About file location

As the EGA is co-managed by the EMBL-EBI and CRG, files could be located in the UK and/or Spain, as indicated by their respective flags.

Alternatively, files could be located in one of the international Federated EGA nodes, as indicated next to the node's flag.
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Datasets of RNA-seq of tumor samples from clear cell renal cell carcinoma patients included in the Translational Program of the NIVOREN GETUG-AFU-26 trial

RNA-seq analyses were performed on tumor tissue samples of 115 advanced clear cell renal cell carcinoma patients who participated in the NIVOREN GETUG-AFU-26 trial. The samples were obtained prior to treatment initiation. RNA-seq was performed to evaluate previously published gene expression signatures. These included: the IMmotion T effector (CD8A, EOMES, PRF1, IFNG and CD274) and the IMmotion Myeloid (IL-6, CXCL1, CXCL2, CXCL3, CXCL8, and PTGS2) gene signatures represent gene expression patterns associated with T effector cells and myeloid cells, respectively, while JAVELIN Renal 101 Immuno (T-cell receptor signaling: CD3G, CD3E, CD8B, THEMIS, TRAT1, GRAP2, CD247; T-cell activation, proliferation, and differentiation: CD2, CD96, PRF1, CD6, IL7R, ITK, GPR18, EOMES, SIT1, NLRC3; Natural killer cell mediated cytotoxicity: D2, CD96, PRF1, CD244, KLRD1, SH2D1A; Chemokine: CCL5, XCL2; and Other immune response genes: CST7, GFI1, KCNA3, PSTPIP1) represents gene expression patterns associated with both innate and adaptive immune response.

Request Access

Policy for DAC RNA-seq of tumor samples from clear cell renal cell carcinoma patients included in the Translational Program of the NIVOREN GETUG-AFU-26 trial.

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 Authorized 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 Authorized Personnel are set out in Appendix II. Data: The managed access datasets to which the User Institution has requested access. Data Producers: The individuals, listed in Appendix I, responsible for the development, organization, 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(s) that has requested access to the Data (detailed in Appendix II). Data Producers Institution(s): The Institution(s) that has produced the Data (detailed in Appendix I). Data Access Committee: The committee responsible for authorizing access to the data. Committee members are listed in Appendix I. 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 Authorized 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 (https://www.sanger.ac.uk/wp-content/uploads/fortlauderdalereport.pdf) and the Toronto Statement (http://www.nature.com/nature/journal/v461/n7261/full/461168a.html). This includes but is not limited to recognizing the contribution of the Data Producers and including a proper acknowledgment 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 analyzing 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.ott.nih.gov/sites/default/files/documents/pdfs/70fr18413.pdf) in conformity with the Organization for Economic Co-operation and Development Guidelines for the Licensing of the Genetic Inventions (2006) (https://www.oecd.org/sti/emerging-tech/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 Data Access Committee within 30 days of any changes or departures of Authorized Personnel. 13. The User Institution will notify the Data Access Committee prior to any significant changes to the protocol for the Project. 14. The User Institution will notify the Data Access Committee as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. The 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. 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 Authorized Personnel. The User Institution will procure that the Authorized 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 France and shall be subject to the exclusive jurisdiction of the France courts. Agreed for User Institution (Name, Title, Date, Signature): Principal Investigator (Name, Title, Date, Signature): I confirm that I have read and understood this Agreement. Agreed for the Data Access Committee (Name, Title, Date, Signature): APPENDIX I – DATASET DETAILS & DATA ACCESS COMMITTEE APPENDIX II – PROJECT DETAILS APPENDIX III – PUBLICATION POLICY APPENDIX I – DATASET DETAILS & DATA ACCESS COMMITTEE Dataset reference (EGA Study ID, Dataset Accession Numbers and Dataset Details): Name of the project that created the dataset : RNA-seq of tumor samples from clear cell renal cell carcinoma patients included in the Translational Program of the NIVOREN GETUG-AFU-26 trial. Data Producers Institution(s): Gustave Roussy, 114, rue Edouard Vaillant – 94805 VILLEJUIF Cedex, FRANCE Names of other data producers/collaborators (Name, Email, Job Title): Specific limitations on areas of research: 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. Name of the Data Access Committee: DAC RNA-seq of tumor samples from clear cell renal cell carcinoma patients included in the Translational Program of the NIVOREN GETUG-AFU-26 trial. Data Access Committee Members (Name, Email, Job Title): Principal Investigator Lucia CARRIL (carrilajuria.lucia@gmail.com) Head of Bioinformatics platform Marc Deloger (Marc.DELOGER@gustaveroussy.fr) Data Manager Alicia TRAN DIEN (alicia.tran-dien@gustaveroussy.fr) Data Protection Officer Clara BECHET (Clara.BECHET@gustaveroussy.fr) 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): User Institution(s): All Individuals who the User Institution to be named as registered users (Name, Email, Job Title, Supervisor): All Individuals that should have an account created at the EGA (Name, Email, Job Title): APPENDIX III – PUBLICATION POLICY The Data Access Committee anticipates 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 the Data Access Committee have published their own global analysis or twelve (12) months after these data were first made available on the relevant hosting database, unless the 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., EGAS00000000029), and acknowledge its use in a form agreed by the User Institution with the 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
EGAS50000001057 RNASeq

