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Sequencing files for "A Unifying Paradigm for Transcriptional Heterogeneity and Squamous Features in Pancreatic Ductal Adenocarcinoma."

Files from DNA and RNA sequencing from primary tumors and metastases from pancreatic cancer patients along with matched normal tissues.

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MSKCC Medical Donation Program 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 the MSKCC Medical Donation Program 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: MSKCC Medical Donation Program Data Access Committee 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. MSKCC Medical Donation Program Data Access Committee: Memorial Sloan Kettering Cancer Center, Medical Donation Program, 1275 York Avenue, New York, NY 10065. 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 the MSKCC Medical Donation Program Data Access Committee within 30 days of any changes or departures of Authorised Personnel. 13. The User Institution will notify the MSKCC Medical Donation Program Data Access Committee prior to any significant changes to the protocol for the Project. 14. The User Institution will notify the MSKCC Medical Donation Program Data Access Committee as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. The MSKCC Medical Donation Program 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. As an example, this may include specific provisions relating to the Data required by Data Producers other than the MSKCC Medical Donation Program Data Access Committee. 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 England and Wales and shall be subject to the exclusive jurisdiction of the English 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 the MSKCC Medical Donation Program Data Access Committee 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) EGAS00001002186 Name of project that created the dataset Sequencing of pancreatic cancer primary tumors and metastases Names of other data producers/collaborators Alvin P. Makohon-Moore Marc Attiyeh Jungeui Hong Nicholas Socci Kenneth Kinzler Christine Iacobuzio-Donahue Specific limitations on areas of research None. Minimum protection measures required None. 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 MSKCC Medical Donation Program Data Access Committee intends 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. The MSKCC Medical Donation Program Data Access Committee 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 the MSKCC Medical Donation Program 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., EGAS00001002186), and acknowledge its use in a form agreed by the User Institution with the MSKCC Medical Donation Program 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
EGAS00001003974 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
EGAF00002872109 bam 9.9 GB
EGAF00002872110 bam 10.9 GB
EGAF00002872111 bam 10.4 GB
