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Finding structural variation from the patient-derived xenografts of pediatric T-cell leukemia at the single-cell level

In this study, we aimed to identify somatic structural variation of T-cell acute lymphoblastic leukemias (T-ALLs_ from patient-derived xenografts (PDX) at the single-cell level. For this purpose, we performed strand-specific single-cell sequencing of PDX-derived T-ALL relapse samples from two juvenile patients (P1, P33). To validate structural variation detected via scTRIP, we profiled whole exome sequencing (WES) data from P33 (samples taken during initial disease, remission, relapse), and mate-pair sequencing data from P1 (relapse).

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Data access policy of EMBL genome biology research group for structural variation (Strand-seq application)

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 EMBL genome biology research group for structural variation (Strand-seq application) 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: EMBL genome biology research group for structural variation (Strand-seq application) 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. 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 EMBL genome biology research group for structural variation (Strand-seq application), within 30 days of any changes or departures of Authorised Personnel. 13. The User Institution will notify EMBL genome biology research group for structural variation (Strand-seq application), prior to any significant changes to the protocol for the Project. 14. The User Institution will notify EMBL genome biology research group for structural variation (Strand-seq application), as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. EMBL genome biology research group for structural variation (Strand-seq application) 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 EMBL genome biology research group for structural variation (Strand-seq application). 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.

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
EGAF00002273266 txt.gz 115.2 MB
EGAF00002273267 txt.gz 115.0 MB
EGAF00002273268 txt.gz 100.9 MB
EGAF00002273269 txt.gz 100.3 MB
EGAF00002273270 txt.gz 76.0 MB
EGAF00002273271 txt.gz 75.7 MB
EGAF00002273272 txt.gz 86.2 MB
EGAF00002273273 txt.gz 86.0 MB
EGAF00002273274 txt.gz 63.7 MB
EGAF00002273275 txt.gz 62.9 MB
EGAF00002273276 txt.gz 89.7 MB
EGAF00002273277 txt.gz 89.2 MB
EGAF00002273278 txt.gz 63.1 MB
EGAF00002273279 txt.gz 62.6 MB
EGAF00002273280 txt.gz 85.5 MB
EGAF00002273281 txt.gz 85.4 MB
EGAF00002273282 txt.gz 80.1 MB
EGAF00002273283 txt.gz 80.0 MB
EGAF00002273284 txt.gz 101.1 MB
EGAF00002273285 txt.gz 101.3 MB
EGAF00002273286 txt.gz 110.3 MB
EGAF00002273287 txt.gz 110.1 MB
EGAF00002273288 txt.gz 79.4 MB
EGAF00002273289 txt.gz 78.7 MB
EGAF00002273290 txt.gz 72.6 MB
EGAF00002273291 txt.gz 72.5 MB
EGAF00002273292 txt.gz 123.9 MB
EGAF00002273293 txt.gz 123.5 MB
EGAF00002273294 txt.gz 31.8 MB
EGAF00002273295 txt.gz 31.7 MB
EGAF00002273296 txt.gz 71.0 MB
EGAF00002273297 txt.gz 70.5 MB
EGAF00002273298 txt.gz 92.9 MB
EGAF00002273299 txt.gz 92.3 MB
EGAF00002273300 txt.gz 93.3 MB
EGAF00002273301 txt.gz 92.4 MB
EGAF00002273302 txt.gz 47.1 MB
EGAF00002273303 txt.gz 46.9 MB
