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Bulk RNAseq

Bulk RNAseq from 183 premalignant gastric biopsies

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Data Access Agreement

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 XXXXX 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: XXXXX 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 2 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/w eb_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 3 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 XXXXX within 30 days of any changes or departures of Authorised Personnel. 13. The User Institution will notify XXXXX prior to any significant changes to the protocol for the Project. 14. The User Institution will notify XXXXX as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. XXXXX 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 XXXXX. 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 4 Signature:   Name:   Title:   Date:   Principal Investigator I confirm that I have read and understood this Agreement. Signature:   Name:   Title:   Date:   Agreed for XXXXX 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) 5 Dataset reference (EGA Study ID and Dataset Details) Name of project that created the dataset Names of other data producers/collaborators 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. 6 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 XXXXX 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. XXXXX 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 XX months after these data were first made available on the relevant hosting database, unless XXXXX 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 XXXXX.

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
EGAS00001007067 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
EGAF00007973145 cram 8.5 GB
EGAF00007973146 cram 1.8 GB
EGAF00007973147 cram 4.1 GB
EGAF00007973148 cram 3.6 GB
EGAF00007973149 cram 1.8 GB
EGAF00007973150 cram 1.9 GB
EGAF00007973151 cram 1.7 GB
EGAF00007973152 cram 16.0 GB
EGAF00007973153 cram 1.9 GB
EGAF00007973154 cram 23.5 GB
EGAF00007973155 cram 17.1 GB
EGAF00007973156 cram 2.7 GB
EGAF00007973157 cram 2.4 GB
EGAF00007973158 cram 3.8 GB
EGAF00007973159 cram 6.1 GB
EGAF00007973160 cram 4.3 GB
EGAF00007973161 cram 3.0 GB
EGAF00007973162 cram 3.2 GB
EGAF00007973163 cram 3.9 GB
EGAF00007973164 cram 3.0 GB
EGAF00007973165 cram 3.5 GB
EGAF00007973166 cram 2.8 GB
EGAF00007973167 cram 5.6 GB
EGAF00007973168 cram 4.0 GB
EGAF00007973169 cram 2.4 GB
EGAF00007973170 cram 3.1 GB
EGAF00007973171 cram 2.2 GB
EGAF00007973172 cram 15.1 GB
EGAF00007973173 cram 2.4 GB
EGAF00007973174 cram 3.3 GB
EGAF00007973175 cram 5.6 GB
EGAF00007973176 cram 2.6 GB
EGAF00007973177 cram 2.0 GB
EGAF00007973178 cram 2.0 GB
EGAF00007973179 cram 2.3 GB
EGAF00007973180 cram 2.7 GB
EGAF00007973181 cram 3.3 GB
EGAF00007973182 cram 15.3 GB
EGAF00007973183 cram 7.8 GB
EGAF00007973184 cram 2.3 GB
EGAF00007973185 cram 11.0 GB
EGAF00007973186 cram 3.1 GB
EGAF00007973187 cram 6.0 GB
EGAF00007973188 cram 2.9 GB
EGAF00007973189 cram 7.1 GB
EGAF00007973190 cram 8.4 GB
EGAF00007973191 cram 4.2 GB
EGAF00007973192 cram 10.1 GB
EGAF00007973193 cram 7.5 GB
EGAF00007973194 cram 10.7 GB
EGAF00007973195 cram 34.3 GB
EGAF00007973196 cram 12.8 GB
EGAF00007973197 cram 1.9 GB
EGAF00007973198 cram 13.0 GB
EGAF00007973199 cram 3.7 GB
EGAF00007973200 cram 3.3 GB
EGAF00007973201 cram 11.6 GB
EGAF00007973202 cram 26.5 GB
EGAF00007973203 cram 4.9 GB