EGAF00002872112 bam 9.8 GB
EGAF00002872113 bam 9.9 GB
EGAF00002872114 bam 2.5 GB
EGAF00002872115 bam 2.6 GB
EGAF00002872116 bam 128.9 GB
EGAF00002872117 bam 337.3 GB
EGAF00002872118 bam 359.0 GB
EGAF00002872119 bam 273.4 GB
EGAF00002872120 bam 270.5 GB
EGAF00002872121 bam 376.5 GB
EGAF00002872122 bam 302.4 GB
EGAF00002872123 bam 315.2 GB
EGAF00002872124 bam 324.7 GB
EGAF00002872125 bam 341.2 GB
EGAF00002872126 bam 310.2 GB
EGAF00002872127 bam 535.8 GB
EGAF00002872128 bam 495.0 GB
EGAF00002872129 bam 414.3 GB
EGAF00002872130 bam 434.8 GB
EGAF00002872131 bam 487.4 GB
EGAF00002872132 bam 457.9 GB
EGAF00002872133 bam 456.8 GB
EGAF00002872134 bam 454.2 GB
EGAF00002872135 bam 452.2 GB
EGAF00002872136 bam 430.7 GB
EGAF00002872137 bam 510.8 GB
EGAF00002872138 bam 573.6 GB
EGAF00002872139 bam 22.6 GB
EGAF00002872140 bam 35.3 GB
EGAF00002872141 bam 36.7 GB
EGAF00002872142 bam 35.6 GB
EGAF00002872143 bam 36.9 GB
EGAF00002872144 bam 15.3 GB
EGAF00002872145 bam 66.9 GB
EGAF00002872146 bam 71.0 GB
EGAF00002872147 bam 67.9 GB
EGAF00002872148 bam 73.0 GB
EGAF00002872149 bam 63.9 GB
EGAF00002872150 bam 63.8 GB
EGAF00002872151 bam 38.4 GB
EGAF00002872152 bam 50.7 GB
EGAF00002872153 bam 57.1 GB
EGAF00002872154 bam 48.6 GB
EGAF00002872155 bam 69.3 GB
EGAF00002872156 bam 66.2 GB
EGAF00002872157 bam 79.2 GB
EGAF00002872158 bam 55.2 GB
EGAF00002872159 bam 69.4 GB
EGAF00002872160 bam 62.4 GB
EGAF00002872161 bam 22.1 GB
EGAF00002872162 bam 62.1 GB
EGAF00002872163 bam 61.3 GB
EGAF00002872164 bam 48.0 GB
EGAF00002872165 bam 64.4 GB
EGAF00002872166 bam 59.3 GB
EGAF00002872167 bam 14.7 GB
EGAF00002872168 bam 50.2 GB
EGAF00002872169 bam 44.6 GB
EGAF00002872170 bam 59.8 GB
EGAF00002872171 bam 47.9 GB
EGAF00002872172 bam 42.6 GB
EGAF00002872173 bam 54.4 GB
EGAF00002872174 bam 15.2 GB
EGAF00002872175 bam 32.4 GB
EGAF00002872176 bam 41.0 GB
EGAF00002872177 bam 35.9 GB
EGAF00002872178 bam 33.7 GB
EGAF00002872179 bam 49.9 GB
EGAF00002872180 bam 35.2 GB
EGAF00002872181 bam 43.8 GB
EGAF00002872182 bam 45.3 GB
EGAF00002872183 bam 36.5 GB
EGAF00002872184 bam 18.7 GB
EGAF00002872185 bam 40.4 GB
EGAF00002872186 bam 41.3 GB
EGAF00002872187 bam 28.9 GB
EGAF00002872188 bam 38.6 GB
EGAF00002872189 bam 80.7 GB
EGAF00002872190 bam 44.2 GB
EGAF00002872191 bam 30.9 GB
EGAF00002872192 bam 38.8 GB
EGAF00002872193 bam 45.3 GB
EGAF00002872194 bam 12.1 GB
EGAF00002872195 bam 33.1 GB
EGAF00002872196 bam 30.2 GB
EGAF00002872197 bam 45.3 GB
EGAF00002872198 bam 34.5 GB
EGAF00002872199 bam 52.4 GB
EGAF00002872200 bam 12.0 GB
EGAF00002872201 bam 50.6 GB
EGAF00002872202 bam 33.3 GB
EGAF00002872203 bam 35.9 GB
EGAF00002872204 bam 34.5 GB
EGAF00002872205 bam 29.0 GB
EGAF00002872206 bam 31.3 GB
EGAF00002872207 bam 30.7 GB
EGAF00002872208 bam 28.5 GB
EGAF00002872209 bam 42.6 GB
EGAF00002872210 bam 11.2 GB
EGAF00002872211 bam 39.8 GB
EGAF00002872212 bam 33.2 GB
EGAF00002872213 bam 34.1 GB
EGAF00002872214 bam 33.3 GB
EGAF00002872215 bam 34.5 GB
