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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RNA sequencing of baseline HCC PDX models

To establish the baseline transcriptional profiles, we performed bulk RNA-seq for 36 of our HCC PDX models. 2-6 samples were collected for each model resulting in a total of 68 samples. Isolated RNA was used as input for library preparation using TruSeq RNA Sample Preparation Kit v2 (Illumina). The libraries were multiplexed and sequenced on Illumina HiSeq 2500 (Illumina) to produce FASTQ files.

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GENENTECH DATA ACCESS COMMITTEEDATA ACCESS AGREEMENT

GENENTECH DATA ACCESS COMMITTEEDATA ACCESS AGREEMENT WITH COMMERCIAL ORGANIZATIONThis Data Access Agreement (“Agreement”) between Genentech, Inc. (“Genentech”) and User and User Organization (as defined below) governs the terms on which access will be granted to the genotype data obtained from Genentech.In signing this Agreement, User and User Organization agree to be bound by the terms and conditions of access set out in this Agreement.For the sake of clarity, the terms of access set out in this Agreement apply both to the User and the User Organization (as defined below). User Organization and User are referred to within the Agreement as “You” and “Your” shall be construed accordingly.Definitions: gRED means Genentech Research and Early Development.Data means all and any human genetic data obtained from Genentech and generated by gRED. Data Subject means a person, who has been informed of the purpose for which the Data is held and has given his/her informed consent thereto.User means a researcher whose User Organization has previously completed this Data Access Agreement and has received acknowledgement of its acceptance.Publications means, without limitation, articles published in print journals, electronic journals, reviews, books, posters and other written and verbal presentations of research.User Organization means the commercial organization at which the User is employed or affiliated.Genentech Data Access Committee means members of the gRED organization that is responsible for making the data access decisions for the genotype data generated by gRED.Terms and Conditions: In signing this Agreement:1.You agree to use the Data only for the advancement of medical research.2.You agree to preserve, at all times, the confidentiality of Data pertaining to Data Subjects. In particular, You undertake not to use, or attempt to use the Data to compromise or otherwise infringe the confidentiality of information on Data Subjects and their right to privacy.3.You agree not to attempt to link the Data provided under this Agreement to other information or archive data available for the data sets provided, even if access to that data has been formally granted to you, or it is freely available without restriction, without specific permission being sought from the relevant access committees.4.You agree not to transfer or disclose the Data, in whole or part, or any identifiable material derived from the Data, to others, except as necessary for data/safety monitoring or program management. Should You wish to share the Data with a collaborator outside the same Organization, the third party must make a separate application for access to the Data.5.You agree to use the Data for the approved purpose and project described in your application; use of the Data for a new purpose or project will require a new application and approval.6.You shall be free to publish the results of the research using the Data for the approved purpose. You agree to acknowledge in any such publication that the research makes use of Data generated by Genentech/gRED.7.You accept that Genentech:a.bears no legal responsibility for the accuracy or comprehensiveness of the Data; and b.accepts no liability for indirect, consequential, or incidental, damages or losses arising from use of the Data, or from the unavailability of, or break in access to, the Data for whatever reason.8.You understand and acknowledge that the Data is protected by copyright and other intellectual property rights, and that duplication, except