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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WGS of clonal organoids, bulk-tumor tissues, and matched blood samples derived from metastatic colorectal cancer patients

This dataset consists of WGS fastq files from 58 clonal organoids and 18 fresh-frozen (FT) bulk-tissue samples from surgically resected primary and metastatic tumors before and after anticancer therapies in 6 patients with matched blood control samples from each patient. After DNA extraction from each sample using DNeasy Blood and Tissue Kit (Qiagen), library preparation was done using TruSeq DNA PCR-free kit. Then, paired-end fastq files were generated using Illumina NovaSeq 6000.

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Data access agreement on human-derived clonal organoids from metastatic colorectal cancer

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 User Institution has requested access. The User Institution agrees to be bound by these terms and conditions. Definitions Authorised Personnel: The individuals at the User Institution to whom Dr. Won Hee Lee grants access to the Data. This includes the User, the individuals listed in Appendix II and any other individuals for whom the User Institution subsequently requests access to the Data. Details of the initial Authorised Personnel are set out in Appendix II. Data: The managed access datasets to which the User Institution has requested access. Data Producers: Dr. Won Hee Lee and the collaborators listed in Appendix I responsible for the development, organisation, and oversight of these Data. External Collaborator: A collaborator of the User, working for an institution other than the User Institution. Project: The project for which the User Institution has requested access to these Data. A description of the Project is set out in Appendix II. Publications: Includes, without limitation, articles published in print journals, electronic journals, reviews, books, posters and other written and verbal presentations of research. Research Participant: An individual whose data form part of these Data. Research Purposes: Shall mean research that is seeking to advance the understanding of genetics and genomics, including the treatment of disorders, and work on statistical methods that may be applied to such research. User: The principal investigator for the Project. User Institution(s): The Institution that has requested access to the Data. YUCM: Yonsei University College of Medicine 1. The User Institution agrees to only use these Data for the purpose of the Project (described in Appendix II) and only for Research Purposes. The User Institution 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. The User Institution agrees to preserve, at all times, the confidentiality of these Data. In particular, it undertakes not to use, or attempt to use these Data to compromise or otherwise infringe the confidentiality of information on Research Participants. Without prejudice to the generality of the foregoing, the User Institution agrees to use at least the measures set out in Appendix I to protect these Data. 3. The User Institution agrees to protect the confidentiality of Research Participants in any research papers or publications that they prepare by taking all reasonable care to limit the possibility of identification. 4. The User Institution agrees not to link or combine these Data to other information or archived data available in a way that could re-identify the Research Participants, even if access to that data has been formally granted to the User Institution or is freely available without restriction. 