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Tumor-derived cell lines as pharmacogenomic models to predict therapeutic vulnerabilities in hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is a heterogeneous aggressive malignancy with low efficacy of current therapies at advanced stages. We integrated molecular and pharmacological profiling of a large panel of liver cancer cell lines (LCCL) to assess their clinical relevance as HCC preclinical models and identify new effective therapies and biomarkers of response. Here, we performed multi-omic analysis including whole-exome, RNA and microRNA sequencing in a series 34 LCCL. Molecular profiles of LCCL and primary HCC were compared and we searched for molecular features associated with drug response. Our panel of LCCL faithfully recapitulated the most aggressive molecular “proliferation class” of HCC.

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FunGeST - Functional Genomics from cancer research to personalized medicine

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 Data Recipient has requested access. The Data Recipient agrees to be bound by these terms and conditions. Definitions GDPR: This DAA makes both parties compliant with the Regulation (EU) 2016/679 of the European Parliament and of the Council, that is, the General Data Protection Regulation (herein referred to as the ‘GDPR’). Data: Refers to managed controlled access datasets (the Data). Under this Agreement, the Data is pseudonymised. Data Access/Transfer: Refers to an Institution’s right to request access to the Data and retrieve them from the Data Controller’s Institution upon approval of this hDAA by the corresponding DAC within the Data Controller’s Institution. Data Handling: Refers to an Institution’s ability to analyse and manipulate the Data within its own computer network. Data Controller(s): Refers to an Institution, responsible for the generation of the Data and its pseudonymisation. A key-code permitting relinkage to Data Subjects is kept by the Data Controller(s). Data Subject: Refers to any individual who is the source of any Data covered by this Agreement. Data Recipient (‘You’): Refers to the Institution who requests Access to the Data through this Agreement. Authorised Personnel: The individual(s) at the Institution requesting Access to the Data. Research Project: The Project for which You have requested Access to the Data. Publications: Refers, without limitation, to any and all articles published in print journals, electronic journals, reviews, books, posters, and other written and verbal presentations of Research that have been accepted by peer review. FunGeST: This DAA was written for the FunGeST functional genomics projects headed at the CRC (Centre de recherche des Cordeliers, Paris, France) 1. You, the Data Recipient, agree to only use the Data for the Purpose of the Project, for Research Purposes only and not in any profit-making activities. You 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. You agree to preserve, at all times, the confidentiality of information and Data pertaining to Data Subjects. 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. Without prejudice to the generality of the foregoing, you agree to use at least the measures set out in Appendix I to protect these Data; 3. You agree not to attempt to identify Data Subjects; 4. You agree not to link or combine the Data to other information or archived data available in a way that could re-identify the Data Subjects, even if access to that data has been formally granted to you or is freely available without restriction. 