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The application of RNA sequencing for the diagnosis and genomic classification of pediatric acute lymphoblastic leukemia

RNA-seq data for ALL patients as described in "The application of RNA sequencing for the diagnosis and genomic classification of pediatric acute lymphoblastic leukemia"

Request Access

DAC for samples from "The application of RNA sequencing for the diagnosis and genomic classification of pediatric acute lymphoblastic leukemia"

DATA ACCESS AGREEMENT The User Institution agrees with the Murdoch Children’s Research Institute of Royal Children’s Hospital, Flemington Rd, Parkville, Victoria, 3052 Australia ABN 21 006 566 972 (MCRI), that access to and use of the specified dataset will be governed by the following terms and conditions. The User Institution agrees to be bound by these terms and conditions. 1. Definitions Authorised 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 Authorised Personnel are set out in Appendix II. Data: The managed access datasets to which the User Institution has requested access. Data Producers: MCRI 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. Recipient: The User Institution 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. 2. 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. 3. 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. 4. 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. 5. 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. 6. 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. 7. 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. 8. 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. 9. 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. 10. 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. 11. 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). 12. 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. 13. The User Institution will notify MCRI within 30 days of any changes or departures of Authorised Personnel. 14. The User Institution will notify MCRI prior to any significant changes to the protocol for the Project. 15. The User Institution will notify MCRI as soon as it becomes aware of a breach of the terms or conditions of this agreement. 16. MCRI 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. 17. 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 MCRI. 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. 18. If requested, the User Institution will allow data security and management documentation to be inspected by an agent of the other party to verify that it is complying with the terms of this agreement. 19. 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. 20. 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 News South Wales, Australia and the parties submit to the exclusive jurisdiction of the courts that operate in New South Wales. 