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RNAseq and WES of CHC patients years before HCC development

We conducted a nested case–control study within a prospective liver biopsy biobank at the University Hospital Basel. Patients with chronic hepatitis C (CHC) who developed hepatocellular carcinoma (HCC) during follow-up (index cases, CHC-HCC) were identified and 1:2 propensity score-matched to CHC controls without HCC (controls, CHC-nonHCC). Matching included clinical, demographic, and virological risk factors for HCC. Liver biopsies were analyzed using RNA and whole-exome sequencing.

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Data access policy for IFNL4 Organoid Transcriptome Profiles

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 Prof. Dr. Markus Heim 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: Prof. Dr. Markus Heim 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 Prof. Dr. Markus Heim within 30 days of any changes or departures of Authorised Personnel. 13. The User Institution will notify Prof. Dr. Markus Heim prior to any significant changes to the protocol for the Project. 14. The User Institution will notify Prof. Dr. Markus Heim as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. Prof. Dr. Markus Heim 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 Prof. Dr. Markus Heim. 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
EGAS50000001096 Exome Sequencing
EGAS50000001097 RNASeq
EGAS50000001098 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
EGAF50000387953 bam 2.9 GB
EGAF50000387954 bam 2.9 GB
EGAF50000387955 bam 2.8 GB
EGAF50000387956 bam 2.9 GB
EGAF50000387957 bam 3.1 GB
EGAF50000387958 bam 2.8 GB
EGAF50000387959 bam 2.6 GB
EGAF50000387960 bam 3.2 GB
EGAF50000387961 bam 3.1 GB
EGAF50000387962 bam 3.5 GB
EGAF50000387963 bam 3.0 GB
EGAF50000387964 bam 6.1 GB
EGAF50000387965 bam 3.2 GB
EGAF50000387966 bam 4.0 GB
EGAF50000387967 bam 3.2 GB
EGAF50000387968 bam 3.9 GB
EGAF50000387969 bam 3.0 GB
EGAF50000387970 bam 3.5 GB
EGAF50000387971 bam 3.2 GB
EGAF50000387972 bam 3.2 GB
EGAF50000387973 bam 3.6 GB
EGAF50000387974 bam 3.4 GB
EGAF50000387975 bam 3.4 GB
EGAF50000387976 bam 3.2 GB
EGAF50000387977 bam 4.4 GB
EGAF50000387978 bam 3.0 GB
EGAF50000387979 bam 4.1 GB
EGAF50000387980 bam 3.7 GB
EGAF50000387981 bam 3.8 GB
EGAF50000387982 bam 2.8 GB
EGAF50000387983 bam 3.6 GB
EGAF50000387984 bam 2.9 GB
EGAF50000387985 bam 3.8 GB
EGAF50000387986 bam 2.9 GB
EGAF50000387987 bam 3.8 GB
EGAF50000387988 bam 3.0 GB
EGAF50000387989 bam 4.3 GB
EGAF50000387990 bam 3.3 GB
EGAF50000387991 bam 4.1 GB
EGAF50000387992 bam 3.1 GB
EGAF50000387993 bam 3.4 GB
EGAF50000387994 bam 3.3 GB
EGAF50000387995 bam 3.2 GB
EGAF50000387996 bam 4.1 GB
EGAF50000387997 bam 3.8 GB