5. You and your Authorised Personnel agree to take into consideration any usage restrictions (if any), stemming from consent, i.e. the appropriate lawful basis for processing the Data, as well as any usage restrictions stemming from any applicable internal policies of your Institution; 6. You agree that in handling this Data You will follow an up-to-date information technology (IT) policy that must include, at a minimum, the following items: a. Logging and auditing of Access to the Data and to the computer network; b. Password protection to computer network and/or strong data encryption; c. Virus and malware protection to computers on the computer network; d. Secure backup procedure; 7. You acknowledge that Access to the Data is granted for the duration of the Project described in Section I, and these restrictions are specific to that particular Project. Any utilization of the Data for a different Project will require prior approval through a new Agreement. 8. You recognize that nothing in this Agreement shall operate to transfer to You any intellectual property rights to the Data. 9. You agree not to make intellectual property claims on the Data and not to use intellectual property protection in ways that would prevent or block Access to, or use of, any element of the Data. 10. You can elect to perform further Research that would add intellectual and resource capital to the Data, and decide to obtain intellectual property rights on these downstream discoveries. In this case, You agree to implement licensing policies that will not obstruct further Research, following the Organisation for Economic Co-operation and Development Guidelines. 11. You agree that the Research Project 1) bears no legal responsibility for the accuracy or comprehensiveness of the Data; 2) accepts no liability for indirect, consequential, or incidental damages or losses arising from use of the Data; and 3) bears no responsibility for the further analysis or interpretation of these Data over and above that published by the Controller(s). 12. You agree to hold the Data Subject(s) and Data Controller(s) harmless and to defend and indemnify all these parties against all liabilities, demands, damages, expenses, and losses arising out of Your use for any Purpose of the Data. 13. You agree to a moratorium on publishing global analyses of the dataset until the Data Controller(s) have published their own global analysis or twelve (12) months, the maximum, have passed from the time the Data were deposited, whichever occurs first. You acknowledge that prompt publication or public disclosure of the results of the Research Project is encouraged. You also agree that by publishing Your global analyses of the Data, you will not disclose any results generated from the Data. 14. You agree to acknowledge the contribution of the Data Controller(s) in all oral and written presentations, disclosures, and Publications resulting from all analyses of the Data. 15. You agree to use the Data in Your laboratory. Any Authorised Personnel shall work under Your direct supervision. You agree to distribute a copy of these terms to the Authorised Personnel. 16. You may not transfer any information included in the Data to anyone unless specifically designated in the Research Project, or by prior specific or general written authorisation of the Data Controller(s) responsible for the generation of the original Data in each case. 17. You may not transfer the Data itself to anyone outside the Institution, unless the Controller(s) has (have) approved such transfer and its terms in writing. 18. Should You wish to share the Data with an external collaborator, the external collaborator must complete a separate Data Access Agreement. 19. You shall ensure that ‘all’ who have Access to the Data, namely You and Your Authorised Personnel, will be listed out, and are made aware and be bound by the terms of this Agreement. You remain solely and fully responsible for Your Authorised Personnel’s non-compliance with the provision of the Agreement and/or applicable laws. 20. In case of a breach of security resulting from ‘accidental’ use of Data by You and Your Authorised Personnel, which leads to disclosure of Data, then You must report this to Data Controller(s) within 72 hours maximum, and follow any relevant rule as provided by the GDPR. 21. In case of a ‘non-accidental or minor’ breach of DAA by You You will further be required to destroy any Data held. 22. You accept that this Agreement will terminate immediately upon ‘any’ breach by You, or its termination (see Section I). 