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 MCRI 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) <currently unassigned> Name of project that created the dataset Deep multi-region whole-genome sequencing reveals heterogeneity and gene-by-environment interactions in treatment-naive, metastatic lung cancer Names of other data producers/collaborators A/Prof Paul Ekert A/Prof Alicia Oshlack Dr Lauren Brown Dr Nadia Davidson Specific limitations on areas of research None. 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 The data requested here have been published in Brown et al, Blood Advances 2020, PubMed ID 32150610. As such, there is no further publication moratorium on these data. 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., EGAS000000000XX), and acknowledge its use in a form agreed by the User Institution with MCRI.

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
EGAS00001004212 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
EGAF00003448266 fastq.gz 4.5 GB
EGAF00003448267 fastq.gz 5.2 GB
EGAF00003448268 fastq.gz 4.0 GB
EGAF00003448269 fastq.gz 4.4 GB
EGAF00003448270 fastq.gz 5.2 GB
EGAF00003448271 fastq.gz 6.0 GB
EGAF00003448272 fastq.gz 3.3 GB
EGAF00003448273 fastq.gz 3.8 GB
EGAF00003448274 fastq.gz 7.8 GB
EGAF00003448275 fastq.gz 7.9 GB
EGAF00003448276 fastq.gz 3.8 GB
EGAF00003448277 fastq.gz 4.4 GB
EGAF00003448278 fastq.gz 3.1 GB
EGAF00003448279 fastq.gz 3.6 GB
EGAF00003448280 fastq.gz 5.9 GB
EGAF00003448281 fastq.gz 6.1 GB
EGAF00003448282 fastq.gz 3.7 GB
EGAF00003448283 fastq.gz 4.1 GB
EGAF00003448284 fastq.gz 5.3 GB
EGAF00003448285 fastq.gz 5.9 GB
EGAF00003448756 fastq.gz 918.9 MB
EGAF00003448757 fastq.gz 1.3 GB
EGAF00004198423 fastq.gz 1.2 GB
EGAF00004198424 fastq.gz 1.8 GB
EGAF00004198425 fastq.gz 916.7 MB
EGAF00004198426 fastq.gz 1.3 GB
EGAF00004198427 fastq.gz 4.2 GB
EGAF00004198428 fastq.gz 4.5 GB
EGAF00004198429 fastq.gz 5.4 GB
EGAF00004198430 fastq.gz 6.2 GB
EGAF00004198431 fastq.gz 4.2 GB
EGAF00004198432 fastq.gz 4.9 GB
EGAF00004198433 fastq.gz 5.9 GB
EGAF00004198434 fastq.gz 6.8 GB
EGAF00004198435 fastq.gz 16.2 GB
EGAF00004198436 fastq.gz 18.2 GB
EGAF00004198437 fastq.gz 3.8 GB
EGAF00004198438 fastq.gz 4.1 GB
EGAF00004198439 fastq.gz 6.6 GB
EGAF00004198440 fastq.gz 6.7 GB
EGAF00004198441 fastq.gz 7.5 GB
EGAF00004198442 fastq.gz 7.6 GB
EGAF00004198443 fastq.gz 2.7 GB
EGAF00004198444 fastq.gz 3.0 GB
EGAF00004198445 fastq.gz 3.8 GB
EGAF00004198446 fastq.gz 4.4 GB
EGAF00004198447 fastq.gz 7.4 GB
EGAF00004198448 fastq.gz 8.5 GB
EGAF00004198449 fastq.gz 3.4 GB
EGAF00004198450 fastq.gz 3.8 GB
EGAF00004198451 fastq.gz 3.5 GB
EGAF00004198452 fastq.gz 3.5 GB
EGAF00004198453 fastq.gz 3.3 GB
EGAF00004198454 fastq.gz 3.4 GB
EGAF00004198455 fastq.gz 4.1 GB
EGAF00004198456 fastq.gz 4.1 GB
EGAF00004198457 fastq.gz 11.3 GB
EGAF00004198458 fastq.gz 11.1 GB
EGAF00004198459 fastq.gz 15.0 GB
EGAF00004198460 fastq.gz 15.2 GB
EGAF00004198461 fastq.gz 3.1 GB
EGAF00004198462 fastq.gz 3.4 GB
EGAF00004198463 fastq.gz 2.7 GB
EGAF00004198464 fastq.gz 3.0 GB
EGAF00004198465 fastq.gz 3.2 GB
EGAF00004198466 fastq.gz 3.6 GB
EGAF00004198467 fastq.gz 4.3 GB
EGAF00004198468 fastq.gz 4.8 GB
EGAF00004198469 fastq.gz 4.9 GB
EGAF00004198470 fastq.gz 5.8 GB
EGAF00004198471 fastq.gz 4.5 GB
EGAF00004198472 fastq.gz 5.1 GB
EGAF00004198473 fastq.gz 5.4 GB
