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RNA Sequencing of Colorectal Liver Metastases

Reverse-stranded paired-end 75 base-pair RNA sequencing libraries of 93 metastatic FFPE samples were constructed using Illumina Total RNA Stranded Kits. Ribosomal RNAs (rRNAs) were depleted by using the Ribo-Zero rRNA Removal Kit (Illumina). Libraries were sequenced on a HiSEQ2500 machine. Five samples were re-sequenced using paired-end 50 base-pair libraries due to the smaller insert sizes.

Request Access

Policy for use of RNA Sequencing data from colorectal liver metastases

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 Sean Pitroda 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: Sean Pitroda 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. Sean Pitroda: Ludwig Center for Metastasis Research, The University of Chicago, Chicago, IL 60637 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 ( ) and the Toronto Statement ( 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) ( ) in conformity with the Organisation for Economic Co-operation and Development Guidelines for the Licensing of the Genetic Inventions (2006) ( ). 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 Sean Pitroda within 30 days of any changes or departures of Authorised Personnel. 13. The User Institution will notify Sean Pitroda prior to any significant changes to the protocol for the Project. 14. The User Institution will notify Sean Pitroda as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. Sean Pitroda 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 Sean Pitroda. 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 Sean Pitroda 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 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. 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 Sean Pitroda and collaborators 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. Sean Pitroda and collaborators 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 Sean Pitroda 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 Sean Pitroda.