EGAF00007973204 cram 2.9 GB
EGAF00007973205 cram 15.1 GB
EGAF00007973206 cram 3.6 GB
EGAF00007973207 cram 2.9 GB
EGAF00007973208 cram 15.4 GB
EGAF00007973209 cram 4.3 GB
EGAF00007973210 cram 2.9 GB
EGAF00007973211 cram 10.2 GB
EGAF00007973212 cram 11.0 GB
EGAF00007973213 cram 5.0 GB
EGAF00007973214 cram 4.3 GB
EGAF00007973215 cram 8.2 GB
EGAF00007973216 cram 5.4 GB
EGAF00007973217 cram 4.1 GB
EGAF00007973218 cram 5.3 GB
EGAF00007973219 cram 19.8 GB
EGAF00007973220 cram 3.7 GB
EGAF00007973221 cram 4.9 GB
EGAF00007973222 cram 6.9 GB
EGAF00007973223 cram 7.9 GB
EGAF00007973224 cram 2.6 GB
EGAF00007973225 cram 3.6 GB
EGAF00007973226 cram 7.2 GB
EGAF00007973227 cram 3.2 GB
EGAF00007973228 cram 9.8 GB
EGAF00007973229 cram 5.4 GB
EGAF00007973230 cram 8.0 GB
EGAF00007973231 cram 32.6 GB
EGAF00007973232 cram 3.6 GB
EGAF00007973233 cram 3.0 GB
EGAF00007973234 cram 9.9 GB
EGAF00007973235 cram 21.6 GB
EGAF00007973236 cram 8.8 GB
EGAF00007973237 cram 11.3 GB
EGAF00007973238 cram 6.7 GB
EGAF00007973239 cram 5.9 GB
EGAF00007973240 cram 7.6 GB
EGAF00007973241 cram 7.7 GB
EGAF00007973242 cram 7.1 GB
EGAF00007973243 cram 6.2 GB
EGAF00007973244 cram 6.8 GB
EGAF00007973245 cram 9.5 GB
EGAF00007973246 cram 10.3 GB
EGAF00007973247 cram 8.0 GB
EGAF00007973248 cram 8.0 GB
EGAF00007973249 cram 6.0 GB
EGAF00007973250 cram 8.8 GB
EGAF00007973251 cram 8.3 GB
EGAF00007973252 cram 7.7 GB
EGAF00007973253 cram 7.3 GB
EGAF00007973254 cram 7.8 GB
EGAF00007973255 cram 6.1 GB
EGAF00007973256 cram 7.8 GB
EGAF00007973257 cram 6.6 GB
EGAF00007973258 cram 8.5 GB
EGAF00007973259 cram 8.1 GB
EGAF00007973260 cram 9.9 GB
EGAF00007973261 cram 8.1 GB
EGAF00007973262 cram 7.6 GB
EGAF00007973263 cram 8.3 GB
EGAF00007973264 cram 7.2 GB
EGAF00007973265 cram 6.9 GB
EGAF00007973266 cram 6.3 GB
EGAF00007973267 cram 9.0 GB
EGAF00007973268 cram 8.7 GB
EGAF00007973269 cram 11.1 GB
EGAF00007973270 cram 8.9 GB
EGAF00007973271 cram 11.8 GB
EGAF00007973272 cram 9.1 GB
EGAF00007973273 cram 10.2 GB
EGAF00007973274 cram 10.0 GB
EGAF00007973275 cram 7.8 GB
EGAF00007973276 cram 6.2 GB
EGAF00007973277 cram 6.9 GB
EGAF00007973278 cram 6.5 GB
EGAF00007973279 cram 10.4 GB
EGAF00007973280 cram 6.2 GB
EGAF00007973281 cram 4.5 GB
EGAF00007973282 cram 7.1 GB
EGAF00007973283 cram 6.4 GB
EGAF00007973284 cram 5.3 GB
EGAF00007973285 cram 7.5 GB
EGAF00007973286 cram 9.4 GB
EGAF00007973287 cram 7.6 GB
EGAF00007973288 cram 6.4 GB
EGAF00007973289 cram 5.3 GB
EGAF00007973290 cram 9.0 GB
EGAF00007973291 cram 10.0 GB
EGAF00007973292 cram 9.6 GB
EGAF00007973293 cram 10.3 GB
EGAF00007973294 cram 10.8 GB
EGAF00007973295 cram 11.4 GB
EGAF00007973296 cram 8.2 GB
EGAF00007973297 cram 10.3 GB
EGAF00007973298 cram 11.7 GB
EGAF00007973299 cram 7.7 GB
EGAF00007973300 cram 6.8 GB
EGAF00007973301 cram 3.4 GB
EGAF00007973302 cram 3.7 GB
EGAF00007973303 cram 6.1 GB
EGAF00007973304 cram 8.5 GB
EGAF00007973305 cram 5.1 GB
EGAF00007973306 cram 5.9 GB
EGAF00007973307 cram 11.6 GB
EGAF00007973308 cram 7.0 GB
EGAF00007973309 cram 4.8 GB
EGAF00007973310 cram 7.6 GB
EGAF00007973311 cram 7.9 GB
EGAF00007973312 cram 7.2 GB
EGAF00007973313 cram 6.8 GB
EGAF00007973314 cram 7.0 GB
EGAF00007973315 cram 16.8 GB
EGAF00007973316 cram 6.9 GB
EGAF00007973317 cram 5.9 GB
EGAF00007973318 cram 4.8 GB
EGAF00007973319 cram 7.5 GB
EGAF00007973320 cram 6.4 GB
EGAF00007973321 cram 3.8 GB
EGAF00007973322 cram 8.6 GB
EGAF00007973323 cram 5.3 GB
EGAF00007973324 cram 8.9 GB
EGAF00007973325 cram 5.1 GB
EGAF00007973326 cram 7.7 GB
EGAF00007973327 cram 5.4 GB
183 Files (1.4 TB)