EGAF00004198474 fastq.gz 6.1 GB
EGAF00004198475 fastq.gz 4.3 GB
EGAF00004198476 fastq.gz 4.6 GB
EGAF00004198477 fastq.gz 7.3 GB
EGAF00004198478 fastq.gz 7.4 GB
EGAF00004198479 fastq.gz 6.6 GB
EGAF00004198480 fastq.gz 6.7 GB
EGAF00004198481 fastq.gz 7.9 GB
EGAF00004198482 fastq.gz 7.9 GB
EGAF00004198483 fastq.gz 3.6 GB
EGAF00004198484 fastq.gz 3.8 GB
EGAF00004198485 fastq.gz 5.1 GB
EGAF00004198486 fastq.gz 4.8 GB
EGAF00004198487 fastq.gz 3.9 GB
EGAF00004198488 fastq.gz 4.1 GB
EGAF00004198489 fastq.gz 2.8 GB
EGAF00004198490 fastq.gz 2.8 GB
EGAF00004198491 fastq.gz 4.3 GB
EGAF00004198492 fastq.gz 4.6 GB
EGAF00004198493 fastq.gz 3.8 GB
EGAF00004198494 fastq.gz 4.1 GB
EGAF00004198495 fastq.gz 3.4 GB
EGAF00004198496 fastq.gz 3.6 GB
EGAF00004198497 fastq.gz 7.1 GB
EGAF00004198498 fastq.gz 7.3 GB
EGAF00004198499 fastq.gz 9.0 GB
EGAF00004198500 fastq.gz 9.1 GB
EGAF00004198501 fastq.gz 5.3 GB
EGAF00004198502 fastq.gz 5.4 GB
EGAF00004198503 fastq.gz 6.9 GB
EGAF00004198504 fastq.gz 6.8 GB
EGAF00004198505 fastq.gz 5.3 GB
EGAF00004198506 fastq.gz 5.3 GB
EGAF00004198507 fastq.gz 6.7 GB
EGAF00004198508 fastq.gz 6.6 GB
EGAF00004198509 fastq.gz 4.2 GB
EGAF00004198510 fastq.gz 4.3 GB
EGAF00004198511 fastq.gz 4.6 GB
EGAF00004198512 fastq.gz 4.6 GB
EGAF00004198513 fastq.gz 3.2 GB
EGAF00004198514 fastq.gz 3.1 GB
EGAF00004198515 fastq.gz 4.2 GB
EGAF00004198516 fastq.gz 4.1 GB
EGAF00004198517 fastq.gz 4.2 GB
EGAF00004198518 fastq.gz 4.2 GB
EGAF00004198519 fastq.gz 3.5 GB
EGAF00004198520 fastq.gz 3.5 GB
EGAF00004198521 fastq.gz 9.7 GB
EGAF00004198522 fastq.gz 9.7 GB
EGAF00004198523 fastq.gz 11.3 GB
EGAF00004198524 fastq.gz 11.1 GB
EGAF00004198525 fastq.gz 9.7 GB
EGAF00004198526 fastq.gz 9.7 GB
EGAF00004198527 fastq.gz 4.3 GB
EGAF00004198528 fastq.gz 4.7 GB
EGAF00004198529 fastq.gz 3.6 GB
EGAF00004198530 fastq.gz 3.6 GB
EGAF00004198531 fastq.gz 4.2 GB
EGAF00004198532 fastq.gz 4.3 GB
EGAF00004198533 fastq.gz 4.4 GB
EGAF00004198534 fastq.gz 4.5 GB
EGAF00004198535 fastq.gz 4.0 GB
EGAF00004198536 fastq.gz 4.0 GB
EGAF00004198537 fastq.gz 4.3 GB
EGAF00004198538 fastq.gz 4.4 GB
EGAF00004198539 fastq.gz 7.1 GB
EGAF00004198540 fastq.gz 6.9 GB
EGAF00004198541 fastq.gz 4.7 GB
EGAF00004198542 fastq.gz 4.5 GB
EGAF00004198543 fastq.gz 5.1 GB
EGAF00004198544 fastq.gz 5.8 GB
EGAF00004198545 fastq.gz 4.8 GB
EGAF00004198546 fastq.gz 5.6 GB
EGAF00004198547 fastq.gz 3.7 GB
EGAF00004198548 fastq.gz 4.1 GB
EGAF00004198549 fastq.gz 4.4 GB
EGAF00004198550 fastq.gz 5.0 GB
EGAF00004198551 fastq.gz 4.8 GB
EGAF00004198552 fastq.gz 5.2 GB
EGAF00004198553 fastq.gz 4.6 GB
EGAF00004198554 fastq.gz 5.2 GB
EGAF00004198555 fastq.gz 4.7 GB
EGAF00004198556 fastq.gz 5.5 GB
EGAF00004198557 fastq.gz 3.6 GB
EGAF00004198558 fastq.gz 4.1 GB
EGAF00004198559 fastq.gz 8.0 GB
EGAF00004198560 fastq.gz 8.2 GB
EGAF00004198561 fastq.gz 3.9 GB
EGAF00004198562 fastq.gz 4.1 GB
EGAF00004198563 fastq.gz 3.4 GB
EGAF00004198564 fastq.gz 3.9 GB
EGAF00004198565 fastq.gz 3.1 GB
EGAF00004198566 fastq.gz 3.3 GB
EGAF00004198567 fastq.gz 4.0 GB
EGAF00004198568 fastq.gz 4.7 GB
EGAF00004198569 fastq.gz 3.2 GB
EGAF00004198570 fastq.gz 3.7 GB