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
EGAS00001002945 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
EGAF00002004122 fastq.gz 1.3 GB
EGAF00002004123 fastq.gz 1.3 GB
EGAF00002004124 fastq.gz 1.7 GB
EGAF00002004125 fastq.gz 1.7 GB
EGAF00002004126 fastq.gz 1.3 GB
EGAF00002004127 fastq.gz 1.4 GB
EGAF00002004128 fastq.gz 999.4 MB
EGAF00002004129 fastq.gz 1.0 GB
EGAF00002004130 fastq.gz 935.0 MB
EGAF00002004131 fastq.gz 953.5 MB
EGAF00002004132 fastq.gz 1.3 GB
EGAF00002004133 fastq.gz 1.3 GB
EGAF00002004134 fastq.gz 1.1 GB
EGAF00002004135 fastq.gz 1.1 GB
EGAF00002004136 fastq.gz 1.1 GB
EGAF00002004137 fastq.gz 1.1 GB
EGAF00002004138 fastq.gz 1.6 GB
EGAF00002004139 fastq.gz 1.6 GB
EGAF00002004140 fastq.gz 1.2 GB
EGAF00002004141 fastq.gz 1.3 GB
EGAF00002004142 fastq.gz 1.6 GB
EGAF00002004143 fastq.gz 1.6 GB
EGAF00002004144 fastq.gz 1.6 GB
EGAF00002004145 fastq.gz 1.6 GB
EGAF00002004146 fastq.gz 1.7 GB
EGAF00002004147 fastq.gz 1.7 GB
EGAF00002004148 fastq.gz 1.9 GB
EGAF00002004149 fastq.gz 2.0 GB
EGAF00002004150 fastq.gz 1.2 GB
EGAF00002004151 fastq.gz 1.2 GB
EGAF00002004152 fastq.gz 1.2 GB
EGAF00002004153 fastq.gz 1.2 GB
EGAF00002004154 fastq.gz 2.6 GB
EGAF00002004155 fastq.gz 2.6 GB
EGAF00002004156 fastq.gz 1.8 GB
EGAF00002004157 fastq.gz 1.8 GB
EGAF00002004158 fastq.gz 1.9 GB
EGAF00002004159 fastq.gz 1.9 GB
EGAF00002004160 fastq.gz 1.0 GB
EGAF00002004161 fastq.gz 1.0 GB
EGAF00002004162 fastq.gz 1.5 GB
EGAF00002004163 fastq.gz 1.5 GB
EGAF00002004164 fastq.gz 1.5 GB
EGAF00002004165 fastq.gz 1.5 GB
EGAF00002004166 fastq.gz 1.4 GB
EGAF00002004167 fastq.gz 1.4 GB
EGAF00002004168 fastq.gz 1.5 GB
EGAF00002004169 fastq.gz 1.5 GB
EGAF00002004170 fastq.gz 2.3 GB
EGAF00002004171 fastq.gz 2.3 GB
EGAF00002004172 fastq.gz 1.3 GB
EGAF00002004173 fastq.gz 1.3 GB
EGAF00002004174 fastq.gz 1.3 GB
EGAF00002004175 fastq.gz 1.3 GB
EGAF00002004176 fastq.gz 1.2 GB
EGAF00002004177 fastq.gz 1.2 GB
EGAF00002004178 fastq.gz 1.4 GB
EGAF00002004179 fastq.gz 1.4 GB
EGAF00002004180 fastq.gz 1.1 GB
EGAF00002004181 fastq.gz 1.1 GB
EGAF00002004182 fastq.gz 1.7 GB
EGAF00002004183 fastq.gz 1.7 GB
EGAF00002004184 fastq.gz 1.7 GB
EGAF00002004185 fastq.gz 1.8 GB
EGAF00002004186 fastq.gz 1.2 GB
EGAF00002004187 fastq.gz 1.2 GB
EGAF00002004188 fastq.gz 2.0 GB
EGAF00002004189 fastq.gz 2.0 GB
EGAF00002004190 fastq.gz 1.7 GB
EGAF00002004191 fastq.gz 1.7 GB
EGAF00002004192 fastq.gz 1.5 GB
EGAF00002004193 fastq.gz 1.5 GB
EGAF00002004194 fastq.gz 1.6 GB
EGAF00002004195 fastq.gz 1.6 GB
EGAF00002004196 fastq.gz 1.8 GB
EGAF00002004197 fastq.gz 1.8 GB
EGAF00002004198 fastq.gz 1.7 GB
EGAF00002004199 fastq.gz 1.7 GB
EGAF00002004200 fastq.gz 1.7 GB
EGAF00002004201 fastq.gz 1.7 GB
EGAF00002004202 fastq.gz 1.3 GB
EGAF00002004203 fastq.gz 1.3 GB
EGAF00002004204 fastq.gz 1.3 GB
EGAF00002004205 fastq.gz 1.3 GB
EGAF00002004206 fastq.gz 959.0 MB
EGAF00002004207 fastq.gz 976.4 MB
EGAF00002004208 fastq.gz 1.9 GB
EGAF00002004209 fastq.gz 1.9 GB
EGAF00002004210 fastq.gz 1.5 GB
EGAF00002004211 fastq.gz 1.5 GB
EGAF00002004212 fastq.gz 1.1 GB
EGAF00002004213 fastq.gz 1.1 GB
EGAF00002004214 fastq.gz 1.4 GB
EGAF00002004215 fastq.gz 1.4 GB
EGAF00002004216 fastq.gz 1.3 GB
EGAF00002004217 fastq.gz 1.3 GB
EGAF00002004218 fastq.gz 1.1 GB
EGAF00002004219 fastq.gz 1.2 GB
EGAF00002004220 fastq.gz 1.2 GB
EGAF00002004221 fastq.gz 1.2 GB
EGAF00002004222 fastq.gz 1.3 GB
EGAF00002004223 fastq.gz 1.3 GB
EGAF00002004224 fastq.gz 2.0 GB
EGAF00002004225 fastq.gz 2.0 GB
