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Single-cell RNA sequencing of control and Notch inhibitor treated HCC PDX model

We generated single-cell RNA-seq data for anti-Notch2 (n=3), anti-JAG1 (n=1) and anti-gD (n=4) treated LIV78 tumors. NCR nude mice bearing similarly sized LIV78 tumors (volumes between 300-900mm3) were injected intravenously with 30mg/kg body weight of either anti-Notch2, anti-Jag1 or anti-gD control antibody 72hrs prior to tumor harvest and tumor cell isolation. Following the depletion of CD45+ and Ter119+ cells, the samples were processed for single-cell RNA-seq (scRNAseq) as described previously (Long et al., 2019) using the Chromium Single Cell 3’ Library and Gel bead kit v2, following the manufacturer’s manual. cDNAs and libraries were prepared following the manufacturer’s manual (10X Genomics). Libraries were profiled by Bioanalyzer High Sensitivity DNA kit (Agilent Technologies) and quantified using Kapa Library Quantification Kit (Kapa Biosystems, Wilmington, MA). Each library was sequenced in one lane of HiSeq 2500 (Illumina) following the manufacturer’s sequencing specification (10X Genomics) to produce the resulting 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
EGAS50000000517 Transcriptome Sequencing

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
EGAF00008544898 fastq.gz 7.0 GB Report
EGAF00008544899 fastq.gz 6.3 GB Report
EGAF00008544910 fastq.gz 7.5 GB Report
EGAF00008544912 fastq.gz 7.3 GB Report
EGAF00008544916 fastq.gz 3.6 GB Report
EGAF00008544917 fastq.gz 11.6 GB Report
EGAF00008544925 fastq.gz 7.3 GB Report
EGAF00008544927 fastq.gz 6.3 GB Report
EGAF00008544928 fastq.gz 22.2 GB Report
EGAF00008544929 fastq.gz 26.6 GB Report
EGAF00008544930 fastq.gz 26.1 GB Report
EGAF00008544934 fastq.gz 25.6 GB Report
EGAF00008544935 fastq.gz 7.5 GB Report
EGAF00008544937 fastq.gz 22.4 GB Report
EGAF00008544940 fastq.gz 26.2 GB Report
EGAF00008544944 fastq.gz 26.7 GB Report
16 Files (240.3 GB)