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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Comprehensive Deep Sequencing Atlas in HCC tumors

The atlas aims to unravel the intricate genetic landscape of HCC, providing a detailed characterization of genomic alterations, transcriptomic profiles, and key mutations associated with liver tumors. The integration of WGS, RNAseq, and WES data offers a holistic perspective, facilitating a deeper understanding of the molecular mechanisms driving HCC pathogenesis. The resulting atlas serves as a valuable resource for researchers, clinicians, and the broader scientific community, contributing to advancements in HCC diagnostics, prognostics, and therapeutic interventions.

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DUO:0000027
version: 2021-02-23

project specific restriction

This data use modifier indicates that use is limited to use within an approved project.

FunGeST - Functional Genomics from cancer research to personalized medicine

DATA ACCESS AGREEMENT These terms and conditions govern access to the managed access datasets to which the Data Recipient has requested access. The Data Recipient agrees to be bound by these terms and conditions. Definitions GDPR: This DAA ensures that both parties comply with the Regulation (EU) 2016/679 of the European Parliament and of the Council, known as the General Data Protection Regulation (herein referred to as the ‘GDPR’). Data: Data means pseudonymised research data, related metadata and associated documentation provided under this Agreement. Data Access/Transfer: Refers to an Institution’s right to request access to the Data and retrieve it from the Data Controller’s Institution upon approval of this DAA by the corresponding Data Access Committee (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): The Institution responsible for data generation and pseudonymization. Data Subject: Refers to any individual who is the source of any Data covered by this Agreement. Data Recipient (‘You’): The Institution that requests access to the Data through this Agreement. Authorized 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 Data Access Agreement (DAA) has been developed for the FunGeST functional genomics projects, with the Centre de Recherche des Cordeliers (CRC) in Paris, France serving as the Data Controller. Terms and Conditions 1. Data Usage: The Data Recipient shall use the Data solely for the Research Project identified in this Agreement and strictly for research purposes, and shall not use the Data for any profit-making or commercial activities. 2. Confidentiality and Data Protection: The Data Recipient shall maintain the confidentiality of all information and Data relating to Data Subjects and shall not use the Data in any manner that compromises or violates the confidentiality or privacy of Data Subjects. The Data Recipient shall comply with all applicable data protection laws (including the GDPR and the French Data Protection Act) and the security measures set out in Clause 6. 3. Data Subject No Re-Identification: The Data Recipient shall not attempt to identify any Data Subject. 4. No Data Linking for Re-identification: The Data Recipient shall not link or combine the Data with other information in a way that could (re)identify Data Subjects, even where such other information is formally accessible or publicly available. 5. Usage Restrictions (Consent / Law / Policy): The Data Recipient shall comply with any use restrictions arising from informed consent, applicable law or regulation, and the Recipient’s institutional policies. 6. IT Security Measures: The Data Recipient shall implement and maintain up-to-date technical and organizational measures, including at a minimum: a) logging and auditing access to the Data and networks. b) password protection and/or strong encryption at rest and in transit; c) protection against viruses and malware; d) secure and tested backup procedures; e) role-based access control, least-privilege, and (where available) multi-factor authentication; f) incident response procedures (including containment, eradication, recovery, and post-incident review). 7. Project Duration: Access to the Data is granted only for the duration of the Research Project. Any new or different use requires prior written approval and a separate agreement. 8. Intellectual Property: No intellectual property rights in the Data are transferred under this Agreement. The Data Recipient shall not assert IP rights over the Data or use IP to restrict access to or use of the Data. The Data Recipient may generate results, analyses, or discoveries based on the Data and may seek IP over such results, provided that any licensing aligns with OECD principles and does not impede further academic research. 9. Warranties and Disclaimer: The Data are provided “as is”. The Data Controller makes no representations or warranties (express or implied) as to accuracy, completeness, fitness for a particular purpose, or non-infringement. 