EGAF00002004226 fastq.gz 1.4 GB
EGAF00002004227 fastq.gz 1.4 GB
EGAF00002004228 fastq.gz 1.4 GB
EGAF00002004229 fastq.gz 1.4 GB
EGAF00002004230 fastq.gz 1.5 GB
EGAF00002004231 fastq.gz 1.5 GB
EGAF00002004232 fastq.gz 1.2 GB
EGAF00002004233 fastq.gz 1.2 GB
EGAF00002004234 fastq.gz 1.4 GB
EGAF00002004235 fastq.gz 1.4 GB
EGAF00002004236 fastq.gz 1.5 GB
EGAF00002004237 fastq.gz 1.5 GB
EGAF00002004238 fastq.gz 1.1 GB
EGAF00002004239 fastq.gz 1.1 GB
EGAF00002004240 fastq.gz 1.2 GB
EGAF00002004241 fastq.gz 1.2 GB
EGAF00002004242 fastq.gz 892.0 MB
EGAF00002004243 fastq.gz 899.4 MB
EGAF00002004244 fastq.gz 1.3 GB
EGAF00002004245 fastq.gz 1.3 GB
EGAF00002004246 fastq.gz 1.3 GB
EGAF00002004247 fastq.gz 1.3 GB
EGAF00002004248 fastq.gz 1.3 GB
EGAF00002004249 fastq.gz 1.3 GB
EGAF00002004250 fastq.gz 1.3 GB
EGAF00002004251 fastq.gz 1.3 GB
EGAF00002004252 fastq.gz 1.6 GB
EGAF00002004253 fastq.gz 1.6 GB
EGAF00002004254 fastq.gz 1.6 GB
EGAF00002004255 fastq.gz 1.7 GB
EGAF00002004256 fastq.gz 3.1 GB
EGAF00002004257 fastq.gz 3.2 GB
EGAF00002004258 fastq.gz 3.2 GB
EGAF00002004259 fastq.gz 3.2 GB
EGAF00002004260 fastq.gz 850.7 MB
EGAF00002004261 fastq.gz 858.7 MB
EGAF00002004262 fastq.gz 859.8 MB
EGAF00002004263 fastq.gz 868.0 MB
EGAF00002004264 fastq.gz 1.4 GB
EGAF00002004265 fastq.gz 1.4 GB
EGAF00002004266 fastq.gz 1.7 GB
EGAF00002004267 fastq.gz 1.7 GB
EGAF00002004268 fastq.gz 1.0 GB
EGAF00002004269 fastq.gz 1.1 GB
EGAF00002004270 fastq.gz 1.2 GB
EGAF00002004271 fastq.gz 1.3 GB
EGAF00002004272 fastq.gz 1.6 GB
EGAF00002004273 fastq.gz 1.7 GB
EGAF00002004274 fastq.gz 1.5 GB
EGAF00002004275 fastq.gz 1.6 GB
EGAF00002004276 fastq.gz 1.2 GB
EGAF00002004277 fastq.gz 1.2 GB
EGAF00002004278 fastq.gz 1.2 GB
EGAF00002004279 fastq.gz 1.2 GB
EGAF00002004280 fastq.gz 914.2 MB
EGAF00002004281 fastq.gz 928.8 MB
EGAF00002004282 fastq.gz 920.9 MB
EGAF00002004283 fastq.gz 936.1 MB
EGAF00002004284 fastq.gz 1.4 GB
EGAF00002004285 fastq.gz 1.4 GB
EGAF00002004286 fastq.gz 1.5 GB
EGAF00002004287 fastq.gz 1.5 GB
EGAF00002004288 fastq.gz 1.5 GB
EGAF00002004289 fastq.gz 1.5 GB
EGAF00002004290 fastq.gz 1.5 GB
EGAF00002004291 fastq.gz 1.5 GB
EGAF00002004292 fastq.gz 2.0 GB
EGAF00002004293 fastq.gz 2.0 GB
EGAF00002004294 fastq.gz 1.1 GB
EGAF00002004295 fastq.gz 1.1 GB
EGAF00002004296 fastq.gz 1.8 GB
EGAF00002004297 fastq.gz 1.8 GB
EGAF00002004298 fastq.gz 1.7 GB
EGAF00002004299 fastq.gz 1.7 GB
EGAF00002004300 fastq.gz 1.1 GB
EGAF00002004301 fastq.gz 1.1 GB
EGAF00002004302 fastq.gz 1.7 GB
EGAF00002004303 fastq.gz 1.7 GB
EGAF00002004304 fastq.gz 1.2 GB
EGAF00002004305 fastq.gz 1.2 GB
EGAF00002004306 fastq.gz 1.2 GB
EGAF00002004307 fastq.gz 1.2 GB
EGAF00002004308 fastq.gz 2.4 GB
EGAF00002004309 fastq.gz 2.5 GB
EGAF00002004310 fastq.gz 1.5 GB
EGAF00002004311 fastq.gz 1.5 GB
EGAF00002004312 fastq.gz 1.5 GB
EGAF00002004313 fastq.gz 1.5 GB
EGAF00002004314 fastq.gz 1.7 GB
EGAF00002004315 fastq.gz 1.8 GB
EGAF00002004316 fastq.gz 1.8 GB
EGAF00002004317 fastq.gz 1.8 GB
EGAF00002004318 fastq.gz 1.6 GB
EGAF00002004319 fastq.gz 1.6 GB
EGAF00002004320 fastq.gz 1.5 GB
EGAF00002004321 fastq.gz 1.5 GB
EGAF00002004322 fastq.gz 1.4 GB
EGAF00002004323 fastq.gz 1.4 GB
EGAF00002004324 fastq.gz 1.8 GB
EGAF00002004325 fastq.gz 1.8 GB
EGAF00002004326 fastq.gz 1.3 GB
EGAF00002004327 fastq.gz 1.3 GB
EGAF00002004328 fastq.gz 1.4 GB
EGAF00002004329 fastq.gz 1.4 GB
EGAF00002004330 fastq.gz 1.3 GB
EGAF00002004331 fastq.gz 1.3 GB
210 Files (308.8 GB)