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RNAseq FASTq files from 82 pre-treatment tumors from PURE01

RNAseq FASTq files from 82 pre-treatment tumors from PURE01

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Data access committee 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 Northwestern University 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: Northwestern University 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 NORTHWESTERN UNIVERSITY within 30 days of any changes or departures of Authorised Personnel. 13. The User Institution will notify NORTHWESTERN UNIVERSITY prior to any significant changes to the protocol for the Project. 14. The User Institution will notify NORTHWESTERN UNIVERSITY as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. NORTHWESTERN UNIVERSITY 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 NORTHWESTERN UNIVERSITY. 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 NORTHWESTERN UNIVERSITY 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) Name of project that created the dataset: PURE01 Trial Names of other data producers/collaborators: Joshua Meeks, Northwestern University Andrea Necchi, MD, 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 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* Joshua Meeks Joshua.meeks@northwestern.edu Associate Professor of Urology All Individuals that should have an account created at the EGA Name of Registered User Email Job Title Joshua Meeks joshua.meeks@northwestern.edu A Gordon Robertson grobertson.bcgsc@gmail.com APPENDIX III – PUBLICATION POLICY NORTHWESTERN UNIVERSITY 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. NORTHWESTERN UNIVERSITY 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 1 months after these data were first made available on the relevant hosting database, unless NORTHWESTERN UNIVERSITY 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., EGAS00000000029), and acknowledge its use in a form agreed by the User Institution with NORTHWESTERN UNIVERSITY.

