
EGAF00004858555 fastq.gz 8.2 GB
EGAF00004858556 fastq.gz 8.5 GB
EGAF00004858557 fastq.gz 1.8 GB
EGAF00004858558 fastq.gz 1.9 GB
EGAF00004858559 fastq.gz 4.4 GB
EGAF00004858560 fastq.gz 4.6 GB
EGAF00004858561 fastq.gz 1.7 GB
EGAF00004858562 fastq.gz 1.8 GB
EGAF00004858563 fastq.gz 4.1 GB
EGAF00004858564 fastq.gz 4.3 GB
EGAF00004858565 fastq.gz 2.5 GB
EGAF00004858566 fastq.gz 2.6 GB
EGAF00004858567 fastq.gz 6.0 GB
EGAF00004858568 fastq.gz 6.3 GB
188 Files (696.4 GB)