5. The User Institution agrees only to transfer or disclose these Data, in whole or part, or any material derived from these Data, to the Authorised Personnel. Should the User Institution wish to share these Data with an External Collaborator, the External Collaborator must complete a separate application for access to these Data. 6. The User Institution agrees that the Data Producers, and all other parties involved in the creation, funding or protection of these Data: a) make no warranty or representation, express or implied as to the accuracy, quality or comprehensiveness of these Data; b) exclude to the fullest extent permitted by law all liability for actions, claims, proceedings, demands, losses (including but not limited to loss of profit), costs, awards damages and payments made by the Recipient that may arise (whether directly or indirectly) in any way whatsoever from the Recipient’s use of these Data or from the unavailability of, or break in access to, these Data for whatever reason and; c) bear no responsibility for the further analysis or interpretation of these Data. 7. The User Institution agrees to follow the Fort Lauderdale Guidelines (http://www.wellcome.ac.uk/stellent/groups/corporatesite/@policy_communications/documents/web_document/wtd003207.pdf ) and the Toronto Statement (http://www.nature.com/nature/journal/v461/n7261/full/461168a.html). This includes but is not limited to recognising the contribution of the Data Producers and including a proper acknowledgement in all reports or publications resulting from the use of these Data. 8. The User Institution agrees to follow the Publication Policy in Appendix III. This includes respecting the moratorium period for the Data Producers to publish the first peer-reviewed report describing and analysing these Data. 9. The User Institution agrees not to make intellectual property claims on these Data and not to use intellectual property protection in ways that would prevent or block access to, or use of, any element of these Data, or conclusion drawn directly from these Data. 10. The User Institution can elect to perform further research that would add intellectual and resource capital to these data and decide to obtain intellectual property rights on these downstream discoveries. In this case, the User Institution agrees to implement licensing policies that will not obstruct further research and to follow the U.S. National Institutes of Health Best Practices for the Licensing of Genomic Inventions (2005) (https://www.icgc.org/files/daco/NIH_BestPracticesLicensingGenomicInventions_2005_en.pdf ) in conformity with the Organisation for Economic Co-operation and Development Guidelines for the Licensing of the Genetic Inventions (2006) (http://www.oecd.org/science/biotech/36198812.pdf ). 11. The User Institution agrees to destroy/discard the Data held, once it is no longer used for the Project, unless obliged to retain the data for archival purposes in conformity with audit or legal requirements. 12. The User Institution will notify YUCM within 30 days of any changes or departures of Authorised Personnel. 13. The User Institution will notify YUCM prior to any significant changes to the protocol for the Project. 14. The User Institution will notify YUCM as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. YUCM may terminate this agreement by written notice to the User Institution. If this agreement terminates for any reason, the User Institution will be required to destroy any Data held, including copies and backup copies. This clause does not prevent the User Institution from retaining these data for archival purpose in conformity with audit or legal requirements. 