10. Liability and Indemnity: To the maximum extent permitted by law, neither Party shall be liable to the other for indirect, consequential, or incidental losses arising from use of the Data. Nothing in this Agreement excludes or limits liability for fraud, wilful misconduct, gross negligence, or breach of applicable data protection law. The Data Recipient remains responsible for its use of the Data and shall indemnify and hold harmless the Data Controller and Data Subjects from losses and claims arising from the Recipient’s breach of this Agreement, misuse of the Data, or violation of law. 11. Publication and Acknowledgement: The Data Recipient agrees that any publications, presentations, or disclosures based on the Data must appropriately cite the Data source. All papers or outputs must include the citations/acknowledgements specified for the relevant EGAD dataset ID. The list of required citations and acknowledgements will be provided along with the dataset and must be followed. 12. Personnel Compliance and Data Confidentiality: Use of the Data is restricted to the Data Recipient’s Institution and Authorized Personnel who are informed of and comply with this Agreement. The Data Recipient shall not disclose Data to third parties except where expressly permitted by the Research Project or with the Data Controller’s prior written consent. The Data shall not be transferred outside the Institution without prior written approval. External collaborators must first enter into a separate Data Access Agreement. 13. Amendments: No modification or waiver of this Agreement is valid unless in writing and signed by duly authorized representatives of both Parties. 14. Security Incidents: In the event of a personal-data breach or security incident affecting the Data, the Data Recipient shall notify the Data Controller without undue delay and in any event within 72 hours of becoming aware, provide all relevant information, cooperate in containment and remediation, and maintain appropriate records. The notification shall include: (i) a description of the nature of the incident, (ii) categories and approximate number of data subjects and records concerned, (iii) likely consequences, (iv) measures taken or proposed to address the incident, and (v) a contact point for further information (e.g., the Recipient’s DPO). Notifications shall be sent to: Jessica.zucman-rossi@inserm.fr. 15. Termination and Post-Termination Duties: This Agreement may be terminated immediately for material breach, or upon completion or termination of the Research Project. Upon termination or expiry, the Data Recipient shall cease all use of the Data and, at the Data Controller’s option, securely delete or return the Data and all copies, subject to mandatory retention laws. Within 30 days of termination or expiry, the Data Recipient shall return or securely destroy all Data and certify destruction in writing (name, role, date, method), unless retention is required by mandatory law (and then only for the minimum period and securely archived). Clauses 2–6, 8–12, 14–18 survive termination. 16. Use of Name and Logos: Neither Party shall use the other’s name, trademarks, or logos in any publicity, or advertising, or news release without prior written approval. Each Party may disclose factual information about the existence and purpose of this Agreement, provided such statements are accurate, describe the relationship of the parties and do not imply endorsement. 17. Dispute Resolution; Urgent Relief: The Parties shall first seek to resolve disputes amicably within 60 days of written notice. Nothing in this clause prevents either Party from seeking urgent injunctive or equitable relief in any court of competent jurisdiction. 18. Governing Law and Jurisdiction: This Agreement, and any non-contractual obligations arising out of or in connection with it, shall be governed by and construed in accordance with the laws of France. The courts of Paris, France shall have exclusive jurisdiction to settle any dispute arising out of or in connection with this Agreement. 19. Cross‑Border Data Transfers: Any transfer of Data outside the EU/EEA or the UK shall rely on appropriate safeguards under applicable law (including EU Standard Contractual Clauses and/or the UK IDTA/Addendum, as applicable). The Data Recipient shall not engage any subprocessor or external service provider for Data hosting or processing without the Data Controller’s prior written consent and a written agreement imposing security and confidentiality obligations no less protective than this Agreement. 20. Boilerplate 20.1 Entire Agreement. This Agreement constitutes the entire agreement between the Parties with respect to its subject matter and supersedes all prior understandings. 20.2 Severability. If any provision is held invalid or unenforceable, the remainder shall continue in full force and effect. 20.3 Assignment. Neither Party may assign this Agreement without the other Party’s prior written consent, except to a successor in connection with a merger or reorganization that assumes all obligations herein. 20.4 Notices. Notices under this Agreement shall be in writing and delivered by email and/or registered mail to the notice contacts most recently notified in writing by each Party to the other. Each Party’s initial notice details shall be those specified in the Section I or in the signature block. Either Party may update its notice details by written notice; such update is effective upon receipt. 20.5 Governing Language. If this Agreement is translated, the English version shall prevail.

