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Transcriptome sequencing of hepatocellular carcinoma biopsies

RNA-sequencing of 122 hepatocellular carcinoma biopsies and 15 normal liver biopsies. RNA-seq library prep was performed with 200 ng total RNA using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (Illumina) according to manufacturer’s specifications. Single-end 126-bp sequencing was performed on an Illumina HiSeq 2500 using v4 SBS chemistry at the Genomics Facility Basel according to the manufacturer’s guidelines. Primary data analysis was performed with the Illumina RTA version 1.18.66.3.

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Data access policy for MERiC

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 MERiC consortium 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: The MERiC consortium 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. The MERiC consortium: The MERiC consortium is a consortium headed by Prof Michael N Hall (Biozentrum, University of Basel), Prof Markus H Heim (Department of Biomedicine, University of Basel), Prof Gerhard Christofori (Department of Biomedicine, University of Basel) and Prof Niko Beerenwinkel (Department of Biosystems Science and Engineering, ETH Zurich). 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 MERiC consortium within 30 days of any changes or departures of Authorised Personnel. 13. The User Institution will notify The MERiC consortium prior to any significant changes to the protocol for the Project. 14. The User Institution will notify The MERiC consortium as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. The MERiC consortium 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 MERiC consortium. 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 Switzerland and shall be subject to the exclusive jurisdiction of the Swiss courts.