16. The User Institution accepts that it may be necessary for the Data Producers to alter the terms of this agreement from time to time. As an example, this may include specific provisions relating to the Data required by Data Producers other than YUCM. In the event that changes are required, the Data Producers or their appointed agent will contact the User Institution to inform it of the changes and the User Institution may elect to accept the changes or terminate the agreement. 17. If requested, the User Institution will allow data security and management documentation to be inspected to verify that it is complying with the terms of this agreement. 18. The User Institution agrees to distribute a copy of these terms to the Authorised Personnel. The User Institution will procure that the Authorised Personnel comply with the terms of this agreement. 19. This agreement (and any dispute, controversy, proceedings or claim of whatever nature arising out of this agreement or its formation) shall be construed, interpreted and governed by the laws of Republic of Korea and shall be subject to the exclusive jurisdiction of the courts of Republic of Korea. Agreed for User Institution Signature: Name: Title: Date: Principal Investigator I confirm that I have read and understood this Agreement. Signature: Name: Title: Date: Agreed for YUCM Signature: Name: Won Hee Lee Title: Doctor Date: May 1st, 2025 APPENDIX I – DATASET DETAILS APPENDIX II ––PROJECT DETAILS APPENDIX III –– PUBLICATION POLICY APPENDIX I – DATASET DETAILS Dataset reference (EGA Study ID and Dataset Details) : EGA study ID - 2181 : Dataset details - To investigate the clonal evolution of metastatic CRC at the single-cell level, we performed WGS in 58 clonal organoids and 18 fresh-frozen (FT) bulk-tissue samples from surgically resected primary and metastatic tumors before and after anticancer therapies in 6 patients. This approach enabled detailed phylogenetic reconstruction of individual clones. We discovered the timing and burden of treatment-related mutations as well as the heterogeneous evolution in driver mutations and genomic rearrangements in late-stage clonal evolution under anticancer therapies in metastatic CRC. Name of project that created the dataset : Clonal evolution of metastatic colorectal cancer under anticancer therapies Names of other data producers/collaborators : Young Seok Ju, Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea : Young Jun Cha, Center for Colorectal Cancer, Research Institute and Hospital, National Cancer Center, Goyang, Korea : Bun Kim, Center for Colorectal Cancer, Research Institute and Hospital, National Cancer Center, Goyang, Korea Specific limitations on areas of research : Use of (part of) the dataset in any shape or form is limited to non-commercial biomedical research. The dataset cannot be used for biomedical research directly sponsored by a commercial entity (e.g. pharmaceutics), unless explicitly agreed otherwise with YUCM. Minimum protection measures required : Only persons involved in the project for which the DAC has approved data use, should be allowed access to the data. Sharing of data beyond the original project group is not allowed under this DAA. File access: Data can be held in unencrypted files on an institutional compute system, with Unix user group read/write access for one or more appropriate groups but not Unix world read/write access behind a secure firewall. Laptops holding these data should have password protected logins and screenlocks (set to lock after 5 min