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
EGAS00001005549 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
EGAF00005441171 fastq.gz 3.2 GB
EGAF00005441172 fastq.gz 3.2 GB
EGAF00005441173 fastq.gz 4.5 GB
EGAF00005441174 fastq.gz 4.4 GB
EGAF00005441175 fastq.gz 3.3 GB
EGAF00005441176 fastq.gz 3.4 GB
EGAF00005441177 fastq.gz 2.6 GB
EGAF00005441178 fastq.gz 2.6 GB
EGAF00005441179 fastq.gz 3.9 GB
EGAF00005441180 fastq.gz 4.0 GB
EGAF00005441181 fastq.gz 3.8 GB
EGAF00005441182 fastq.gz 3.8 GB
EGAF00005441183 fastq.gz 3.0 GB
EGAF00005441184 fastq.gz 2.9 GB
EGAF00005441185 fastq.gz 3.7 GB
EGAF00005441186 fastq.gz 3.7 GB
EGAF00005441187 fastq.gz 3.6 GB
EGAF00005441188 fastq.gz 3.5 GB
EGAF00005441189 fastq.gz 2.5 GB
EGAF00005441190 fastq.gz 2.5 GB
EGAF00005441191 fastq.gz 3.8 GB
EGAF00005441192 fastq.gz 3.8 GB
EGAF00005441193 fastq.gz 2.3 GB
EGAF00005441194 fastq.gz 2.2 GB
EGAF00005441195 fastq.gz 2.9 GB
EGAF00005441196 fastq.gz 3.0 GB
EGAF00005441197 fastq.gz 1.7 GB
EGAF00005441198 fastq.gz 1.7 GB
EGAF00005441199 fastq.gz 2.6 GB
EGAF00005441200 fastq.gz 2.6 GB
EGAF00005441201 fastq.gz 2.7 GB
EGAF00005441202 fastq.gz 2.6 GB
EGAF00005441203 fastq.gz 3.0 GB
EGAF00005441204 fastq.gz 2.9 GB
EGAF00005441205 fastq.gz 2.5 GB
EGAF00005441206 fastq.gz 2.5 GB
EGAF00005441207 fastq.gz 3.0 GB
EGAF00005441208 fastq.gz 2.9 GB
EGAF00005441209 fastq.gz 2.3 GB
EGAF00005441210 fastq.gz 2.3 GB
EGAF00005441211 fastq.gz 2.4 GB
EGAF00005441212 fastq.gz 2.4 GB
EGAF00005441213 fastq.gz 2.9 GB
EGAF00005441214 fastq.gz 2.9 GB
EGAF00005441215 fastq.gz 2.3 GB
EGAF00005441216 fastq.gz 2.2 GB
EGAF00005441217 fastq.gz 2.6 GB
EGAF00005441218 fastq.gz 2.6 GB
EGAF00005441219 fastq.gz 3.0 GB
EGAF00005441220 fastq.gz 2.9 GB
EGAF00005441221 fastq.gz 3.8 GB
EGAF00005441222 fastq.gz 3.9 GB
EGAF00005441223 fastq.gz 3.2 GB
EGAF00005441224 fastq.gz 3.2 GB
EGAF00005441225 fastq.gz 4.7 GB
EGAF00005441226 fastq.gz 4.7 GB
EGAF00005441227 fastq.gz 3.9 GB
EGAF00005441228 fastq.gz 4.0 GB
EGAF00005441229 fastq.gz 4.0 GB
EGAF00005441230 fastq.gz 4.0 GB
EGAF00005441231 fastq.gz 2.5 GB
EGAF00005441232 fastq.gz 2.4 GB
EGAF00005441233 fastq.gz 3.5 GB
EGAF00005441234 fastq.gz 3.6 GB
EGAF00005441235 fastq.gz 3.1 GB
EGAF00005441236 fastq.gz 3.0 GB
EGAF00005441237 fastq.gz 3.3 GB
EGAF00005441238 fastq.gz 3.3 GB
EGAF00005441239 fastq.gz 4.9 GB
EGAF00005441240 fastq.gz 4.5 GB
EGAF00005441241 fastq.gz 4.7 GB
EGAF00005441242 fastq.gz 4.3 GB
EGAF00005441243 fastq.gz 3.0 GB
EGAF00005441244 fastq.gz 3.1 GB
EGAF00005441245 fastq.gz 2.2 GB
EGAF00005441246 fastq.gz 2.2 GB
EGAF00005441247 fastq.gz 1.8 GB
EGAF00005441248 fastq.gz 1.7 GB
EGAF00005441249 fastq.gz 3.7 GB
EGAF00005441250 fastq.gz 3.8 GB
EGAF00005441251 fastq.gz 2.5 GB
EGAF00005441252 fastq.gz 2.5 GB
EGAF00005441253 fastq.gz 2.7 GB
EGAF00005441254 fastq.gz 2.6 GB
EGAF00005441255 fastq.gz 3.9 GB
EGAF00005441256 fastq.gz 4.1 GB
EGAF00005441257 fastq.gz 2.5 GB
EGAF00005441258 fastq.gz 2.4 GB
EGAF00005441259 fastq.gz 2.9 GB
EGAF00005441260 fastq.gz 2.9 GB
EGAF00005441261 fastq.gz 3.6 GB
EGAF00005441262 fastq.gz 3.6 GB
EGAF00005441263 fastq.gz 4.1 GB
EGAF00005441264 fastq.gz 4.2 GB
EGAF00005441265 fastq.gz 2.6 GB
EGAF00005441266 fastq.gz 2.5 GB
EGAF00005441267 fastq.gz 2.4 GB
EGAF00005441268 fastq.gz 2.3 GB
EGAF00005441269 fastq.gz 2.5 GB
EGAF00005441270 fastq.gz 2.4 GB
EGAF00005441271 fastq.gz 2.8 GB
EGAF00005441272 fastq.gz 2.8 GB
EGAF00005441273 fastq.gz 3.4 GB
EGAF00005441274 fastq.gz 3.3 GB
EGAF00005441275 fastq.gz 2.5 GB
EGAF00005441276 fastq.gz 2.4 GB
EGAF00005441277 fastq.gz 2.5 GB
EGAF00005441278 fastq.gz 2.5 GB
EGAF00005441279 fastq.gz 4.8 GB
EGAF00005441280 fastq.gz 4.9 GB
EGAF00005441281 fastq.gz 4.5 GB
EGAF00005441282 fastq.gz 4.6 GB
EGAF00005441283 fastq.gz 2.2 GB
EGAF00005441284 fastq.gz 2.2 GB
EGAF00005441285 fastq.gz 2.9 GB
EGAF00005441286 fastq.gz 2.8 GB
EGAF00005441287 fastq.gz 2.8 GB
EGAF00005441288 fastq.gz 2.7 GB
EGAF00005441289 fastq.gz 3.0 GB
EGAF00005441290 fastq.gz 2.9 GB
EGAF00005441291 fastq.gz 2.6 GB
EGAF00005441292 fastq.gz 2.6 GB
EGAF00005441293 fastq.gz 3.5 GB
EGAF00005441294 fastq.gz 3.5 GB
EGAF00005441295 fastq.gz 4.3 GB
EGAF00005441296 fastq.gz 4.4 GB
EGAF00005441297 fastq.gz 3.3 GB
EGAF00005441298 fastq.gz 3.2 GB
EGAF00005441299 fastq.gz 3.5 GB
EGAF00005441300 fastq.gz 3.5 GB
EGAF00005441301 fastq.gz 2.6 GB
EGAF00005441302 fastq.gz 2.5 GB
EGAF00005441303 fastq.gz 4.2 GB
EGAF00005441304 fastq.gz 4.4 GB
EGAF00005441305 fastq.gz 2.8 GB
EGAF00005441306 fastq.gz 2.7 GB
EGAF00005441307 fastq.gz 4.0 GB
EGAF00005441308 fastq.gz 4.2 GB
EGAF00005441309 fastq.gz 3.7 GB
EGAF00005441310 fastq.gz 3.7 GB
EGAF00005441311 fastq.gz 3.7 GB
EGAF00005441312 fastq.gz 3.7 GB
EGAF00005441313 fastq.gz 2.4 GB
EGAF00005441314 fastq.gz 2.4 GB
EGAF00005441315 fastq.gz 4.9 GB
EGAF00005441316 fastq.gz 5.0 GB
EGAF00005441317 fastq.gz 2.6 GB
EGAF00005441318 fastq.gz 2.5 GB
EGAF00005441319 fastq.gz 4.4 GB
EGAF00005441320 fastq.gz 4.5 GB
EGAF00005441321 fastq.gz 3.3 GB
EGAF00005441322 fastq.gz 3.3 GB
EGAF00005441323 fastq.gz 2.5 GB
EGAF00005441324 fastq.gz 2.5 GB
EGAF00005441325 fastq.gz 4.2 GB
EGAF00005441326 fastq.gz 4.1 GB
EGAF00005441327 fastq.gz 3.4 GB
EGAF00005441328 fastq.gz 3.6 GB
EGAF00005441329 fastq.gz 2.2 GB
EGAF00005441330 fastq.gz 2.2 GB
EGAF00005441331 fastq.gz 3.5 GB
EGAF00005441332 fastq.gz 3.4 GB
EGAF00005441333 fastq.gz 3.7 GB
EGAF00005441334 fastq.gz 3.7 GB
EGAF00005441462 txt 16.6 MB
EGAF00005441465 xlsx 29.7 kB
EGAF00005441466 xlsx 13.0 kB
EGAF00005441467 xlsx 58.1 kB
168 Files (524.3 GB)