EGAF00002872216 bam 35.5 GB
EGAF00002872217 bam 29.6 GB
EGAF00002872218 bam 30.7 GB
EGAF00002872219 bam 29.6 GB
EGAF00002872220 bam 32.8 GB
EGAF00002872221 bam 12.1 GB
EGAF00002872222 bam 11.6 GB
EGAF00002872223 bam 11.8 GB
EGAF00002872224 bam 10.7 GB
EGAF00002872225 bam 9.6 GB
EGAF00002872226 bam 12.0 GB
EGAF00002872227 bam 8.8 GB
EGAF00002872228 bam 8.8 GB
EGAF00002872229 bam 10.3 GB
EGAF00002872230 bam 9.8 GB
EGAF00002872231 bam 11.0 GB
EGAF00002872232 bam 10.6 GB
EGAF00002872233 bam 11.7 GB
EGAF00002872234 bam 10.0 GB
EGAF00002872235 bam 9.4 GB
EGAF00002872236 bam 10.5 GB
EGAF00002872237 bam 12.0 GB
EGAF00002872238 bam 11.1 GB
EGAF00002872239 bam 11.7 GB
EGAF00002872240 bam 11.6 GB
EGAF00002872241 bam 9.3 GB
EGAF00002872242 bam 10.1 GB
EGAF00002872243 bam 8.5 GB
EGAF00002872244 bam 11.3 GB
EGAF00002872245 bam 8.5 GB
EGAF00002872246 bam 9.8 GB
EGAF00002872247 bam 9.9 GB
EGAF00002872248 bam 9.0 GB
EGAF00002872249 bam 8.7 GB
EGAF00002872250 bam 8.6 GB
EGAF00002872251 bam 9.8 GB
EGAF00002872252 bam 10.1 GB
EGAF00002872253 bam 10.8 GB
EGAF00002872254 bam 11.0 GB
EGAF00002872255 bam 12.5 GB
EGAF00002872256 bam 9.8 GB
EGAF00002872257 bam 10.5 GB
EGAF00002872258 bam 9.8 GB
EGAF00002872259 bam 11.2 GB
EGAF00002872260 bam 11.6 GB
EGAF00002872261 bam 11.3 GB
EGAF00002872262 bam 11.0 GB
EGAF00002872263 bam 9.8 GB
EGAF00002872264 bam 9.7 GB
EGAF00002872265 bam 10.4 GB
EGAF00002872266 bam 11.5 GB
EGAF00002872267 bam 9.8 GB
EGAF00002872268 bam 9.7 GB
EGAF00002872269 bam 8.9 GB
EGAF00002872270 bam 9.2 GB
EGAF00002872271 bam 10.6 GB
EGAF00002872272 bam 8.6 GB
EGAF00002872273 bam 12.4 GB
EGAF00002872274 bam 12.2 GB
EGAF00002872275 bam 10.2 GB
EGAF00002872276 bam 11.6 GB
EGAF00002872277 bam 9.9 GB
EGAF00002872278 bam 9.5 GB
EGAF00002872279 bam 9.0 GB
EGAF00002872280 bam 10.9 GB
EGAF00002872281 bam 10.7 GB
EGAF00002872282 bam 10.4 GB
EGAF00002872283 bam 11.2 GB
EGAF00002872284 bam 10.0 GB
EGAF00002872285 bam 10.1 GB
EGAF00002872286 bam 9.2 GB
EGAF00002872287 bam 11.8 GB
EGAF00002872288 bam 11.8 GB
EGAF00002872289 bam 10.2 GB
EGAF00002872290 bam 11.1 GB
EGAF00002872291 bam 9.0 GB
EGAF00002872292 bam 10.6 GB
EGAF00002872293 bam 9.8 GB
EGAF00002872294 bam 9.4 GB
EGAF00002872295 bam 10.7 GB
EGAF00002872296 bam 10.8 GB
EGAF00002872297 bam 10.7 GB
EGAF00002872298 bam 10.2 GB
EGAF00002872299 bam 11.6 GB
EGAF00002872300 bam 10.3 GB
EGAF00002872301 bam 10.0 GB
EGAF00002872302 bam 9.5 GB
EGAF00002872303 bam 11.7 GB
EGAF00002872304 bam 9.6 GB
EGAF00002872305 bam 9.3 GB
EGAF00002872306 bam 8.7 GB
EGAF00002872307 bam 10.2 GB
EGAF00002872308 bam 12.1 GB
EGAF00002872309 bam 10.9 GB
EGAF00002872310 bam 10.8 GB
EGAF00002872311 bam 10.9 GB
EGAF00002872312 bam 8.0 GB
EGAF00002872313 bam 9.0 GB
EGAF00002872314 bam 10.0 GB
EGAF00002872315 bam 10.3 GB
EGAF00002872316 bam 11.4 GB
EGAF00002872317 bam 9.7 GB
EGAF00002872318 bam 9.3 GB
EGAF00002872319 bam 9.3 GB
EGAF00002872320 bam 9.1 GB
EGAF00002872321 bam 6.5 GB