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 Quality Report
Located in
i
EGAF50000383241 fastq.gz 661.5 MB
EGAF50000383242 fastq.gz 1.2 GB
EGAF50000383243 fastq.gz 203.6 MB
EGAF50000383244 fastq.gz 279.1 MB
EGAF50000383245 fastq.gz 979.1 MB
EGAF50000383246 fastq.gz 290.9 MB
EGAF50000383247 fastq.gz 647.8 MB
EGAF50000383248 fastq.gz 276.2 MB
EGAF50000383249 fastq.gz 390.3 MB
EGAF50000383250 fastq.gz 105.3 MB
EGAF50000383251 fastq.gz 812.4 MB
EGAF50000383252 fastq.gz 418.0 MB
EGAF50000383253 fastq.gz 270.2 MB
EGAF50000383254 fastq.gz 256.2 MB
EGAF50000383255 fastq.gz 122.0 MB
EGAF50000383256 fastq.gz 284.0 MB
EGAF50000383257 fastq.gz 618.6 MB
EGAF50000383258 fastq.gz 280.3 MB
EGAF50000383259 fastq.gz 218.4 MB
EGAF50000383260 fastq.gz 227.3 MB
EGAF50000383261 fastq.gz 407.4 MB
EGAF50000383262 fastq.gz 321.3 MB
EGAF50000383263 fastq.gz 333.2 MB
EGAF50000383264 fastq.gz 496.3 MB
EGAF50000383265 fastq.gz 178.9 MB
EGAF50000383266 fastq.gz 483.2 MB
EGAF50000383267 fastq.gz 361.8 MB
EGAF50000383268 fastq.gz 468.4 MB
EGAF50000383269 fastq.gz 272.9 MB
EGAF50000383270 fastq.gz 668.6 MB
EGAF50000383271 fastq.gz 789.9 MB
EGAF50000383272 fastq.gz 708.0 MB
EGAF50000383273 fastq.gz 407.3 MB
EGAF50000383274 fastq.gz 379.2 MB
EGAF50000383275 fastq.gz 135.4 MB
EGAF50000383276 fastq.gz 332.0 MB
EGAF50000383277 fastq.gz 322.8 MB
EGAF50000383278 fastq.gz 643.3 MB
EGAF50000383279 fastq.gz 216.3 MB
EGAF50000383280 fastq.gz 509.9 MB
EGAF50000383281 fastq.gz 404.4 MB
EGAF50000383282 fastq.gz 770.9 MB
EGAF50000383283 fastq.gz 656.9 MB
EGAF50000383284 fastq.gz 190.9 MB
EGAF50000383285 fastq.gz 243.9 MB
EGAF50000383286 fastq.gz 40.7 MB
EGAF50000383287 fastq.gz 47.4 MB
EGAF50000383288 fastq.gz 71.8 MB
EGAF50000383289 fastq.gz 12.4 MB
EGAF50000383290 fastq.gz 17.5 MB
EGAF50000383291 fastq.gz 70.8 MB
EGAF50000383292 fastq.gz 62.4 MB
EGAF50000383293 fastq.gz 215.8 MB
EGAF50000383294 fastq.gz 680.8 MB
EGAF50000383295 fastq.gz 44.2 MB
EGAF50000383296 fastq.gz 89.4 MB
EGAF50000383297 fastq.gz 516.0 MB