as reasonably required to carry out Your research with the Data, or sale of all or part of the Data on any media is not permitted.9.You recognize that nothing in this Agreement shall operate to transfer to the User Organization any intellectual property rights relating to the Data. The User Organization has the right to develop intellectual property based on the comparisons with their own data. Any invention or discovery made by User and/or User Organization arising out of the use of the Data (each a “Data Invention”) shall be promptly disclosed to Genentech in writing. User Organization hereby grants to Genentech a royalty-free, fully-paid, non-exclusive license (i) to make, use and import such Data Invention for internal research purposes; and (ii) to make, use, offer to sell, sell and import such Data Invention to the extent necessary to commercialize Genentech product(s), which license shall be sublicensable to Genentech’s affiliates and development and commercialization collaborators on such product(s). 10.You agree that you will submit a report to the Genentech Data Access Committee, if requested, on completion of the agreed purpose. The Genentech Data Access Committee agrees to treat the report and all information, data, results, and conclusions contained within such report as confidential information belonging to the User Organization.11.(a) You agree to use the Data in accordance with all applicable laws, including but not limited to applicable data privacy laws.(b) The Genentech Data Access Committee reserves the right to request and inspect data security and management documentation to ensure the adequacy of data protection measures. 12.This Agreement shall be effective as of the date of the last party to sign below (“Effective Date”) and shall terminate three (3) years after the Effective Date, unless terminated sooner pursuant to Section 13 below.13.You accept that this Agreement will terminate immediately upon any breach of this Agreement by You and You will be required to destroy any Data held. Either Party may terminate this Agreement upon thirty (30) days written notice for any reason. The following Sections of this Agreement shall survive its expiration or termination: Sections 1 – 10, 11(a), and 13. For and on behalf of User/Applicant:___________________________Signature of User/Applicant___________________________Print Name of User/Applicant___________________________Title___________________________DateFor and on behalf of User Organization:___________________________Signature of Organizational or Administrative Authority___________________________Print Name___________________________Title___________________________Name of User Organization___________________________DateFor Genentech, Inc.:___________________________Signature___________________________Print Name___________________________Title___________________________Date

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
EGAS50000000515 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
EGAF00008544709 fastq.gz 4.1 GB Report
EGAF00008544710 fastq.gz 3.9 GB Report
EGAF00008544711 fastq.gz 4.1 GB Report
EGAF00008544712 fastq.gz 4.0 GB Report
EGAF00008544713 fastq.gz 4.0 GB Report
EGAF00008544714 fastq.gz 4.0 GB Report
EGAF00008544715 fastq.gz 4.0 GB Report
EGAF00008544716 fastq.gz 4.3 GB Report
EGAF00008544717 fastq.gz 3.8 GB Report
EGAF00008544718 fastq.gz 4.5 GB Report
EGAF00008544719 fastq.gz 4.3 GB Report
EGAF00008544720 fastq.gz 4.4 GB Report
EGAF00008544721 fastq.gz 4.7 GB Report
EGAF00008544722 fastq.gz 3.9 GB Report
EGAF00008544723 fastq.gz 4.7 GB Report
EGAF00008544724 fastq.gz 4.4 GB Report
EGAF00008544725 fastq.gz 4.1 GB Report
EGAF00008544726 fastq.gz 3.5 GB Report
EGAF00008544727 fastq.gz 4.0 GB Report
EGAF00008544728 fastq.gz 3.5 GB Report
EGAF00008544729 fastq.gz 4.2 GB Report
EGAF00008544730 fastq.gz 4.0 GB Report
EGAF00008544731 fastq.gz 4.0 GB Report
EGAF00008544732 fastq.gz 3.6 GB Report
EGAF00008544733 fastq.gz 3.6 GB Report
EGAF00008544734 fastq.gz 3.8 GB Report
EGAF00008544735 fastq.gz 3.7 GB Report
EGAF00008544736 fastq.gz 4.5 GB Report
EGAF00008544737 fastq.gz 3.7 GB Report
