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Transcriptome profiling of head and neck squamous cell carcinomas with paired patient-derived xenografts

This dataset includes transcriptome profiling of 88 head and neck primary patient tumor samples and 45 paired patient-derived xenograft samples that successfully engrafted in mice. NGS was performed using the Illumina TruSeq stranded total RNA sample preparation kit on the Illumina NovaSeq X Plus platform at the Princess Margaret Genomics Centre. This dataset consists of paired-end fastq files.

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
EGAS50000000714 RNASeq

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
EGAF50000241639 fastq.gz 3.3 GB
EGAF50000241640 fastq.gz 3.4 GB
EGAF50000241641 fastq.gz 4.3 GB
EGAF50000241642 fastq.gz 4.4 GB
EGAF50000241643 fastq.gz 4.6 GB
EGAF50000241644 fastq.gz 4.6 GB
EGAF50000241645 fastq.gz 5.0 GB
EGAF50000241646 fastq.gz 5.2 GB
EGAF50000241647 fastq.gz 5.3 GB
EGAF50000241648 fastq.gz 5.9 GB
EGAF50000241649 fastq.gz 3.7 GB
EGAF50000241650 fastq.gz 3.8 GB
EGAF50000241651 fastq.gz 3.9 GB
EGAF50000241652 fastq.gz 4.1 GB
EGAF50000241653 fastq.gz 4.7 GB
EGAF50000241654 fastq.gz 4.9 GB
EGAF50000241655 fastq.gz 4.3 GB
EGAF50000241656 fastq.gz 4.2 GB
EGAF50000241657 fastq.gz 4.5 GB
EGAF50000241658 fastq.gz 4.5 GB
EGAF50000241659 fastq.gz 5.0 GB
EGAF50000241660 fastq.gz 4.0 GB
EGAF50000241661 fastq.gz 3.8 GB
EGAF50000241662 fastq.gz 5.3 GB
EGAF50000241663 fastq.gz 5.3 GB
EGAF50000241664 fastq.gz 5.2 GB
EGAF50000241665 fastq.gz 5.2 GB
EGAF50000241666 fastq.gz 5.5 GB
EGAF50000241667 fastq.gz 5.4 GB
EGAF50000241668 fastq.gz 5.6 GB
EGAF50000241669 fastq.gz 5.0 GB
EGAF50000241670 fastq.gz 4.1 GB
EGAF50000241671 fastq.gz 4.7 GB
EGAF50000241672 fastq.gz 4.0 GB
EGAF50000241673 fastq.gz 4.2 GB
EGAF50000241674 fastq.gz 4.1 GB
EGAF50000241675 fastq.gz 4.3 GB
EGAF50000241676 fastq.gz 4.5 GB
EGAF50000241677 fastq.gz 4.7 GB
EGAF50000241678 fastq.gz 4.9 GB
EGAF50000241679 fastq.gz 4.2 GB
EGAF50000241680 fastq.gz 4.5 GB
EGAF50000241681 fastq.gz 4.5 GB
EGAF50000241682 fastq.gz 4.8 GB
EGAF50000241683 fastq.gz 5.4 GB
EGAF50000241684 fastq.gz 5.7 GB
EGAF50000241685 fastq.gz 3.9 GB
EGAF50000241686 fastq.gz 5.7 GB
EGAF50000241687 fastq.gz 4.1 GB
EGAF50000241688 fastq.gz 5.9 GB