EGAF50000387998 bam 3.4 GB
EGAF50000387999 bam 2.7 GB
EGAF50000388000 bam 7.0 GB
EGAF50000388001 bam 20.8 GB
EGAF50000388002 bam 34.0 GB
EGAF50000388003 bam 23.1 GB
EGAF50000388004 bam 36.6 GB
EGAF50000388005 bam 19.4 GB
EGAF50000388006 bam 34.2 GB
EGAF50000388007 bam 19.6 GB
EGAF50000388008 bam 36.4 GB
EGAF50000388009 bam 19.9 GB
EGAF50000388010 bam 34.9 GB
EGAF50000388011 bam 20.0 GB
EGAF50000388012 bam 36.3 GB
EGAF50000388013 bam 20.8 GB
EGAF50000388014 bam 36.9 GB
EGAF50000388015 bam 20.4 GB
EGAF50000388016 bam 35.8 GB
EGAF50000388017 bam 20.7 GB
EGAF50000388018 bam 33.7 GB
EGAF50000388019 bam 18.7 GB
EGAF50000388020 bam 36.9 GB
EGAF50000388021 bam 20.9 GB
EGAF50000388022 bam 33.2 GB
EGAF50000388023 bam 20.1 GB
EGAF50000388024 bam 35.5 GB
EGAF50000388025 bam 18.7 GB
EGAF50000388026 bam 35.5 GB
EGAF50000388027 bam 24.6 GB
EGAF50000388028 bam 38.6 GB
EGAF50000388029 bam 19.9 GB
EGAF50000388030 bam 35.4 GB
EGAF50000388031 bam 23.4 GB
EGAF50000388032 bam 33.2 GB
EGAF50000388033 bam 19.2 GB
EGAF50000388034 bam 33.6 GB
EGAF50000388035 bam 24.4 GB
EGAF50000388036 bam 33.3 GB
EGAF50000388037 bam 21.1 GB
EGAF50000388038 bam 32.8 GB
EGAF50000388039 bam 21.4 GB
EGAF50000388040 bam 35.3 GB
EGAF50000388041 bam 25.2 GB
EGAF50000388042 bam 36.2 GB
EGAF50000388043 bam 18.6 GB
EGAF50000388044 bam 38.3 GB
EGAF50000388045 bam 23.4 GB
EGAF50000388046 bam 36.7 GB
EGAF50000388047 bam 21.8 GB
EGAF50000388048 bam 37.5 GB
EGAF50000388049 bam 21.6 GB
EGAF50000388050 bam 35.6 GB
EGAF50000388051 bam 21.2 GB
EGAF50000388052 bam 34.4 GB
EGAF50000388053 bam 18.4 GB
EGAF50000388054 bam 37.8 GB
EGAF50000388055 bam 19.2 GB
EGAF50000388056 bam 38.2 GB
EGAF50000388057 bam 21.3 GB
EGAF50000388058 bam 35.1 GB
EGAF50000388059 bam 22.1 GB
EGAF50000388060 bam 36.3 GB
EGAF50000388061 bam 18.6 GB
EGAF50000388062 bam 35.2 GB
EGAF50000388063 bam 19.6 GB
EGAF50000388064 bam 36.4 GB
EGAF50000388065 bam 18.6 GB
EGAF50000388066 bam 33.6 GB
EGAF50000388067 bam 20.5 GB
EGAF50000388068 bam 36.0 GB
EGAF50000388069 bam 21.3 GB
EGAF50000388070 bam 33.7 GB
EGAF50000388071 bam 18.6 GB
EGAF50000388072 bam 37.1 GB
EGAF50000388073 bam 20.2 GB
EGAF50000388074 bam 35.7 GB
EGAF50000388075 bam 20.1 GB
EGAF50000388076 bam 35.3 GB
EGAF50000388077 bam 34.9 GB
EGAF50000388079 csv 9.6 MB
EGAF50000388080 csv 28.2 MB
EGAF50000388082 csv 3.6 kB
EGAF50000388083 csv 2.2 kB
EGAF50000577641 bam 3.7 GB
EGAF50000577642 bam 4.0 GB
EGAF50000577643 bam 4.0 GB
EGAF50000577644 bam 4.4 GB
EGAF50000577645 bam 4.1 GB
EGAF50000577646 bam 4.2 GB
EGAF50000577647 bam 4.6 GB
EGAF50000577648 bam 4.4 GB
EGAF50000577649 bam 4.7 GB
EGAF50000577650 bam 5.0 GB
EGAF50000577651 bam 5.1 GB
EGAF50000577652 bam 5.4 GB
EGAF50000577653 bam 6.3 GB
EGAF50000577654 bam 7.7 GB
EGAF50000577655 bam 5.9 GB
144 Files (2.4 TB)