23. You endeavour to settle any dispute with the Data Controller(s) amicably. If you are unable to reach an Agreement, you will meet and negotiate in good faith in an effort to resolve the issue. If the issue has not been resolved within a reasonable period (e.g. 30 calendar days), you are both entitled to submit it for resolution by an arbitrator. 24. Further, the language of the proceedings will be ‘English’ if not otherwise agreed. The award of the arbitration will be final and binding upon the parties concerned. 25. This Agreement (and any dispute, controversy, proceedings, or claim of whatever nature arising out of it or its formation) shall be interpreted, governed by and construed in accordance with the Laws of France, and shall be subject to the exclusive jurisdiction of the French 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
EGAF00002440990 bam 6.4 GB
EGAF00002440991 bam 6.3 GB
EGAF00002440992 bam 6.9 GB
EGAF00002440993 bam 7.1 GB
EGAF00002440994 bam 6.3 GB
EGAF00002440995 bam 6.1 GB
EGAF00002440996 bam 6.8 GB
EGAF00002440997 bam 7.0 GB
EGAF00002440998 bam 5.8 GB
EGAF00002440999 bam 6.3 GB
EGAF00002441000 bam 6.8 GB
EGAF00002441001 bam 6.3 GB
EGAF00002441002 bam 6.3 GB
EGAF00002441003 bam 6.9 GB
EGAF00002441004 bam 6.5 GB
EGAF00002441005 bam 6.7 GB
EGAF00002441006 bam 7.5 GB
EGAF00002441007 bam 9.4 GB
EGAF00002441008 bam 6.7 GB
EGAF00002441009 bam 6.2 GB
EGAF00002441010 bam 5.9 GB
EGAF00002441011 bam 7.5 GB
EGAF00002441012 bam 6.9 GB
EGAF00002441013 bam 6.3 GB
EGAF00002441014 bam 6.2 GB
EGAF00002441015 bam 6.3 GB
EGAF00002441016 bam 6.4 GB
EGAF00002441017 bam 7.1 GB
EGAF00002441018 bam 7.0 GB
EGAF00002441019 bam 7.1 GB
EGAF00002441020 bam 9.2 GB
EGAF00002441021 bam 5.6 GB
EGAF00002441022 bam 6.2 GB
EGAF00002441023 bam 6.2 GB
EGAF00002441024 bam 9.0 GB
EGAF00002441025 bam 8.0 GB
EGAF00002441026 bam 8.5 GB
EGAF00002441027 bam 9.6 GB
EGAF00002441028 bam 9.0 GB
EGAF00002441029 bam 8.2 GB
EGAF00002441030 bam 8.9 GB
EGAF00002441031 bam 8.7 GB
EGAF00002441032 bam 8.4 GB
EGAF00002441033 bam 7.3 GB
EGAF00002441034 bam 9.5 GB
EGAF00002441035 bam 7.8 GB
EGAF00002441036 bam 7.8 GB
EGAF00002441037 bam 8.6 GB
EGAF00002441038 bam 7.7 GB
EGAF00002441039 bam 9.7 GB
EGAF00002441040 bam 7.7 GB
EGAF00002441041 bam 8.6 GB
EGAF00002441042 bam 8.9 GB
EGAF00002441043 bam 8.8 GB
EGAF00002441044 bam 9.2 GB
EGAF00002441045 bam 8.1 GB
EGAF00002441046 bam 9.6 GB
EGAF00002441047 bam 8.2 GB
EGAF00002441048 bam 8.6 GB
EGAF00002441049 bam 8.6 GB
EGAF00002441050 bam 8.9 GB
EGAF00002441051 bam 8.5 GB
EGAF00002441052 bam 9.1 GB
EGAF00002441053 bam 9.9 GB
EGAF00002441054 bam 7.3 GB
EGAF00002441055 bam 9.6 GB
EGAF00002441056 bam 7.5 GB
EGAF00002441057 bam 8.2 GB
EGAF00002441058 trim.gz 314.2 MB
EGAF00002441059 trim.gz 219.2 MB
EGAF00002441060 trim.gz 312.1 MB
EGAF00002441061 trim.gz 263.4 MB
EGAF00002441062 trim.gz 244.9 MB
EGAF00002441063 trim.gz 312.0 MB
EGAF00002441064 trim.gz 319.2 MB
EGAF00002441065 trim.gz 393.8 MB
EGAF00002441066 trim.gz 202.9 MB
EGAF00002441067 trim.gz 719.0 MB
EGAF00002441068 trim.gz 271.4 MB
EGAF00002441069 trim.gz 262.0 MB
EGAF00002441070 trim.gz 253.9 MB
EGAF00002441071 trim.gz 194.1 MB
EGAF00002441072 trim.gz 276.3 MB
EGAF00002441073 trim.gz 245.7 MB
EGAF00002441074 trim.gz 241.0 MB
EGAF00002441075 trim.gz 444.6 MB
EGAF00002441076 trim.gz 219.6 MB
EGAF00002441077 trim.gz 285.8 MB
EGAF00002441078 trim.gz 295.2 MB
EGAF00002441079 trim.gz 180.7 MB
EGAF00002441080 trim.gz 276.3 MB
EGAF00002441081 trim.gz 240.9 MB
EGAF00002441082 trim.gz 385.5 MB
EGAF00002441083 trim.gz 300.2 MB
EGAF00002441084 trim.gz 326.5 MB
EGAF00002441085 trim.gz 247.4 MB
EGAF00002441086 trim.gz 249.5 MB
EGAF00002441087 trim.gz 223.2 MB
EGAF00002441088 trim.gz 226.6 MB
EGAF00002441089 trim.gz 229.9 MB
EGAF00002441090 trim.gz 248.0 MB
EGAF00002441091 trim.gz 258.6 MB
102 Files (529.9 GB)