EGAF00002872322 bam 6.5 GB
EGAF00002872323 bam 7.2 GB
EGAF00002872324 bam 11.4 GB
EGAF00002872325 bam 10.3 GB
EGAF00002872326 bam 10.2 GB
EGAF00002872327 bam 9.3 GB
EGAF00002872328 bam 9.9 GB
EGAF00002872329 bam 9.7 GB
EGAF00002872330 bam 10.6 GB
EGAF00002872331 bam 9.2 GB
EGAF00002872332 bam 9.4 GB
EGAF00002872333 bam 8.9 GB
EGAF00002872334 bam 9.1 GB
EGAF00002872335 bam 7.9 GB
EGAF00002872336 bam 9.2 GB
EGAF00002872337 bam 8.7 GB
EGAF00002872338 bam 11.1 GB
EGAF00002872339 bam 9.1 GB
EGAF00002872340 bam 9.5 GB
EGAF00002872341 bam 2.7 GB
EGAF00002872342 bam 10.2 GB
EGAF00002872343 bam 7.9 GB
EGAF00002872344 bam 9.7 GB
EGAF00002872345 bam 9.0 GB
EGAF00002872346 bam 9.1 GB
EGAF00002872347 bam 8.8 GB
EGAF00002872348 bam 10.4 GB
EGAF00002872349 bam 11.7 GB
EGAF00002872350 bam 9.3 GB
EGAF00002872351 bam 8.7 GB
EGAF00002872352 bam 10.8 GB
EGAF00002872353 bam 10.8 GB
EGAF00002872354 bam 10.1 GB
EGAF00002872355 bam 11.8 GB
EGAF00002872356 bam 11.1 GB
EGAF00002872357 bam 10.8 GB
EGAF00002872358 bam 11.4 GB
EGAF00002872359 bam 9.5 GB
EGAF00002872360 bam 12.1 GB
EGAF00002872361 bam 9.8 GB
EGAF00002872362 bam 10.2 GB
EGAF00002872363 bam 10.8 GB
EGAF00002872364 bam 9.8 GB
EGAF00002872365 bam 10.0 GB
EGAF00002872366 bam 9.9 GB
EGAF00002872367 bam 9.1 GB
EGAF00002872368 bam 9.5 GB
EGAF00002872369 bam 9.3 GB
EGAF00002872370 bam 12.3 GB
EGAF00002872371 bam 11.4 GB
EGAF00002872372 bam 10.1 GB
EGAF00002872373 bam 9.5 GB
EGAF00002872374 bam 10.3 GB
EGAF00002872375 bam 9.9 GB
EGAF00002872376 bam 9.9 GB
EGAF00002872377 bam 10.4 GB
EGAF00002872378 bam 10.1 GB
EGAF00002872379 bam 9.9 GB
EGAF00002872380 bam 11.0 GB
EGAF00002872381 bam 10.1 GB
EGAF00002872382 bam 9.1 GB
EGAF00002872383 bam 9.4 GB
EGAF00002872384 bam 10.0 GB
EGAF00002872385 bam 9.2 GB
EGAF00002872386 bam 9.7 GB
EGAF00002872387 bam 9.6 GB
EGAF00002872388 bam 9.8 GB
EGAF00002872389 bam 9.5 GB
EGAF00002872390 bam 9.5 GB
EGAF00002872391 bam 10.4 GB
EGAF00002872392 bam 8.7 GB
EGAF00002872393 bam 8.2 GB
EGAF00002872394 bam 10.0 GB
EGAF00002872395 bam 9.7 GB
EGAF00002872396 bam 12.3 GB
EGAF00002872397 bam 10.7 GB
EGAF00002872398 bam 10.8 GB
EGAF00002872399 bam 10.0 GB
EGAF00002872400 bam 8.9 GB
EGAF00002872401 bam 12.2 GB
EGAF00002872402 bam 9.2 GB
EGAF00002872403 bam 10.5 GB
EGAF00002872404 bam 9.7 GB
EGAF00002872405 bam 9.0 GB
EGAF00002872406 bam 10.9 GB
EGAF00002872407 bam 9.8 GB
EGAF00002872408 bam 9.6 GB
EGAF00002872409 bam 11.5 GB
EGAF00002872410 bam 11.7 GB
EGAF00002872411 bam 13.5 GB
EGAF00002872412 bam 9.7 GB
EGAF00002872413 bam 10.9 GB
EGAF00002872414 bam 11.6 GB
EGAF00002872415 bam 8.7 GB
EGAF00002872416 bam 12.3 GB
EGAF00002872417 bam 9.8 GB
EGAF00002872418 bam 10.1 GB
EGAF00002872419 bam 10.8 GB
EGAF00002872420 bam 10.6 GB
EGAF00002872421 bam 10.1 GB
EGAF00002872422 bam 10.2 GB
EGAF00002872423 bam 11.2 GB
EGAF00002872424 bam 9.5 GB
EGAF00002872425 bam 9.7 GB
EGAF00002872426 bam 9.0 GB
EGAF00002872427 bam 8.9 GB
319 Files (14.7 TB)