EGAF00002273304 txt.gz 50.9 MB
EGAF00002273305 txt.gz 50.8 MB
EGAF00002273306 txt.gz 49.9 MB
EGAF00002273307 txt.gz 49.7 MB
EGAF00002273308 txt.gz 65.0 MB
EGAF00002273309 txt.gz 64.8 MB
EGAF00002273310 txt.gz 130.3 MB
EGAF00002273311 txt.gz 129.9 MB
EGAF00002273312 txt.gz 54.9 MB
EGAF00002273313 txt.gz 54.4 MB
EGAF00002273314 txt.gz 51.0 MB
EGAF00002273315 txt.gz 50.9 MB
EGAF00002273316 txt.gz 70.4 MB
EGAF00002273317 txt.gz 69.8 MB
EGAF00002273318 txt.gz 69.0 MB
EGAF00002273319 txt.gz 68.8 MB
EGAF00002273320 txt.gz 70.0 MB
EGAF00002273321 txt.gz 69.9 MB
EGAF00002273322 txt.gz 39.2 MB
EGAF00002273323 txt.gz 39.2 MB
EGAF00002273324 txt.gz 43.4 MB
EGAF00002273325 txt.gz 43.0 MB
EGAF00002273326 txt.gz 96.4 MB
EGAF00002273327 txt.gz 96.0 MB
EGAF00002273328 txt.gz 103.6 MB
EGAF00002273329 txt.gz 103.0 MB
EGAF00002273330 txt.gz 89.8 MB
EGAF00002273331 txt.gz 89.4 MB
EGAF00002273332 txt.gz 118.1 MB
EGAF00002273333 txt.gz 117.8 MB
EGAF00002273334 txt.gz 116.3 MB
EGAF00002273335 txt.gz 115.5 MB
EGAF00002273336 txt.gz 41.8 MB
EGAF00002273337 txt.gz 41.6 MB
EGAF00002273338 txt.gz 37.4 MB
EGAF00002273339 txt.gz 37.3 MB
EGAF00002273340 txt.gz 39.5 MB
EGAF00002273341 txt.gz 39.4 MB
EGAF00002273342 txt.gz 165.6 MB
EGAF00002273343 txt.gz 164.0 MB
EGAF00002273344 txt.gz 113.4 MB
EGAF00002273345 txt.gz 112.8 MB
EGAF00002273346 txt.gz 74.6 MB
EGAF00002273347 txt.gz 74.5 MB
EGAF00002273348 txt.gz 175.1 MB
EGAF00002273349 txt.gz 175.5 MB
EGAF00002273350 txt.gz 83.0 MB
EGAF00002273351 txt.gz 82.9 MB
EGAF00002273352 txt.gz 178.2 MB
EGAF00002273353 txt.gz 178.7 MB
EGAF00002273354 txt.gz 29.0 MB
EGAF00002273355 txt.gz 28.9 MB
EGAF00002273356 txt.gz 150.2 MB
EGAF00002273357 txt.gz 151.1 MB
EGAF00002273358 txt.gz 29.7 MB
EGAF00002273359 txt.gz 29.9 MB
EGAF00002273360 txt.gz 104.7 MB
EGAF00002273361 txt.gz 104.5 MB
EGAF00002273362 txt.gz 189.9 MB
EGAF00002273363 txt.gz 190.0 MB
EGAF00002273364 txt.gz 150.3 MB
EGAF00002273365 txt.gz 150.8 MB
EGAF00002273366 txt.gz 117.3 MB
EGAF00002273367 txt.gz 117.4 MB
EGAF00002273368 txt.gz 147.2 MB
EGAF00002273369 txt.gz 148.4 MB
EGAF00002273370 txt.gz 74.6 MB
EGAF00002273371 txt.gz 74.4 MB
EGAF00002273372 txt.gz 44.8 MB
EGAF00002273373 txt.gz 45.0 MB
EGAF00002273374 txt.gz 103.5 MB
EGAF00002273375 txt.gz 103.9 MB
EGAF00002273376 txt.gz 100.4 MB
EGAF00002273377 txt.gz 100.5 MB
EGAF00002273378 txt.gz 124.8 MB
EGAF00002273379 txt.gz 124.8 MB
EGAF00002273380 txt.gz 206.0 MB
EGAF00002273381 txt.gz 205.2 MB
EGAF00002273382 txt.gz 23.2 MB
EGAF00002273383 txt.gz 23.3 MB
EGAF00002273384 txt.gz 60.6 MB
EGAF00002273385 txt.gz 60.7 MB
EGAF00002273386 txt.gz 117.2 MB
EGAF00002273387 txt.gz 117.5 MB
EGAF00002273388 txt.gz 86.9 MB
EGAF00002273389 txt.gz 87.1 MB
EGAF00002273390 txt.gz 91.9 MB
EGAF00002273391 txt.gz 92.2 MB
EGAF00002273392 txt.gz 37.6 MB
EGAF00002273393 txt.gz 37.9 MB
EGAF00002273394 txt.gz 110.4 MB
EGAF00002273395 txt.gz 110.6 MB
EGAF00002273396 txt.gz 97.5 MB
EGAF00002273397 txt.gz 97.7 MB
EGAF00002273398 txt.gz 77.5 MB
EGAF00002273399 txt.gz 77.8 MB
EGAF00002273400 txt.gz 67.0 MB
EGAF00002273401 txt.gz 67.1 MB
EGAF00002273402 txt.gz 40.6 MB
EGAF00002273403 txt.gz 40.6 MB
EGAF00002273404 txt.gz 49.1 MB
EGAF00002273405 txt.gz 49.3 MB
EGAF00002273406 txt.gz 116.4 MB
EGAF00002273407 txt.gz 116.9 MB
EGAF00002273408 txt.gz 122.6 MB
