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Glioblastoma stem cell lines WGS data

WGS data for 20 Glioblastoma stem cell (GSC) lines and matched blood samples. Fastq files are available. For 10 GSC samples and the 10 matched blood samples the reads are on 3 fastq files per sample

Request Access

Data access policy for the SU2C Brain Tumour Stem Cell datasets (Whitley et al)

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 Authorized Personnel: The individuals at the User Institution to whom the SU2C Brain Tumour Stem Cell Group Data Access Committee (DAC) 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 Authorized Personnel are set out in Appendix II. Data: The managed access datasets to which the User Institution has requested access. Data Producers: Dr. Peter Dirks and the collaborators listed in Appendix I responsible for the development, organization, 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 molecular biology (genetics, genomics, transcriptomics, epigenetics, and epigenomics) 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. The Hospital for Sick Children, University Health Network, and University of Toronto: Institutions of data production and governance over data included here, by collaborating data producing institutions. 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 Authorized 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 ( ) and the Toronto Statement ( This includes but is not limited to recognizing 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 analyzing 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) ( ) in conformity with the Organisation for Economic Co-operation and Development Guidelines for the Licensing of the Genetic Inventions (2006) ( ). 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 SU2C Brain Tumour Stem Cell Group DAC within 30 days of any changes or departures of Authorized Personnel. 13. The User Institution will notify SU2C Brain Tumour Stem Cell Group DAC prior to any significant changes to the protocol for the Project. 14. The User Institution will notify SU2C Brain Tumour Stem Cell Group DAC as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. SU2C Brain Tumour Stem Cell Group DAC 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 Dr. Peter Dirks. 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 Authorized Personnel. The User Institution will procure that the Authorized 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 Ontario and PHIPA (Personal Health Information Protection Act) and shall be subject to the exclusive jurisdiction of the Canadian courts. 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 SU2C Brain Tumour Stem Cell Group Signature: Name: Dr. Peter Dirks Title: Senior Scientist, The Hospital for Sick Children Date: APPENDIX I – DATASET DETAILS APPENDIX II ––PROJECT DETAILS APPENDIX III –– PUBLICATION POLICY APPENDIX I – DATASET DETAILS (to be completed by the data producer before passing to applicant) Dataset reference (EGA Study ID and Dataset Details) Study ID: EGAS00001004395 Dataset Details: RNA-seq for GSC lines and WGS data for GSC line and matched GBM tissues Name of project that created the dataset SU2C Canada Cancer Stem Cell Dream Team Names of other data producers/collaborators Trevor Pugh, University Health Network ( Laura Richards, University Health Network ( Gary Bader, University of Toronto ( Owen Whitley, University of Toronto ( Florence Cavalli, The Hospital for Sick Children ( Specific limitations on areas of research No limitations Minimum protection measures required 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 SU2C Brain Tumour Stem Cell Group 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. SU2C Brain Tumour Stem Cell Group 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 Dr. Peter Dirks or an authorized designate from SU2C Brain Tumour Stem Cell Group 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 SU2C Brain Tumour Stem Cell Group.

