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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Spatial transcriptomic profiling of INSPIRE samples

This study aimed t o define the spatial tumor microenvironment features associated with response to immune checkpoint blockade in recurrent/metastatic head and neck squamous cell carcinoma (RM-HNSCC). Spatial transcriptomic profiling was performed on tumor biopsies from ICB-naive patients to characterize malignant, stromal, and immune cell states and their spatial interactions. The study investigated how intratumoral heterogeneity, cancer-associated fibroblast programs, immune contexture, and tumor-microenvironment signaling relate to subsequent clinical response and progression-free survival following immunotherapy.

Request Access

Access to data generated by UHN is made available by completing the data access agreement for review by the data access committee and will be granted to qualified investigators for appropriate use.

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 the 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 Authorised Personnel are set out in Appendix II. Data: The managed access datasets to which the User Institution has requested access. Data Producers: The Principal Investigator 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. University Health Network: The University Health Network (UHN) is the largest clinical and research hospital in Canada. UHN is affiliated with the University of Toronto and is a member of the Toronto Academic Health Science Network. 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 the DAC within 30 days of any changes or departures of Authorised Personnel. 13. The User Institution will notify the DAC prior to any significant changes to the protocol for the Project. 14. The User Institution will notify the DAC as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. The 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. 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 the province of Ontario and PHIPA. 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 The Data Access Committee Signature: Name: Title: Date: APPENDIX I – DATASET DETAILS APPENDIX II ––PROJECT DETAILS APPENDIX III –– PUBLICATION POLICY

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
EGAS00001003280 Cancer Genomics