EGAF50000241689 fastq.gz 4.0 GB
EGAF50000241690 fastq.gz 4.5 GB
EGAF50000241691 fastq.gz 4.9 GB
EGAF50000241692 fastq.gz 4.7 GB
EGAF50000241693 fastq.gz 5.2 GB
EGAF50000241694 fastq.gz 5.1 GB
EGAF50000241695 fastq.gz 5.7 GB
EGAF50000241696 fastq.gz 4.4 GB
EGAF50000241697 fastq.gz 5.3 GB
EGAF50000241698 fastq.gz 6.0 GB
EGAF50000241699 fastq.gz 5.6 GB
EGAF50000241700 fastq.gz 4.7 GB
EGAF50000241701 fastq.gz 4.2 GB
EGAF50000241702 fastq.gz 4.4 GB
EGAF50000241703 fastq.gz 5.0 GB
EGAF50000241704 fastq.gz 6.6 GB
EGAF50000241705 fastq.gz 5.3 GB
EGAF50000241706 fastq.gz 5.1 GB
EGAF50000241707 fastq.gz 6.9 GB
EGAF50000241708 fastq.gz 5.3 GB
EGAF50000241709 fastq.gz 5.7 GB
EGAF50000241710 fastq.gz 5.9 GB
EGAF50000241711 fastq.gz 6.3 GB
EGAF50000241712 fastq.gz 4.5 GB
EGAF50000241713 fastq.gz 6.6 GB
EGAF50000241714 fastq.gz 4.8 GB
EGAF50000241715 fastq.gz 5.1 GB
EGAF50000241716 fastq.gz 5.2 GB
EGAF50000241717 fastq.gz 4.5 GB
EGAF50000241718 fastq.gz 5.3 GB
EGAF50000241719 fastq.gz 5.5 GB
EGAF50000241720 fastq.gz 4.7 GB
EGAF50000241721 fastq.gz 3.8 GB
EGAF50000241722 fastq.gz 3.4 GB
EGAF50000241723 fastq.gz 4.0 GB
EGAF50000241724 fastq.gz 3.3 GB
EGAF50000241725 fastq.gz 4.5 GB
EGAF50000241726 fastq.gz 5.3 GB
EGAF50000241727 fastq.gz 3.6 GB
EGAF50000241728 fastq.gz 5.7 GB
EGAF50000241729 fastq.gz 4.1 GB
EGAF50000241730 fastq.gz 4.7 GB
EGAF50000241731 fastq.gz 4.6 GB
EGAF50000241732 fastq.gz 4.8 GB
EGAF50000241733 fastq.gz 4.4 GB
EGAF50000241734 fastq.gz 4.0 GB
EGAF50000241735 fastq.gz 4.9 GB
EGAF50000241736 fastq.gz 4.2 GB
EGAF50000241737 fastq.gz 4.2 GB
EGAF50000241738 fastq.gz 4.1 GB
EGAF50000241739 fastq.gz 4.4 GB
EGAF50000241740 fastq.gz 4.4 GB
EGAF50000241741 fastq.gz 6.3 GB
EGAF50000241742 fastq.gz 6.7 GB
EGAF50000241743 fastq.gz 5.8 GB
EGAF50000241744 fastq.gz 5.5 GB
EGAF50000241745 fastq.gz 4.8 GB
EGAF50000241746 fastq.gz 4.2 GB
EGAF50000241747 fastq.gz 5.2 GB
EGAF50000241748 fastq.gz 4.0 GB
EGAF50000241749 fastq.gz 6.1 GB
EGAF50000241750 fastq.gz 4.4 GB
EGAF50000241751 fastq.gz 6.5 GB
EGAF50000241752 fastq.gz 4.7 GB
EGAF50000241753 fastq.gz 3.5 GB
EGAF50000241754 fastq.gz 3.7 GB
EGAF50000241755 fastq.gz 3.8 GB
EGAF50000241756 fastq.gz 6.5 GB
EGAF50000241757 fastq.gz 3.2 GB
EGAF50000241758 fastq.gz 4.0 GB
EGAF50000241759 fastq.gz 4.1 GB
EGAF50000241760 fastq.gz 4.3 GB