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
EGAS00001004395 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
EGAF00004039354 fastq.gz 11.9 GB
EGAF00004039355 fastq.gz 13.7 GB
EGAF00004039357 fastq.gz 12.3 GB
EGAF00004039358 fastq.gz 14.2 GB
EGAF00004039365 fastq.gz 12.3 GB
EGAF00004039366 fastq.gz 14.2 GB
EGAF00004039367 fastq.gz 13.5 GB
EGAF00004039368 fastq.gz 15.1 GB
EGAF00004039369 fastq.gz 13.4 GB
EGAF00004039370 fastq.gz 15.1 GB
EGAF00004039375 fastq.gz 13.1 GB
EGAF00004039376 fastq.gz 14.6 GB
EGAF00004039387 fastq.gz 19.1 GB
EGAF00004039388 fastq.gz 22.2 GB
EGAF00004039389 fastq.gz 19.3 GB
EGAF00004039390 fastq.gz 22.1 GB
EGAF00004039391 fastq.gz 17.5 GB
EGAF00004039392 fastq.gz 20.2 GB
EGAF00004039393 fastq.gz 19.5 GB
EGAF00004039394 fastq.gz 22.4 GB
EGAF00004039396 fastq.gz 17.4 GB
EGAF00004039397 fastq.gz 20.0 GB
EGAF00004039398 fastq.gz 17.5 GB
EGAF00004039399 fastq.gz 20.0 GB
EGAF00004039426 fastq.gz 18.3 GB
EGAF00004039427 fastq.gz 21.4 GB
EGAF00004039428 fastq.gz 18.5 GB
EGAF00004039429 fastq.gz 21.8 GB
EGAF00004039430 fastq.gz 18.9 GB
EGAF00004039431 fastq.gz 22.3 GB
EGAF00004039434 fastq.gz 21.2 GB
EGAF00004039435 fastq.gz 24.7 GB
EGAF00004039436 fastq.gz 21.2 GB
EGAF00004039437 fastq.gz 24.7 GB
EGAF00004039441 fastq.gz 21.2 GB
EGAF00004039442 fastq.gz 24.5 GB
EGAF00004039445 fastq.gz 18.1 GB
EGAF00004039446 fastq.gz 20.9 GB
EGAF00004039447 fastq.gz 18.4 GB
EGAF00004039448 fastq.gz 21.3 GB
EGAF00004039452 fastq.gz 19.0 GB
EGAF00004039453 fastq.gz 21.7 GB
EGAF00004039454 fastq.gz 17.2 GB
EGAF00004039455 fastq.gz 19.2 GB
EGAF00004039456 fastq.gz 15.2 GB
EGAF00004039457 fastq.gz 17.6 GB
EGAF00004039458 fastq.gz 14.9 GB
EGAF00004039459 fastq.gz 17.3 GB
EGAF00004039460 fastq.gz 18.2 GB
EGAF00004039461 fastq.gz 21.0 GB
EGAF00004039462 fastq.gz 18.1 GB
EGAF00004039463 fastq.gz 21.0 GB
EGAF00004039466 fastq.gz 18.3 GB
EGAF00004039467 fastq.gz 21.0 GB
EGAF00004039492 fastq.gz 20.6 GB
EGAF00004039493 fastq.gz 23.6 GB
EGAF00004039496 fastq.gz 20.5 GB
EGAF00004039497 fastq.gz 23.5 GB
EGAF00004039498 fastq.gz 18.6 GB
EGAF00004039499 fastq.gz 21.7 GB
EGAF00004039500 fastq.gz 18.7 GB
EGAF00004039501 fastq.gz 21.6 GB
EGAF00004039502 fastq.gz 19.8 GB
EGAF00004039503 fastq.gz 22.7 GB
EGAF00004039505 fastq.gz 14.7 GB
EGAF00004039506 fastq.gz 17.0 GB
EGAF00004039507 fastq.gz 16.9 GB
EGAF00004039508 fastq.gz 19.5 GB
EGAF00004039509 fastq.gz 17.1 GB
EGAF00004039510 fastq.gz 19.7 GB
EGAF00004039511 fastq.gz 20.4 GB
EGAF00004039512 fastq.gz 23.2 GB
EGAF00004039513 fastq.gz 20.1 GB
EGAF00004039514 fastq.gz 23.0 GB
EGAF00004039515 fastq.gz 20.9 GB
EGAF00004039516 fastq.gz 23.4 GB
EGAF00004039518 fastq.gz 20.8 GB
EGAF00004039519 fastq.gz 23.3 GB