of inactivity). If held on USB keys or other portable hard drives, the data must be encrypted. APPENDIX II – PROJECT DETAILS (to be completed by the Requestor) Details of dataset requested i.e., EGA Study and Dataset Accession Number Brief abstract of the Project in which the Data will be used (500 words max) All Individuals who the User Institution to be named as registered users Name of Registered User Email Job Title Supervisor* All Individuals that should have an account created at the EGA Name of Registered User Email Job Title APPENDIX III – PUBLICATION POLICY YUCM intend to publish the results of their analysis of this dataset and do not consider its deposition into public databases to be the equivalent of such publications. YUCM anticipate that the dataset could be useful to other qualified researchers for a variety of purposes. However, some areas of work are subject to a publication moratorium. The publication moratorium covers any publications (including oral communications) that describe the use of the dataset. For research papers, submission for publication should not occur until 12 months after these data were first made available on the relevant hosting database, unless YUCM has provided written consent to earlier submission. In any publications based on these data, please describe how the data can be accessed, including the name of the hosting database (e.g., The European Genome-phenome Archive at the European Bioinformatics Institute) and its accession numbers (e.g., EGAS00000000029), and acknowledge its use in a form agreed by the User Institution with YUCM.

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
EGAS50000001023 Whole Genome 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
i
EGAF00008721444 fastq.gz 31.4 GB
EGAF00008721445 fastq.gz 32.9 GB
EGAF00008721447 fastq.gz 78.8 GB
EGAF00008721449 fastq.gz 83.6 GB
EGAF00008721974 fastq.gz 31.2 GB
EGAF00008721975 fastq.gz 33.1 GB
EGAF00008721976 fastq.gz 32.9 GB
EGAF00008721977 fastq.gz 31.8 GB
EGAF00008721978 fastq.gz 32.1 GB
EGAF00008721979 fastq.gz 32.6 GB
EGAF00008721980 fastq.gz 34.0 GB
EGAF00008721981 fastq.gz 31.0 GB
EGAF00008721982 fastq.gz 33.3 GB
EGAF00008721983 fastq.gz 35.8 GB
EGAF00008721984 fastq.gz 32.3 GB
EGAF00008721985 fastq.gz 34.7 GB
EGAF00008721986 fastq.gz 32.8 GB
EGAF00008721987 fastq.gz 33.9 GB
EGAF00008721988 fastq.gz 33.2 GB
EGAF00008721989 fastq.gz 35.0 GB
EGAF00008721990 fastq.gz 43.9 GB
EGAF00008721991 fastq.gz 35.2 GB
EGAF00008721992 fastq.gz 33.2 GB
EGAF00008721993 fastq.gz 33.5 GB
EGAF00008721994 fastq.gz 34.0 GB
EGAF00008721995 fastq.gz 32.7 GB
EGAF00008721996 fastq.gz 31.7 GB
EGAF00008721997 fastq.gz 34.7 GB
EGAF00008721998 fastq.gz 34.3 GB
EGAF00008721999 fastq.gz 32.8 GB
EGAF00008722000 fastq.gz 35.9 GB
EGAF00008722001 fastq.gz 43.1 GB
EGAF00008722002 fastq.gz 79.6 GB
EGAF00008722003 fastq.gz 33.2 GB
EGAF00008722004 fastq.gz 32.1 GB
EGAF00008722005 fastq.gz 33.4 GB
EGAF00008722006 fastq.gz 32.4 GB
EGAF00008722007 fastq.gz 32.6 GB
EGAF00008722008 fastq.gz 33.5 GB
EGAF00008722009 fastq.gz 32.1 GB
EGAF00008722010 fastq.gz 111.5 GB
EGAF00008722011 fastq.gz 33.5 GB
EGAF00008722012 fastq.gz 32.2 GB
EGAF00008722013 fastq.gz 115.6 GB
EGAF00008722014 fastq.gz 32.3 GB
EGAF00008722015 fastq.gz 32.0 GB
EGAF00008722016 fastq.gz 33.9 GB
EGAF00008722017 fastq.gz 32.6 GB
EGAF00008722018 fastq.gz 112.0 GB
EGAF00008722019 fastq.gz 33.2 GB
EGAF00008722020 fastq.gz 116.7 GB
EGAF00008722021 fastq.gz 112.7 GB
EGAF00008722022 fastq.gz 102.0 GB
EGAF00008722023 fastq.gz 119.5 GB
EGAF00008722024 fastq.gz 32.2 GB
EGAF00008722025 fastq.gz 42.0 GB
EGAF00008722026 fastq.gz 34.4 GB