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
EGAS00001007694 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 Quality Report
Located in
i
EGAF00008388342 fastq.gz 43.1 GB
EGAF00008388343 fastq.gz 45.3 GB
EGAF00008388344 fastq.gz 45.2 GB
EGAF00008388345 fastq.gz 47.2 GB
EGAF00008388346 fastq.gz 36.6 GB
EGAF00008388347 fastq.gz 39.9 GB
EGAF00008388348 fastq.gz 69.1 GB
EGAF00008388349 fastq.gz 73.2 GB
EGAF00008388350 fastq.gz 32.0 GB
EGAF00008388351 fastq.gz 33.4 GB
EGAF00008388352 fastq.gz 50.5 GB
EGAF00008388353 fastq.gz 53.3 GB
EGAF00008388354 fastq.gz 36.5 GB
EGAF00008388355 fastq.gz 41.5 GB
EGAF00008388356 fastq.gz 111.7 GB
EGAF00008388357 fastq.gz 124.3 GB
EGAF00008388358 fastq.gz 38.9 GB
EGAF00008388359 fastq.gz 41.1 GB
EGAF00008388360 fastq.gz 41.9 GB
EGAF00008388361 fastq.gz 44.0 GB
EGAF00008388362 fastq.gz 34.9 GB
EGAF00008388363 fastq.gz 38.5 GB
EGAF00008388364 fastq.gz 111.3 GB
EGAF00008388365 fastq.gz 123.9 GB
EGAF00008388366 fastq.gz 113.8 GB
EGAF00008388367 fastq.gz 125.4 GB
EGAF00008388368 fastq.gz 47.6 GB
EGAF00008388369 fastq.gz 49.9 GB
EGAF00008388370 fastq.gz 46.7 GB
EGAF00008388371 fastq.gz 48.8 GB
EGAF00008388372 fastq.gz 38.6 GB
EGAF00008388373 fastq.gz 40.5 GB
EGAF00008388374 fastq.gz 70.1 GB
EGAF00008388375 fastq.gz 72.8 GB
EGAF00008388376 fastq.gz 36.0 GB
EGAF00008388377 fastq.gz 39.7 GB
EGAF00008388378 fastq.gz 107.7 GB
EGAF00008388379 fastq.gz 121.9 GB
EGAF00008388380 fastq.gz 37.5 GB
EGAF00008388381 fastq.gz 39.8 GB
EGAF00008388382 fastq.gz 49.5 GB
EGAF00008388383 fastq.gz 52.2 GB
EGAF00008388384 fastq.gz 97.6 GB
EGAF00008388385 fastq.gz 109.0 GB
EGAF00008388386 fastq.gz 114.3 GB
EGAF00008388387 fastq.gz 124.9 GB
EGAF00008388388 fastq.gz 119.3 GB
EGAF00008388389 fastq.gz 127.6 GB
EGAF00008388390 fastq.gz 35.1 GB
EGAF00008388391 fastq.gz 37.5 GB
EGAF00008388392 fastq.gz 110.3 GB
EGAF00008388393 fastq.gz 118.2 GB
EGAF00008388394 fastq.gz 32.4 GB
EGAF00008388395 fastq.gz 36.3 GB
EGAF00008388396 fastq.gz 108.4 GB
EGAF00008388397 fastq.gz 120.9 GB
EGAF00008388398 fastq.gz 36.3 GB
EGAF00008388399 fastq.gz 41.0 GB
EGAF00008388400 fastq.gz 109.9 GB
EGAF00008388401 fastq.gz 118.7 GB
EGAF00008388402 fastq.gz 32.5 GB
EGAF00008388403 fastq.gz 35.2 GB
EGAF00008388404 fastq.gz 32.0 GB
EGAF00008388405 fastq.gz 36.0 GB