EGAF00002273409 txt.gz 123.2 MB
EGAF00002273410 txt.gz 67.2 MB
EGAF00002273411 txt.gz 67.0 MB
EGAF00002273412 txt.gz 62.4 MB
EGAF00002273413 txt.gz 62.4 MB
EGAF00002273414 txt.gz 99.7 MB
EGAF00002273415 txt.gz 99.5 MB
EGAF00002273416 txt.gz 100.3 MB
EGAF00002273417 txt.gz 100.4 MB
EGAF00002273418 txt.gz 63.3 MB
EGAF00002273419 txt.gz 63.5 MB
EGAF00002273420 txt.gz 106.5 MB
EGAF00002273421 txt.gz 106.0 MB
EGAF00002273422 txt.gz 91.4 MB
EGAF00002273423 txt.gz 91.6 MB
EGAF00002273424 txt.gz 83.0 MB
EGAF00002273425 txt.gz 83.3 MB
EGAF00002273426 txt.gz 64.9 MB
EGAF00002273427 txt.gz 65.3 MB
EGAF00002273428 txt.gz 114.0 MB
EGAF00002273429 txt.gz 115.6 MB
EGAF00002273430 txt.gz 107.0 MB
EGAF00002273431 txt.gz 108.5 MB
EGAF00002273432 txt.gz 199.6 MB
EGAF00002273433 txt.gz 202.5 MB
EGAF00002273434 txt.gz 90.7 MB
EGAF00002273435 txt.gz 92.3 MB
EGAF00002273436 txt.gz 32.9 MB
EGAF00002273437 txt.gz 33.6 MB
EGAF00002273438 txt.gz 107.8 MB
EGAF00002273439 txt.gz 109.3 MB
EGAF00002273440 txt.gz 76.1 MB
EGAF00002273441 txt.gz 77.0 MB
EGAF00002273442 txt.gz 46.6 MB
EGAF00002273443 txt.gz 47.4 MB
EGAF00002273444 txt.gz 73.5 MB
EGAF00002273445 txt.gz 74.7 MB
EGAF00002273446 txt.gz 129.2 MB
EGAF00002273447 txt.gz 131.3 MB
EGAF00002273448 txt.gz 97.8 MB
EGAF00002273449 txt.gz 99.4 MB
EGAF00002273450 txt.gz 107.2 MB
EGAF00002273451 txt.gz 109.6 MB
EGAF00002273452 txt.gz 107.6 MB
EGAF00002273453 txt.gz 109.3 MB
EGAF00002273454 txt.gz 118.8 MB
EGAF00002273455 txt.gz 120.5 MB
EGAF00002273456 txt.gz 134.9 MB
EGAF00002273457 txt.gz 136.9 MB
EGAF00002273458 txt.gz 95.0 MB
EGAF00002273459 txt.gz 96.4 MB
EGAF00002273460 txt.gz 87.9 MB
EGAF00002273461 txt.gz 89.2 MB
EGAF00002273462 txt.gz 95.1 MB
EGAF00002273463 txt.gz 96.2 MB
EGAF00002273464 txt.gz 61.8 MB
EGAF00002273465 txt.gz 62.7 MB
EGAF00002273466 txt.gz 66.8 MB
EGAF00002273467 txt.gz 67.6 MB
EGAF00002273468 txt.gz 64.2 MB
EGAF00002273469 txt.gz 65.3 MB
EGAF00002273470 txt.gz 131.3 MB
EGAF00002273471 txt.gz 133.4 MB
EGAF00002273472 txt.gz 26.9 MB
EGAF00002273473 txt.gz 28.2 MB
EGAF00002273474 txt.gz 89.4 MB
EGAF00002273475 txt.gz 90.6 MB
EGAF00002273476 txt.gz 187.6 MB
EGAF00002273477 txt.gz 190.0 MB
EGAF00002273478 txt.gz 86.8 MB
EGAF00002273479 txt.gz 87.8 MB
EGAF00002273480 txt.gz 85.2 MB
EGAF00002273481 txt.gz 86.5 MB
EGAF00002273482 txt.gz 193.0 MB
EGAF00002273483 txt.gz 195.1 MB
EGAF00002273484 txt.gz 78.7 MB
EGAF00002273485 txt.gz 80.2 MB
EGAF00002273486 txt.gz 86.5 MB
EGAF00002273487 txt.gz 87.6 MB
EGAF00002273488 txt.gz 197.0 MB
EGAF00002273489 txt.gz 199.9 MB
EGAF00002273490 txt.gz 94.2 MB
EGAF00002273491 txt.gz 95.2 MB
EGAF00002273492 txt.gz 95.3 MB
EGAF00002273493 txt.gz 96.5 MB
EGAF00002273494 txt.gz 38.7 MB
EGAF00002273495 txt.gz 39.5 MB
EGAF00002273496 txt.gz 117.5 MB
EGAF00002273497 txt.gz 119.5 MB
EGAF00002273498 txt.gz 95.1 MB
EGAF00002273499 txt.gz 96.1 MB
EGAF00002273500 txt.gz 168.0 MB
EGAF00002273501 txt.gz 170.3 MB
EGAF00002273502 txt.gz 167.0 MB
EGAF00002273503 txt.gz 169.1 MB
EGAF00002273504 txt.gz 156.1 MB
EGAF00002273505 txt.gz 158.8 MB
EGAF00002273506 txt.gz 3.1 GB
EGAF00002273507 txt.gz 3.1 GB
EGAF00002273508 txt.gz 3.4 GB
EGAF00002273509 txt.gz 3.5 GB
EGAF00002273510 txt.gz 2.9 GB
EGAF00002273511 txt.gz 3.0 GB
EGAF00002273512 fq.gz 5.6 GB
EGAF00002273513 fq.gz 5.7 GB
248 Files (52.9 GB)