EGAF50000241761 fastq.gz 6.9 GB
EGAF50000241762 fastq.gz 3.3 GB
EGAF50000241763 fastq.gz 4.3 GB
EGAF50000241764 fastq.gz 4.6 GB
EGAF50000241765 fastq.gz 4.9 GB
EGAF50000241766 fastq.gz 4.6 GB
EGAF50000241767 fastq.gz 4.3 GB
EGAF50000241768 fastq.gz 5.2 GB
EGAF50000241769 fastq.gz 7.1 GB
EGAF50000241770 fastq.gz 6.0 GB
EGAF50000241771 fastq.gz 4.5 GB
EGAF50000241772 fastq.gz 7.4 GB
EGAF50000241773 fastq.gz 6.1 GB
EGAF50000241774 fastq.gz 6.4 GB
EGAF50000241775 fastq.gz 6.3 GB
EGAF50000241776 fastq.gz 4.8 GB
EGAF50000241777 fastq.gz 5.8 GB
EGAF50000241778 fastq.gz 6.1 GB
EGAF50000241779 fastq.gz 5.3 GB
EGAF50000241780 fastq.gz 4.8 GB
EGAF50000241781 fastq.gz 4.6 GB
EGAF50000241782 fastq.gz 5.6 GB
EGAF50000241783 fastq.gz 4.4 GB
EGAF50000241784 fastq.gz 7.6 GB
EGAF50000241785 fastq.gz 4.6 GB
EGAF50000241786 fastq.gz 3.1 GB
EGAF50000241787 fastq.gz 4.9 GB
EGAF50000241788 fastq.gz 5.0 GB
EGAF50000241789 fastq.gz 2.9 GB
EGAF50000241790 fastq.gz 4.9 GB
EGAF50000241791 fastq.gz 5.2 GB
EGAF50000241792 fastq.gz 8.1 GB
EGAF50000241793 fastq.gz 5.3 GB
EGAF50000241794 fastq.gz 4.7 GB
EGAF50000241795 fastq.gz 5.3 GB
EGAF50000241796 fastq.gz 5.1 GB
EGAF50000241797 fastq.gz 4.3 GB
EGAF50000241798 fastq.gz 4.8 GB
EGAF50000241799 fastq.gz 4.2 GB
EGAF50000241800 fastq.gz 7.0 GB
EGAF50000241801 fastq.gz 5.0 GB
EGAF50000241802 fastq.gz 4.2 GB
EGAF50000241803 fastq.gz 6.7 GB
EGAF50000241804 fastq.gz 4.8 GB
EGAF50000241805 fastq.gz 4.7 GB
EGAF50000241806 fastq.gz 4.9 GB
EGAF50000241807 fastq.gz 5.1 GB
EGAF50000241808 fastq.gz 4.4 GB
EGAF50000241809 fastq.gz 5.3 GB
EGAF50000241810 fastq.gz 4.7 GB
EGAF50000241811 fastq.gz 5.1 GB
EGAF50000241812 fastq.gz 4.4 GB
EGAF50000241813 fastq.gz 4.9 GB
EGAF50000241814 fastq.gz 5.2 GB
EGAF50000241815 fastq.gz 5.1 GB
EGAF50000241816 fastq.gz 5.4 GB
EGAF50000241817 fastq.gz 4.1 GB
EGAF50000241818 fastq.gz 3.4 GB
EGAF50000241819 fastq.gz 3.5 GB
EGAF50000241820 fastq.gz 4.2 GB
EGAF50000241821 fastq.gz 6.8 GB
EGAF50000241822 fastq.gz 7.1 GB
EGAF50000241823 fastq.gz 4.8 GB
EGAF50000241824 fastq.gz 3.5 GB
EGAF50000241825 fastq.gz 3.7 GB
EGAF50000241826 fastq.gz 3.4 GB
EGAF50000241827 fastq.gz 5.0 GB
EGAF50000241828 fastq.gz 3.6 GB
EGAF50000241829 fastq.gz 3.9 GB
EGAF50000241830 fastq.gz 4.8 GB
EGAF50000241831 fastq.gz 4.6 GB
EGAF50000241832 fastq.gz 5.2 GB
EGAF50000241833 fastq.gz 4.9 GB