EGAF00004198571 fastq.gz 4.0 GB
EGAF00004198572 fastq.gz 4.7 GB
EGAF00004198573 fastq.gz 5.3 GB
EGAF00004198574 fastq.gz 6.1 GB
EGAF00004198575 fastq.gz 3.8 GB
EGAF00004198576 fastq.gz 4.2 GB
EGAF00004198577 fastq.gz 3.6 GB
EGAF00004198578 fastq.gz 4.0 GB
EGAF00004198579 fastq.gz 3.4 GB
EGAF00004198580 fastq.gz 4.0 GB
EGAF00004198581 fastq.gz 7.1 GB
EGAF00004198582 fastq.gz 6.8 GB
EGAF00004198583 fastq.gz 5.7 GB
EGAF00004198584 fastq.gz 6.0 GB
EGAF00004198585 fastq.gz 4.9 GB
EGAF00004198586 fastq.gz 5.2 GB
EGAF00004198587 fastq.gz 5.3 GB
EGAF00004198588 fastq.gz 6.0 GB
EGAF00004198589 fastq.gz 3.2 GB
EGAF00004198590 fastq.gz 3.2 GB
EGAF00004198591 fastq.gz 3.8 GB
EGAF00004198592 fastq.gz 4.0 GB
EGAF00004198593 fastq.gz 4.3 GB
EGAF00004198594 fastq.gz 4.7 GB
EGAF00004198595 fastq.gz 5.7 GB
EGAF00004198596 fastq.gz 6.3 GB
EGAF00004198597 fastq.gz 4.2 GB
EGAF00004198598 fastq.gz 4.6 GB
EGAF00004198599 fastq.gz 5.4 GB
EGAF00004198600 fastq.gz 6.1 GB
EGAF00004198601 fastq.gz 3.5 GB
EGAF00004198602 fastq.gz 3.8 GB
EGAF00004198603 fastq.gz 4.1 GB
EGAF00004198604 fastq.gz 4.5 GB
EGAF00004198605 fastq.gz 3.6 GB
EGAF00004198606 fastq.gz 3.9 GB
EGAF00004198607 fastq.gz 3.8 GB
EGAF00004198608 fastq.gz 4.2 GB
EGAF00004198609 fastq.gz 3.9 GB
EGAF00004198610 fastq.gz 4.2 GB
EGAF00004198611 fastq.gz 3.7 GB
EGAF00004198612 fastq.gz 4.0 GB
EGAF00004198613 fastq.gz 3.3 GB
EGAF00004198614 fastq.gz 3.7 GB
EGAF00004198615 fastq.gz 3.7 GB
EGAF00004198616 fastq.gz 4.1 GB
EGAF00004198617 fastq.gz 3.4 GB
EGAF00004198618 fastq.gz 3.8 GB
EGAF00004198619 fastq.gz 3.7 GB
EGAF00004198620 fastq.gz 4.1 GB
EGAF00004198621 fastq.gz 4.4 GB
EGAF00004198622 fastq.gz 4.9 GB
EGAF00004198623 fastq.gz 4.3 GB
EGAF00004198624 fastq.gz 4.9 GB
EGAF00004198625 fastq.gz 4.8 GB
EGAF00004198626 fastq.gz 5.3 GB
EGAF00004198627 fastq.gz 4.2 GB
EGAF00004198628 fastq.gz 5.0 GB
EGAF00004198629 fastq.gz 4.5 GB
EGAF00004198630 fastq.gz 5.1 GB
EGAF00004198631 fastq.gz 1.9 GB
EGAF00004198632 fastq.gz 1.9 GB
EGAF00004198633 fastq.gz 1.8 GB
EGAF00004198634 fastq.gz 1.8 GB
EGAF00004198635 fastq.gz 1.0 GB
EGAF00004198636 fastq.gz 1.5 GB
EGAF00004198637 fastq.gz 828.8 MB
EGAF00004198638 fastq.gz 1.2 GB
EGAF00004198639 fastq.gz 1.4 GB
EGAF00004198640 fastq.gz 2.0 GB
EGAF00004198641 fastq.gz 963.0 MB
EGAF00004198642 fastq.gz 1.4 GB
EGAF00004198643 fastq.gz 3.3 GB
EGAF00004198644 fastq.gz 3.7 GB
EGAF00004198645 fastq.gz 3.6 GB
EGAF00004198646 fastq.gz 4.1 GB
EGAF00004198647 fastq.gz 3.1 GB
EGAF00004198648 fastq.gz 3.5 GB
EGAF00004198649 fastq.gz 4.9 GB
EGAF00004198650 fastq.gz 5.6 GB
EGAF00004198651 fastq.gz 3.3 GB
EGAF00004198652 fastq.gz 3.7 GB
EGAF00004198653 fastq.gz 5.7 GB
EGAF00004198654 fastq.gz 6.3 GB
EGAF00004198655 fastq.gz 504.4 MB
EGAF00004198656 fastq.gz 518.9 MB
EGAF00004198657 fastq.gz 5.9 GB
EGAF00004198658 fastq.gz 5.9 GB
EGAF00004198659 fastq.gz 7.7 GB
EGAF00004198660 fastq.gz 7.6 GB
EGAF00004198661 fastq.gz 8.0 GB
EGAF00004198662 fastq.gz 8.7 GB
EGAF00004198663 fastq.gz 3.0 GB
EGAF00004198664 fastq.gz 3.2 GB
EGAF00004198665 fastq.gz 7.4 GB
EGAF00004198666 fastq.gz 8.6 GB
266 Files (1.3 TB)