EGAF50000383298 fastq.gz 494.1 MB
EGAF50000383299 fastq.gz 1.2 GB
EGAF50000383300 fastq.gz 822.9 MB
EGAF50000383301 fastq.gz 290.4 MB
EGAF50000383302 fastq.gz 482.5 MB
EGAF50000383303 fastq.gz 499.9 MB
EGAF50000383304 fastq.gz 434.0 MB
EGAF50000383305 fastq.gz 1.4 GB
EGAF50000383306 fastq.gz 2.0 GB
EGAF50000383307 fastq.gz 481.7 MB
EGAF50000383308 fastq.gz 124.3 MB
EGAF50000383309 fastq.gz 432.4 MB
EGAF50000383310 fastq.gz 128.5 MB
EGAF50000383311 fastq.gz 447.8 MB
EGAF50000383312 fastq.gz 174.9 MB
EGAF50000383313 fastq.gz 474.9 MB
EGAF50000383314 fastq.gz 384.1 MB
EGAF50000383315 fastq.gz 384.9 MB
EGAF50000383316 fastq.gz 208.8 MB
EGAF50000383317 fastq.gz 77.3 MB
EGAF50000383318 fastq.gz 70.3 MB
EGAF50000383319 fastq.gz 474.4 MB
EGAF50000383320 fastq.gz 230.5 MB
EGAF50000383321 fastq.gz 399.9 MB
EGAF50000383322 fastq.gz 2.8 GB
EGAF50000383323 fastq.gz 221.2 MB
EGAF50000383324 fastq.gz 201.0 MB
EGAF50000383325 fastq.gz 420.3 MB
EGAF50000383326 fastq.gz 394.8 MB
EGAF50000383327 fastq.gz 517.0 MB
EGAF50000383328 fastq.gz 222.2 MB
EGAF50000383329 fastq.gz 560.8 MB
EGAF50000383330 fastq.gz 288.0 MB
EGAF50000383331 fastq.gz 119.8 MB
EGAF50000383332 fastq.gz 156.0 MB
EGAF50000383333 fastq.gz 255.8 MB
EGAF50000383334 fastq.gz 301.3 MB
EGAF50000383335 fastq.gz 341.5 MB
EGAF50000383336 fastq.gz 146.6 MB
EGAF50000383337 fastq.gz 534.1 MB
EGAF50000383338 fastq.gz 176.4 MB
EGAF50000383339 fastq.gz 293.9 MB
EGAF50000383340 fastq.gz 153.3 MB
EGAF50000383341 fastq.gz 423.5 MB
EGAF50000383342 fastq.gz 806.2 MB
EGAF50000383343 fastq.gz 389.5 MB
EGAF50000383344 fastq.gz 236.7 MB
EGAF50000383345 fastq.gz 191.6 MB
EGAF50000383346 fastq.gz 261.1 MB
EGAF50000383347 fastq.gz 135.9 MB
EGAF50000383348 fastq.gz 368.3 MB
EGAF50000383349 fastq.gz 1.6 GB
EGAF50000383350 fastq.gz 133.0 MB
EGAF50000383351 fastq.gz 2.7 GB
EGAF50000383352 fastq.gz 276.2 MB
EGAF50000383353 fastq.gz 400.2 MB
EGAF50000383354 fastq.gz 392.3 MB
EGAF50000383355 fastq.gz 200.9 MB
115 Files (49.9 GB)