EGAF00008544738 fastq.gz 2.9 GB Report
EGAF00008544739 fastq.gz 4.1 GB Report
EGAF00008544740 fastq.gz 4.4 GB Report
EGAF00008544741 fastq.gz 3.8 GB Report
EGAF00008544742 fastq.gz 4.4 GB Report
EGAF00008544743 fastq.gz 4.4 GB Report
EGAF00008544744 fastq.gz 4.2 GB Report
EGAF00008544745 fastq.gz 4.2 GB Report
EGAF00008544746 fastq.gz 3.8 GB Report
EGAF00008544747 fastq.gz 2.9 GB Report
EGAF00008544748 fastq.gz 4.4 GB Report
EGAF00008544749 fastq.gz 3.7 GB Report
EGAF00008544750 fastq.gz 5.2 GB Report
EGAF00008544751 fastq.gz 5.1 GB Report
EGAF00008544752 fastq.gz 3.9 GB Report
EGAF00008544753 fastq.gz 4.3 GB Report
EGAF00008544754 fastq.gz 4.3 GB Report
EGAF00008544755 fastq.gz 3.8 GB Report
EGAF00008544756 fastq.gz 5.1 GB Report
EGAF00008544757 fastq.gz 4.3 GB Report
EGAF00008544758 fastq.gz 4.1 GB Report
EGAF00008544759 fastq.gz 5.3 GB Report
EGAF00008544760 fastq.gz 4.4 GB Report
EGAF00008544761 fastq.gz 5.2 GB Report
EGAF00008544762 fastq.gz 4.4 GB Report
EGAF00008544763 fastq.gz 5.2 GB Report
EGAF00008544764 fastq.gz 5.2 GB Report
EGAF00008544765 fastq.gz 5.5 GB Report
EGAF00008544766 fastq.gz 5.8 GB Report
EGAF00008544767 fastq.gz 3.4 GB Report
EGAF00008544768 fastq.gz 3.4 GB Report
EGAF00008544769 fastq.gz 5.8 GB Report
EGAF00008544770 fastq.gz 5.1 GB Report
EGAF00008544771 fastq.gz 3.7 GB Report
EGAF00008544772 fastq.gz 6.3 GB Report
EGAF00008544773 fastq.gz 6.3 GB Report
EGAF00008544774 fastq.gz 5.4 GB Report
EGAF00008544775 fastq.gz 5.5 GB Report
EGAF00008544776 fastq.gz 4.4 GB Report
EGAF00008544777 fastq.gz 4.5 GB Report
EGAF00008544778 fastq.gz 4.2 GB Report
EGAF00008544779 fastq.gz 3.9 GB Report
EGAF00008544780 fastq.gz 5.1 GB Report
EGAF00008544781 fastq.gz 4.2 GB Report
EGAF00008544783 fastq.gz 5.2 GB Report
EGAF00008544784 fastq.gz 5.9 GB Report
EGAF00008544785 fastq.gz 5.4 GB Report
EGAF00008544789 fastq.gz 4.4 GB Report
EGAF00008544790 fastq.gz 5.4 GB Report
EGAF00008544791 fastq.gz 5.2 GB Report
EGAF00008544793 fastq.gz 4.9 GB Report
EGAF00008544794 fastq.gz 3.5 GB Report
EGAF00008544797 fastq.gz 5.4 GB Report
EGAF00008544798 fastq.gz 5.9 GB Report
EGAF00008544799 fastq.gz 4.2 GB Report
EGAF00008544801 fastq.gz 5.2 GB Report
EGAF00008544802 fastq.gz 5.2 GB Report
EGAF00008544804 fastq.gz 5.2 GB Report
EGAF00008544809 fastq.gz 5.2 GB Report
EGAF00008544811 fastq.gz 5.1 GB Report
EGAF00008544812 fastq.gz 4.6 GB Report
EGAF00008544813 fastq.gz 5.2 GB Report
EGAF00008544815 fastq.gz 3.6 GB Report
EGAF00008544816 fastq.gz 6.0 GB Report
EGAF00008544818 fastq.gz 5.2 GB Report
EGAF00008544821 fastq.gz 5.1 GB Report
EGAF00008544823 fastq.gz 4.3 GB Report
EGAF00008544824 fastq.gz 5.8 GB Report
EGAF00008544826 fastq.gz 4.5 GB Report
EGAF00008544827 fastq.gz 5.1 GB Report
EGAF00008544828 fastq.gz 5.2 GB Report
EGAF00008544829 fastq.gz 3.5 GB Report
EGAF00008544830 fastq.gz 3.4 GB Report
EGAF00008544831 fastq.gz 5.1 GB Report
EGAF00008544832 fastq.gz 5.1 GB Report
EGAF00008544833 fastq.gz 4.4 GB Report
EGAF00008544834 fastq.gz 3.8 GB Report
EGAF00008544835 fastq.gz 5.3 GB Report
EGAF00008544837 fastq.gz 5.3 GB Report
EGAF00008544839 fastq.gz 3.4 GB Report
EGAF00008544840 fastq.gz 3.8 GB Report
EGAF00008544843 fastq.gz 4.3 GB Report
EGAF00008544844 fastq.gz 4.4 GB Report
EGAF00008544846 fastq.gz 4.2 GB Report
EGAF00008544850 fastq.gz 4.2 GB Report
EGAF00008544853 fastq.gz 5.5 GB Report
EGAF00008544854 fastq.gz 3.8 GB Report
EGAF00008544856 fastq.gz 4.0 GB Report
EGAF00008544857 fastq.gz 3.5 GB Report
EGAF00008544859 fastq.gz 4.3 GB Report
EGAF00008544862 fastq.gz 4.8 GB Report
EGAF00008544867 fastq.gz 3.6 GB Report
EGAF00008544871 fastq.gz 4.2 GB Report
EGAF00008544876 fastq.gz 4.1 GB Report
EGAF00008544877 fastq.gz 4.4 GB Report
EGAF00008544878 fastq.gz 3.9 GB Report
EGAF00008544880 fastq.gz 5.4 GB Report
EGAF00008544888 fastq.gz 5.4 GB Report
EGAF00008544894 fastq.gz 3.9 GB Report
EGAF00008544895 fastq.gz 3.9 GB Report
EGAF00008544901 fastq.gz 4.2 GB Report
EGAF00008544902 fastq.gz 4.2 GB Report
EGAF00008544903 fastq.gz 12.3 GB Report
EGAF00008544904 fastq.gz 12.1 GB Report
EGAF00008544907 fastq.gz 3.9 GB Report
EGAF00008544918 fastq.gz 4.3 GB Report
EGAF00008544919 fastq.gz 3.5 GB Report
136 Files (621.5 GB)