EGAF50000241834 fastq.gz 4.1 GB
EGAF50000241835 fastq.gz 5.5 GB
EGAF50000241836 fastq.gz 4.4 GB
EGAF50000241837 fastq.gz 3.4 GB
EGAF50000241838 fastq.gz 3.6 GB
EGAF50000241839 fastq.gz 3.2 GB
EGAF50000241840 fastq.gz 4.6 GB
EGAF50000241841 fastq.gz 4.7 GB
EGAF50000241842 fastq.gz 7.3 GB
EGAF50000241843 fastq.gz 4.0 GB
EGAF50000241844 fastq.gz 4.9 GB
EGAF50000241845 fastq.gz 4.2 GB
EGAF50000241846 fastq.gz 3.4 GB
EGAF50000241847 fastq.gz 4.2 GB
EGAF50000241848 fastq.gz 3.7 GB
EGAF50000241849 fastq.gz 3.9 GB
EGAF50000241850 fastq.gz 4.5 GB
EGAF50000241851 fastq.gz 4.3 GB
EGAF50000241852 fastq.gz 4.2 GB
EGAF50000241853 fastq.gz 4.5 GB
EGAF50000241854 fastq.gz 7.0 GB
EGAF50000241855 fastq.gz 4.8 GB
EGAF50000241856 fastq.gz 5.1 GB
EGAF50000241857 fastq.gz 4.9 GB
EGAF50000241858 fastq.gz 4.0 GB
EGAF50000241859 fastq.gz 4.3 GB
EGAF50000241860 fastq.gz 5.2 GB
EGAF50000241861 fastq.gz 4.5 GB
EGAF50000241862 fastq.gz 4.7 GB
EGAF50000241863 fastq.gz 5.7 GB
EGAF50000241864 fastq.gz 5.9 GB
EGAF50000241865 fastq.gz 4.9 GB
EGAF50000241866 fastq.gz 3.9 GB
EGAF50000241867 fastq.gz 4.0 GB
EGAF50000241868 fastq.gz 5.1 GB
EGAF50000241869 fastq.gz 5.0 GB
EGAF50000241870 fastq.gz 4.1 GB
EGAF50000241871 fastq.gz 3.8 GB
EGAF50000241872 fastq.gz 4.3 GB
EGAF50000241873 fastq.gz 4.1 GB
EGAF50000241874 fastq.gz 5.3 GB
EGAF50000241875 fastq.gz 4.0 GB
EGAF50000241876 fastq.gz 4.8 GB
EGAF50000241877 fastq.gz 4.3 GB
EGAF50000241878 fastq.gz 4.2 GB
EGAF50000241879 fastq.gz 3.7 GB
EGAF50000241880 fastq.gz 5.4 GB
EGAF50000241881 fastq.gz 4.5 GB
EGAF50000241882 fastq.gz 5.4 GB
EGAF50000241883 fastq.gz 3.8 GB
EGAF50000241884 fastq.gz 5.2 GB
EGAF50000241885 fastq.gz 2.9 GB
EGAF50000241886 fastq.gz 4.4 GB
EGAF50000241887 fastq.gz 3.1 GB
EGAF50000241888 fastq.gz 4.6 GB
EGAF50000241889 fastq.gz 4.4 GB
EGAF50000241890 fastq.gz 4.5 GB
EGAF50000241891 fastq.gz 6.1 GB
EGAF50000241892 fastq.gz 4.6 GB
EGAF50000241893 fastq.gz 6.4 GB
EGAF50000241894 fastq.gz 4.8 GB
EGAF50000241895 fastq.gz 4.3 GB
EGAF50000241896 fastq.gz 3.8 GB
EGAF50000241897 fastq.gz 4.5 GB
EGAF50000241898 fastq.gz 4.0 GB
EGAF50000241899 fastq.gz 4.7 GB
EGAF50000241900 fastq.gz 5.0 GB
EGAF50000241901 fastq.gz 5.1 GB
EGAF50000241902 fastq.gz 5.3 GB
EGAF50000241903 fastq.gz 6.0 GB
EGAF50000241904 fastq.gz 6.3 GB
266 Files (1.3 TB)