EGAF00008388406 fastq.gz 69.9 GB
EGAF00008388407 fastq.gz 76.5 GB
EGAF00008388408 fastq.gz 43.2 GB
EGAF00008388409 fastq.gz 46.1 GB
EGAF00008388410 fastq.gz 38.4 GB
EGAF00008388411 fastq.gz 40.7 GB
EGAF00008388412 fastq.gz 37.8 GB
EGAF00008388413 fastq.gz 40.0 GB
EGAF00008388414 fastq.gz 41.3 GB
EGAF00008388415 fastq.gz 43.2 GB
EGAF00008388416 fastq.gz 28.4 GB
EGAF00008388417 fastq.gz 30.3 GB
EGAF00008388418 fastq.gz 50.2 GB
EGAF00008388419 fastq.gz 53.1 GB
EGAF00008388420 fastq.gz 33.6 GB
EGAF00008388421 fastq.gz 36.5 GB
EGAF00008388422 fastq.gz 69.3 GB
EGAF00008388423 fastq.gz 74.9 GB
EGAF00008388424 fastq.gz 36.6 GB
EGAF00008388425 fastq.gz 38.0 GB
EGAF00008388426 fastq.gz 73.1 GB
EGAF00008388427 fastq.gz 79.1 GB
EGAF00008388428 fastq.gz 33.7 GB
EGAF00008388429 fastq.gz 35.0 GB
EGAF00008388430 fastq.gz 69.3 GB
EGAF00008388431 fastq.gz 71.9 GB
EGAF00008388432 fastq.gz 107.3 GB
EGAF00008388433 fastq.gz 117.3 GB
EGAF00008388434 fastq.gz 114.1 GB
EGAF00008388435 fastq.gz 128.2 GB
EGAF00008388436 fastq.gz 105.1 GB
EGAF00008388437 fastq.gz 113.0 GB
EGAF00008388438 fastq.gz 114.1 GB
EGAF00008388439 fastq.gz 124.6 GB
EGAF00008388440 fastq.gz 112.7 GB
EGAF00008388441 fastq.gz 120.6 GB
EGAF00008388442 fastq.gz 37.4 GB
EGAF00008388443 fastq.gz 43.6 GB
EGAF00008388444 fastq.gz 110.4 GB
EGAF00008388445 fastq.gz 118.3 GB
EGAF00008388446 fastq.gz 106.9 GB
EGAF00008388447 fastq.gz 116.8 GB
EGAF00008398229 fastq.gz 112.0 GB
EGAF00008398230 fastq.gz 120.2 GB
EGAF00008398231 fastq.gz 113.8 GB
EGAF00008398232 fastq.gz 125.8 GB
EGAF00008398233 fastq.gz 112.3 GB
EGAF00008398234 fastq.gz 122.0 GB
EGAF00008398235 fastq.gz 108.7 GB
EGAF00008398236 fastq.gz 119.2 GB
EGAF00008398237 fastq.gz 36.6 GB
EGAF00008398238 fastq.gz 40.4 GB
EGAF00008398239 fastq.gz 110.5 GB
EGAF00008398240 fastq.gz 123.5 GB
EGAF00008398241 fastq.gz 35.0 GB
EGAF00008398242 fastq.gz 39.0 GB
EGAF00008398243 fastq.gz 94.2 GB
EGAF00008398244 fastq.gz 102.9 GB
EGAF00008398245 fastq.gz 35.5 GB
EGAF00008398246 fastq.gz 39.1 GB
EGAF00008398247 fastq.gz 119.2 GB
EGAF00008398248 fastq.gz 129.5 GB
EGAF00008398249 fastq.gz 111.9 GB
EGAF00008398250 fastq.gz 121.8 GB
EGAF00008398251 fastq.gz 35.9 GB
EGAF00008398252 fastq.gz 37.5 GB
EGAF00008398253 fastq.gz 46.0 GB
EGAF00008398254 fastq.gz 48.6 GB
132 Files (9.5 TB)