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
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
EGAF00005502362 1645827744240 3.4 GB
EGAF00005502363 1645827744240 3.2 GB
EGAF00005502364 1645827744241 3.2 GB
EGAF00005502365 1645827744242 3.2 GB
EGAF00005502366 1645827744242 3.9 GB
EGAF00005502367 1645827744242 2.7 GB
EGAF00005502368 1645827744242 2.8 GB
EGAF00005502369 1645827744241 3.5 GB
EGAF00005502370 1645827744241 3.2 GB
EGAF00005502371 1645827744241 2.6 GB
EGAF00005502372 1645827744241 4.5 GB
EGAF00005502373 1645827744242 3.9 GB
EGAF00005502374 1645827744242 4.4 GB
EGAF00005502375 1645827744242 3.0 GB
EGAF00005502376 1645827744242 3.0 GB
EGAF00005502377 1645849410706 2.9 GB
EGAF00005502378 1645827744239 2.9 GB
EGAF00005502379 1645827744239 2.9 GB
EGAF00005502380 1645827744239 3.8 GB
EGAF00005502381 1645880549363 3.1 GB
EGAF00005502382 1645827744239 4.4 GB
EGAF00005502383 1645827744240 2.5 GB
EGAF00005502384 1645827744240 3.5 GB
EGAF00005502385 1645827744240 3.8 GB
EGAF00005502386 1645827744240 6.8 GB
EGAF00005502387 1645827744240 3.8 GB
EGAF00005502388 1645827744240 3.4 GB
EGAF00005502389 1645827744240 2.4 GB
EGAF00005502390 1645827744241 2.8 GB
EGAF00005502391 1645827744241 2.7 GB
EGAF00005502392 1645827744241 2.7 GB
EGAF00005502393 1645827744241 2.9 GB
EGAF00005502394 1645827744241 2.5 GB
EGAF00005502395 1645872395785 3.0 GB
EGAF00005502396 1645827744236 2.9 GB
EGAF00005502397 1645827744237 3.2 GB
EGAF00005502398 1645827744237 2.7 GB
EGAF00005502399 1645827744237 4.5 GB
EGAF00005502400 1645827744237 2.5 GB
EGAF00005502401 1645827744237 3.2 GB
EGAF00005502402 1645827744237 2.8 GB
EGAF00005502403 1645827744235 2.9 GB
EGAF00005502404 1645827744235 3.4 GB
EGAF00005502405 1645827744235 2.8 GB
EGAF00005502406 1645827744236 3.0 GB
EGAF00005502407 1645827744236 2.7 GB
EGAF00005502408 1645827744236 3.1 GB
EGAF00005502409 1645827744236 3.1 GB
EGAF00005502410 1645827744236 2.9 GB
EGAF00005502411 1645827744239 3.3 GB
EGAF00005502412 1645827744239 3.9 GB
EGAF00005502413 1645827744239 2.9 GB
EGAF00005502414 1645849410706 5.3 GB
EGAF00005502415 1645827744239 3.5 GB
EGAF00005502416 1645827744239 2.6 GB
EGAF00005502417 1645827744240 2.7 GB
EGAF00005502418 1645872395785 3.3 GB
EGAF00005502419 1645838802871 3.2 GB
EGAF00005502420 1645827744240 2.8 GB
EGAF00005502421 1645827744240 3.9 GB
EGAF00005502422 1645827744238 2.6 GB
EGAF00005502423 1645872395785 2.7 GB
EGAF00005502424 1645827744238 3.1 GB
EGAF00005502425 1645827744238 2.7 GB
EGAF00005502426 1645880549363 2.5 GB
EGAF00005502427 1645827744238 5.6 GB
EGAF00005502428 1645827744238 3.6 GB
EGAF00005502429 1645827744238 2.6 GB
EGAF00005502430 1645827744238 2.6 GB
EGAF00005502431 1645854163636 3.9 GB
EGAF00005502432 1645827744239 2.6 GB
EGAF00005502433 1645827744237 4.0 GB
EGAF00005502434 1645827744237 2.8 GB
EGAF00005502435 1645827744237 2.5 GB
EGAF00005502436 1645838802871 4.7 GB
EGAF00005502437 1645827744238 2.7 GB
EGAF00005502438 1645827744238 3.0 GB
EGAF00005502439 1645827744238 3.1 GB
EGAF00005502440 1645827744238 3.2 GB
EGAF00005502441 1645827744236 4.0 GB
EGAF00005502442 1645827744236 3.3 GB
EGAF00005502443 1645827744236 3.7 GB
EGAF00005502444 1645861818462 2.8 GB
EGAF00005502445 1645838802871 2.8 GB
EGAF00005502446 1645827744236 2.7 GB
EGAF00005502447 1645827744237 3.8 GB
EGAF00005502448 1645827744237 3.1 GB
EGAF00005502449 1645827744237 2.9 GB
EGAF00005502450 1645827744237 1.9 GB
EGAF00005502451 1645838802871 3.1 GB
EGAF00005502452 1645872395785 3.7 GB
EGAF00005502453 1645838802871 2.4 GB
EGAF00005502454 1645827744225 2.5 GB
EGAF00005502455 1645844190933 3.1 GB
EGAF00005502456 1645867601432 2.5 GB
EGAF00005502457 1645880549363 3.4 GB
EGAF00005502458 1645872395785 3.0 GB
EGAF00005502459 1645827744226 3.3 GB
EGAF00005502460 1645827744226 2.7 GB
EGAF00005502461 1645893893837 2.5 GB
EGAF00005502462 1645838802871 3.5 GB
EGAF00005502463 1645838802871 2.8 GB
EGAF00005502464 1645867601432 3.1 GB
EGAF00005502465 1645827744226 3.3 GB
EGAF00005502466 1645830478786 3.7 GB
EGAF00005502467 1645827744227 3.5 GB
EGAF00005502468 1645827744227 3.0 GB
EGAF00005502469 1645827744227 3.2 GB
EGAF00005502470 1645872395785 3.6 GB
EGAF00005502471 1645838802871 3.6 GB
EGAF00005502472 1645827744227 2.6 GB
EGAF00005502473 1645827744235 3.3 GB
EGAF00005502474 1645827744235 3.0 GB
EGAF00005502475 1645867601432 4.3 GB
EGAF00005502476 1645880549363 3.0 GB
EGAF00005502477 1645838802871 3.2 GB
EGAF00005502478 1645827744235 2.8 GB
EGAF00005502479 1645827744235 3.2 GB
EGAF00005502480 1645827744235 2.6 GB
EGAF00005502481 1645827744235 2.9 GB
EGAF00005502482 1645827744236 2.5 GB
EGAF00005502483 1645827744236 2.9 GB
EGAF00005502484 1645838802871 2.8 GB
EGAF00005502485 1645827744239 2.9 GB
EGAF00005502486 1645827744239 2.5 GB
EGAF00005502487 1645827744240 3.3 GB
EGAF00005502488 1645827744240 2.9 GB
EGAF00005502489 1645827744240 3.5 GB
EGAF00005502490 1645827744240 3.1 GB
EGAF00005502491 1645827744240 3.6 GB
EGAF00005502492 1645827744240 2.6 GB
EGAF00005502493 1645827744237 4.3 GB
EGAF00005502494 1633799526367 20.7 GB
133 Files (441.8 GB)