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 Notch inhibitor treated HCC PDX models across timepoints

To study the effect of Notch inhibition on the transcriptional profiles our PDX models, we generated bulk RNA-seq data for two Notch inhibition sensitive and three Notch inhibition insensitive models across multiple timepoints (8h, 24h, 48h, 7d, 17d) using anti-JAG1, anti-Notch2, anti-Notch1 or anti-gD antibodies. 3-5 samples were collected for each treatment condition, resulting in a total of 96 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
EGAF00008544692 fastq.gz 1.4 GB Report
EGAF00008544693 fastq.gz 1.7 GB Report
EGAF00008544695 fastq.gz 1.9 GB Report
EGAF00008544696 fastq.gz 2.1 GB Report
EGAF00008544697 fastq.gz 1.9 GB Report
EGAF00008544698 fastq.gz 1.7 GB Report
EGAF00008544699 fastq.gz 2.0 GB Report
EGAF00008544700 fastq.gz 1.9 GB Report
EGAF00008544701 fastq.gz 1.8 GB Report
EGAF00008544702 fastq.gz 2.1 GB Report
EGAF00008544703 fastq.gz 1.9 GB Report
EGAF00008544705 fastq.gz 1.7 GB Report
EGAF00008544706 fastq.gz 2.0 GB Report
EGAF00008544707 fastq.gz 1.8 GB Report
EGAF00008544708 fastq.gz 1.8 GB Report
EGAF00008544782 fastq.gz 1.9 GB Report
EGAF00008544786 fastq.gz 1.6 GB Report
EGAF00008544787 fastq.gz 2.0 GB Report
EGAF00008544788 fastq.gz 1.7 GB Report
EGAF00008544792 fastq.gz 2.2 GB Report
EGAF00008544795 fastq.gz 1.6 GB Report
EGAF00008544796 fastq.gz 1.3 GB Report
EGAF00008544800 fastq.gz 1.3 GB Report
EGAF00008544803 fastq.gz 1.8 GB Report
EGAF00008544805 fastq.gz 1.4 GB Report
EGAF00008544806 fastq.gz 1.3 GB Report
EGAF00008544807 fastq.gz 1.4 GB Report
EGAF00008544808 fastq.gz 1.6 GB Report
EGAF00008544810 fastq.gz 1.8 GB Report
EGAF00008544814 fastq.gz 1.3 GB Report
EGAF00008544817 fastq.gz 1.9 GB Report
EGAF00008544819 fastq.gz 1.3 GB Report
EGAF00008544820 fastq.gz 1.7 GB Report
EGAF00008544822 fastq.gz 2.3 GB Report
EGAF00008544825 fastq.gz 1.7 GB Report
EGAF00008544836 fastq.gz 2.0 GB Report
EGAF00008544838 fastq.gz 1.6 GB Report
EGAF00008544841 fastq.gz 2.1 GB Report
EGAF00008544842 fastq.gz 2.0 GB Report
EGAF00008544845 fastq.gz 2.2 GB Report
EGAF00008544847 fastq.gz 2.0 GB Report
EGAF00008544848 fastq.gz 2.1 GB Report
EGAF00008544849 fastq.gz 1.9 GB Report
EGAF00008544851 fastq.gz 1.5 GB Report
EGAF00008544852 fastq.gz 2.3 GB Report
EGAF00008544855 fastq.gz 2.4 GB Report
EGAF00008544858 fastq.gz 2.1 GB Report
EGAF00008544860 fastq.gz 2.2 GB Report
EGAF00008544861 fastq.gz 2.1 GB Report
EGAF00008544863 fastq.gz 971.7 MB Report
EGAF00008544864 fastq.gz 1.9 GB Report
EGAF00008544865 fastq.gz 2.4 GB Report
EGAF00008544866 fastq.gz 2.3 GB Report
EGAF00008544868 fastq.gz 2.2 GB Report
EGAF00008544869 fastq.gz 1.5 GB Report
EGAF00008544870 fastq.gz 1.8 GB Report
EGAF00008544872 fastq.gz 2.1 GB Report
EGAF00008544873 fastq.gz 1.7 GB Report
EGAF00008544874 fastq.gz 1.8 GB Report
EGAF00008544875 fastq.gz 1.5 GB Report
EGAF00008544879 fastq.gz 1.8 GB Report
EGAF00008544881 fastq.gz 2.1 GB Report
EGAF00008544882 fastq.gz 2.1 GB Report
EGAF00008544883 fastq.gz 2.4 GB Report
EGAF00008544884 fastq.gz 1.4 GB Report
EGAF00008544885 fastq.gz 1.1 GB Report
EGAF00008544886 fastq.gz 1.2 GB Report
EGAF00008544887 fastq.gz 924.8 MB Report
EGAF00008544889 fastq.gz 860.3 MB Report
EGAF00008544890 fastq.gz 2.0 GB Report
EGAF00008544891 fastq.gz 912.0 MB Report
EGAF00008544892 fastq.gz 944.2 MB Report
EGAF00008544893 fastq.gz 1.1 GB Report
EGAF00008544897 fastq.gz 1.6 GB Report
EGAF00008544900 fastq.gz 2.0 GB Report
EGAF00008544905 fastq.gz 2.0 GB Report
EGAF00008544906 fastq.gz 2.4 GB Report
EGAF00008544908 fastq.gz 1.8 GB Report
EGAF00008544909 fastq.gz 2.3 GB Report
EGAF00008544911 fastq.gz 886.7 MB Report
EGAF00008544913 fastq.gz 1.7 GB Report
EGAF00008544914 fastq.gz 970.1 MB Report
EGAF00008544915 fastq.gz 1.8 GB Report
EGAF00008544920 fastq.gz 1.1 GB Report
EGAF00008544921 fastq.gz 2.6 GB Report
EGAF00008544922 fastq.gz 2.3 GB Report
EGAF00008544923 fastq.gz 2.3 GB Report
EGAF00008544924 fastq.gz 2.6 GB Report
EGAF00008544926 fastq.gz 1.4 GB Report
EGAF00008544931 fastq.gz 1.7 GB Report
EGAF00008544932 fastq.gz 1.5 GB Report
EGAF00008544938 fastq.gz 884.3 MB Report
EGAF00008544939 fastq.gz 964.8 MB Report
EGAF00008544941 fastq.gz 1.8 GB Report
EGAF00008544942 fastq.gz 1.3 GB Report
EGAF00008544943 fastq.gz 1.6 GB Report
96 Files (167.5 GB)