EGAF00004039520 fastq.gz 20.3 GB
EGAF00004039521 fastq.gz 22.6 GB
EGAF00004039528 fastq.gz 20.3 GB
EGAF00004039529 fastq.gz 23.6 GB
EGAF00004039530 fastq.gz 20.3 GB
EGAF00004039531 fastq.gz 23.0 GB
EGAF00004457894 fastq.gz 57.9 GB
EGAF00004457895 fastq.gz 67.2 GB
EGAF00004457896 fastq.gz 60.7 GB
EGAF00004457897 fastq.gz 71.2 GB
EGAF00004457898 fastq.gz 63.7 GB
EGAF00004457899 fastq.gz 75.0 GB
EGAF00004457900 fastq.gz 59.6 GB
EGAF00004457901 fastq.gz 69.6 GB
EGAF00004457902 fastq.gz 58.6 GB
EGAF00004457903 fastq.gz 68.8 GB
EGAF00004457904 fastq.gz 60.6 GB
EGAF00004457905 fastq.gz 72.1 GB
EGAF00004457906 fastq.gz 61.5 GB
EGAF00004457907 fastq.gz 72.0 GB
EGAF00004457908 fastq.gz 59.7 GB
EGAF00004457909 fastq.gz 71.3 GB
EGAF00004457910 fastq.gz 59.7 GB
EGAF00004457911 fastq.gz 70.1 GB
EGAF00004457912 fastq.gz 61.8 GB
EGAF00004457913 fastq.gz 73.6 GB
EGAF00004457914 fastq.gz 61.8 GB
EGAF00004457915 fastq.gz 72.3 GB
EGAF00004457916 fastq.gz 63.2 GB
EGAF00004457917 fastq.gz 73.9 GB
EGAF00004457918 fastq.gz 58.4 GB
EGAF00004457919 fastq.gz 66.5 GB
EGAF00004457920 fastq.gz 61.8 GB
EGAF00004457921 fastq.gz 69.4 GB
EGAF00004457922 fastq.gz 60.8 GB
EGAF00004457923 fastq.gz 69.6 GB
EGAF00004457924 fastq.gz 61.4 GB
EGAF00004457925 fastq.gz 70.8 GB
EGAF00004457926 fastq.gz 17.8 GB
EGAF00004457927 fastq.gz 20.7 GB
EGAF00004457928 fastq.gz 61.0 GB
EGAF00004457929 fastq.gz 68.9 GB
EGAF00004457930 fastq.gz 17.6 GB
EGAF00004457931 fastq.gz 20.2 GB
EGAF00004457932 fastq.gz 17.9 GB
EGAF00004457933 fastq.gz 20.6 GB
EGAF00004457934 fastq.gz 19.4 GB
EGAF00004457935 fastq.gz 22.2 GB
EGAF00004457936 fastq.gz 19.2 GB
EGAF00004457937 fastq.gz 22.2 GB
EGAF00004457938 fastq.gz 18.4 GB
EGAF00004457939 fastq.gz 20.9 GB
EGAF00004457940 fastq.gz 18.6 GB
EGAF00004457941 fastq.gz 21.5 GB
EGAF00004457942 fastq.gz 18.4 GB
EGAF00004457943 fastq.gz 21.1 GB
EGAF00004457944 fastq.gz 18.2 GB
EGAF00004457945 fastq.gz 21.0 GB
EGAF00004457946 fastq.gz 13.7 GB
EGAF00004457947 fastq.gz 16.0 GB
EGAF00004457948 fastq.gz 13.9 GB
EGAF00004457949 fastq.gz 15.9 GB
EGAF00004457950 fastq.gz 13.9 GB
EGAF00004457951 fastq.gz 16.0 GB
EGAF00004457952 fastq.gz 17.7 GB
EGAF00004457953 fastq.gz 20.2 GB
EGAF00004457954 fastq.gz 17.9 GB
EGAF00004457955 fastq.gz 20.4 GB
EGAF00004457956 fastq.gz 18.0 GB
EGAF00004457957 fastq.gz 20.5 GB
EGAF00004457958 fastq.gz 18.4 GB
EGAF00004457959 fastq.gz 21.2 GB
EGAF00004457960 fastq.gz 19.6 GB
EGAF00004457961 fastq.gz 23.1 GB
EGAF00004457962 fastq.gz 20.8 GB
EGAF00004457963 fastq.gz 22.3 GB
EGAF00004457964 fastq.gz 59.7 GB
EGAF00004457965 fastq.gz 69.7 GB
EGAF00004677449 fastq.gz 59.9 GB
EGAF00004677450 fastq.gz 69.8 GB
EGAF00004677451 fastq.gz 62.1 GB
EGAF00004677452 fastq.gz 72.1 GB
160 Files (4.9 TB)