EGAF00008722027 fastq.gz 98.1 GB
EGAF00008722028 fastq.gz 112.6 GB
EGAF00008722029 fastq.gz 84.5 GB
EGAF00008722030 fastq.gz 33.7 GB
EGAF00008722031 fastq.gz 33.4 GB
EGAF00008722032 fastq.gz 33.4 GB
EGAF00008722033 fastq.gz 98.8 GB
EGAF00008722034 fastq.gz 34.3 GB
EGAF00008722035 fastq.gz 113.6 GB
EGAF00008722036 fastq.gz 119.5 GB
EGAF00008722037 fastq.gz 34.0 GB
EGAF00008722038 fastq.gz 114.7 GB
EGAF00008722039 fastq.gz 32.8 GB
EGAF00008722040 fastq.gz 117.2 GB
EGAF00008722041 fastq.gz 117.6 GB
EGAF00008722042 fastq.gz 31.9 GB
EGAF00008722043 fastq.gz 33.8 GB
EGAF00008722044 fastq.gz 34.0 GB
EGAF00008722045 fastq.gz 103.0 GB
EGAF00008722046 fastq.gz 39.8 GB
EGAF00008722047 fastq.gz 41.4 GB
EGAF00008722048 fastq.gz 102.3 GB
EGAF00008722049 fastq.gz 33.4 GB
EGAF00008722104 fastq.gz 32.2 GB
EGAF00008722105 fastq.gz 32.4 GB
EGAF00008722106 fastq.gz 33.2 GB
EGAF00008722107 fastq.gz 30.9 GB
EGAF00008722108 fastq.gz 32.6 GB
EGAF00008722109 fastq.gz 32.1 GB
EGAF00008722110 fastq.gz 31.6 GB
EGAF00008722111 fastq.gz 31.7 GB
EGAF00008722112 fastq.gz 33.9 GB
EGAF00008722113 fastq.gz 32.5 GB
EGAF00008722114 fastq.gz 32.0 GB
EGAF00008722115 fastq.gz 40.9 GB
EGAF00008722116 fastq.gz 35.5 GB
EGAF00008722117 fastq.gz 42.8 GB
EGAF00008722118 fastq.gz 38.6 GB
EGAF00008722119 fastq.gz 31.4 GB
EGAF00008722120 fastq.gz 31.8 GB
EGAF00008722121 fastq.gz 31.7 GB
EGAF00008722122 fastq.gz 33.2 GB
EGAF00008722123 fastq.gz 32.0 GB
EGAF00008722124 fastq.gz 33.7 GB
EGAF00008722125 fastq.gz 31.9 GB
EGAF00008722126 fastq.gz 31.4 GB
EGAF00008722127 fastq.gz 33.0 GB
EGAF00008722128 fastq.gz 31.2 GB
EGAF00008722129 fastq.gz 32.3 GB
EGAF00008722130 fastq.gz 32.9 GB
EGAF00008722131 fastq.gz 33.2 GB
EGAF00008722132 fastq.gz 33.0 GB
EGAF00008722133 fastq.gz 31.3 GB
EGAF00008722134 fastq.gz 32.4 GB
EGAF00008722135 fastq.gz 33.3 GB
EGAF00008722136 fastq.gz 32.5 GB
EGAF00008722137 fastq.gz 31.5 GB
EGAF00008722138 fastq.gz 33.9 GB
EGAF00008722139 fastq.gz 32.9 GB
EGAF00008722140 fastq.gz 35.8 GB
EGAF00008722141 fastq.gz 30.9 GB
EGAF00008722142 fastq.gz 34.0 GB
EGAF00008722143 fastq.gz 112.9 GB
EGAF00008722144 fastq.gz 112.7 GB
EGAF00008722145 fastq.gz 32.9 GB
EGAF00008722146 fastq.gz 36.5 GB
EGAF00008722147 fastq.gz 117.7 GB
EGAF00008722148 fastq.gz 37.1 GB
EGAF00008722149 fastq.gz 34.8 GB
EGAF00008722150 fastq.gz 28.4 GB
EGAF00008722151 fastq.gz 31.7 GB
EGAF00008722152 fastq.gz 113.8 GB
EGAF00008722153 fastq.gz 117.7 GB
EGAF00008722154 fastq.gz 32.8 GB
EGAF00008722155 fastq.gz 31.5 GB
EGAF00008722156 fastq.gz 31.3 GB
EGAF00008722165 fastq.gz 33.6 GB
EGAF00008722170 fastq.gz 113.4 GB
EGAF00008722172 fastq.gz 117.5 GB
EGAF00008722174 fastq.gz 35.4 GB
EGAF00008722184 fastq.gz 119.4 GB
EGAF00008722185 fastq.gz 31.6 GB
EGAF00008722186 fastq.gz 32.4 GB
EGAF00008722188 fastq.gz 34.9 GB
EGAF00008722189 fastq.gz 113.5 GB
EGAF00008722192 fastq.gz 27.4 GB
EGAF00008722193 fastq.gz 112.7 GB
EGAF00008722194 fastq.gz 119.0 GB
EGAF00008722198 fastq.gz 114.1 GB
EGAF00008722199 fastq.gz 31.9 GB
EGAF00008722200 fastq.gz 31.6 GB
EGAF00008722202 fastq.gz 31.1 GB
EGAF00008722203 fastq.gz 32.0 GB
EGAF00008722204 fastq.gz 117.2 GB
EGAF00008722205 fastq.gz 29.7 GB
EGAF00008722206 fastq.gz 118.5 GB
EGAF00008722207 fastq.gz 32.1 GB
EGAF00008722210 fastq.gz 34.8 GB
EGAF00008722212 fastq.gz 30.7 GB
EGAF00008722215 fastq.gz 113.3 GB
EGAF00008722218 fastq.gz 32.3 GB
EGAF00008722219 fastq.gz 34.0 GB
EGAF00008722224 fastq.gz 32.7 GB
EGAF00008722227 fastq.gz 118.2 GB
EGAF00008722364 fastq.gz 32.0 GB
EGAF00008722365 fastq.gz 32.0 GB
EGAF00008722366 fastq.gz 36.2 GB
EGAF00008722367 fastq.gz 41.4 GB
EGAF00008722368 fastq.gz 98.5 GB
166 Files (8.4 TB)