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
EGAF50001043811 fastq.gz 123.9 MB
EGAF50001043812 fastq.gz 97.2 MB
EGAF50001043813 fastq.gz 85.4 MB
EGAF50001043814 fastq.gz 84.1 MB
EGAF50001043815 fastq.gz 220.5 MB
EGAF50001043816 fastq.gz 315.8 MB
EGAF50001043817 fastq.gz 680.1 MB
EGAF50001043818 fastq.gz 31.5 MB
EGAF50001043819 fastq.gz 51.1 MB
EGAF50001043820 fastq.gz 40.4 MB
EGAF50001043821 fastq.gz 40.7 MB
EGAF50001043822 fastq.gz 3.4 GB
EGAF50001043823 fastq.gz 1.6 GB
EGAF50001043824 fastq.gz 134.4 MB
EGAF50001043825 fastq.gz 139.6 MB
EGAF50001043826 fastq.gz 447.9 MB
EGAF50001043827 fastq.gz 149.1 MB
EGAF50001043828 fastq.gz 63.0 MB
EGAF50001043829 fastq.gz 55.4 MB
EGAF50001043830 fastq.gz 110.5 MB
EGAF50001043831 fastq.gz 50.0 MB
EGAF50001043832 fastq.gz 99.7 MB
EGAF50001043833 fastq.gz 58.4 MB
EGAF50001043834 fastq.gz 116.9 MB
EGAF50001043835 fastq.gz 80.7 MB
EGAF50001043836 fastq.gz 40.5 MB
EGAF50001043837 fastq.gz 81.0 MB
EGAF50001043838 fastq.gz 40.0 MB
EGAF50001043839 fastq.gz 79.7 MB
EGAF50001043840 fastq.gz 38.7 MB
EGAF50001043841 fastq.gz 77.0 MB
EGAF50001043842 fastq.gz 81.3 MB
EGAF50001043843 fastq.gz 34.8 MB
EGAF50001043844 fastq.gz 70.5 MB
EGAF50001043845 fastq.gz 63.6 MB
EGAF50001043846 fastq.gz 258.3 MB
EGAF50001043847 fastq.gz 532.8 MB
EGAF50001043848 fastq.gz 235.7 MB
EGAF50001043849 fastq.gz 485.0 MB
EGAF50001043850 fastq.gz 229.4 MB
EGAF50001043851 fastq.gz 478.7 MB
EGAF50001043852 fastq.gz 214.8 MB
EGAF50001043853 fastq.gz 170.8 MB
EGAF50001043854 fastq.gz 254.1 MB
EGAF50001043855 fastq.gz 123.5 MB
EGAF50001043856 fastq.gz 251.8 MB
EGAF50001043857 fastq.gz 141.0 MB
EGAF50001043858 fastq.gz 284.7 MB
EGAF50001043859 fastq.gz 306.5 MB
EGAF50001043860 fastq.gz 195.5 MB
EGAF50001043861 fastq.gz 219.3 MB
EGAF50001043862 fastq.gz 564.2 MB
EGAF50001043863 fastq.gz 219.7 MB
EGAF50001043864 fastq.gz 504.8 MB
EGAF50001043865 fastq.gz 1.1 GB
EGAF50001043866 fastq.gz 58.0 MB
EGAF50001043867 fastq.gz 116.2 MB
EGAF50001043868 fastq.gz 56.3 MB
EGAF50001043869 fastq.gz 112.6 MB
EGAF50001043870 fastq.gz 156.3 MB
EGAF50001043871 fastq.gz 330.0 MB
EGAF50001043872 fastq.gz 156.2 MB
EGAF50001043873 fastq.gz 219.2 MB
EGAF50001043874 fastq.gz 451.3 MB
EGAF50001043875 fastq.gz 63.7 MB
EGAF50001043876 fastq.gz 128.7 MB
EGAF50001043877 fastq.gz 59.5 MB
EGAF50001043878 fastq.gz 119.9 MB
EGAF50001043879 fastq.gz 127.2 MB
EGAF50001043880 fastq.gz 197.8 MB
EGAF50001043881 fastq.gz 97.9 MB
EGAF50001043882 fastq.gz 198.7 MB
EGAF50001043883 fastq.gz 96.1 MB
EGAF50001043884 fastq.gz 29.8 MB
EGAF50001043885 fastq.gz 60.0 MB
EGAF50001043886 fastq.gz 25.4 MB
EGAF50001043887 fastq.gz 31.8 MB
EGAF50001043888 fastq.gz 64.5 MB
EGAF50001043889 fastq.gz 339.5 MB
EGAF50001043890 fastq.gz 168.5 MB
EGAF50001043891 fastq.gz 336.9 MB
EGAF50001043892 fastq.gz 164.0 MB
EGAF50001043893 fastq.gz 327.5 MB
EGAF50001043894 fastq.gz 144.6 MB
EGAF50001043895 fastq.gz 287.5 MB
EGAF50001043896 fastq.gz 164.8 MB
EGAF50001043897 fastq.gz 330.1 MB
EGAF50001043898 fastq.gz 635.6 MB
EGAF50001043899 fastq.gz 1.3 GB
EGAF50001043900 fastq.gz 570.1 MB
EGAF50001043901 fastq.gz 540.7 MB
EGAF50001043902 fastq.gz 1.2 GB
EGAF50001043903 fastq.gz 66.7 MB
EGAF50001043904 fastq.gz 137.1 MB
EGAF50001043905 fastq.gz 67.0 MB
EGAF50001043906 fastq.gz 137.6 MB
EGAF50001043907 fastq.gz 67.1 MB
EGAF50001043908 fastq.gz 137.9 MB
EGAF50001043909 fastq.gz 67.8 MB
EGAF50001043910 fastq.gz 356.8 MB
EGAF50001043911 fastq.gz 151.3 MB
EGAF50001043912 fastq.gz 316.4 MB
EGAF50001043913 fastq.gz 366.9 MB
EGAF50001043914 fastq.gz 750.1 MB
EGAF50001043915 fastq.gz 343.4 MB
EGAF50001043916 fastq.gz 703.5 MB
EGAF50001043917 fastq.gz 252.6 MB
EGAF50001043918 fastq.gz 124.6 MB
EGAF50001043919 fastq.gz 138.2 MB
EGAF50001043920 fastq.gz 278.8 MB
EGAF50001043921 fastq.gz 142.8 MB
EGAF50001043922 fastq.gz 292.2 MB
EGAF50001043923 fastq.gz 296.5 MB
EGAF50001043924 fastq.gz 169.9 MB
EGAF50001043925 fastq.gz 1.2 GB
EGAF50001043926 fastq.gz 65.5 MB
EGAF50001043927 fastq.gz 645.6 MB
EGAF50001043928 fastq.gz 328.5 MB
EGAF50001043929 fastq.gz 158.5 MB
EGAF50001043930 fastq.gz 334.5 MB
EGAF50001043931 fastq.gz 158.2 MB
EGAF50001043932 fastq.gz 332.6 MB
EGAF50001043933 fastq.gz 94.1 MB
EGAF50001043934 fastq.gz 189.0 MB
EGAF50001043935 fastq.gz 94.4 MB
EGAF50001043936 fastq.gz 189.5 MB
EGAF50001043937 fastq.gz 94.0 MB
EGAF50001043938 fastq.gz 188.8 MB
EGAF50001043939 fastq.gz 173.9 MB
EGAF50001043940 fastq.gz 85.2 MB
EGAF50001043941 fastq.gz 176.0 MB
EGAF50001043942 fastq.gz 83.9 MB
EGAF50001043943 fastq.gz 173.5 MB
EGAF50001043944 fastq.gz 453.9 MB
EGAF50001043945 fastq.gz 220.8 MB
EGAF50001043946 fastq.gz 454.7 MB
EGAF50001068894 tsv 3.9 kB
137 Files (36.3 GB)