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Breast Cancer - immune clusters - RNA-seq

In this study we use expression data from breast cancer tumors to define immune clusters in breast cancer. Immune clusters have gradual levels of immune infiltration. In the intermediate immune infiltration cluster, we found a worse prognosis which is independent of known clinicopathological features. We also found the immune clusters associated with treatment response. Further using gene expression data and deconvolution algorithms to dissect the immune contexture of the clusters.

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RNA-seq fastq files from paired-end RNA-seq

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 OSBREAC 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: OSBREAC 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. OSBREAC: Oslo Breast Cancer Research Consortium (www.osbreac.no) 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 on request from one of the Data Producers to provide reasonable assistant so that the Data Producer in question is able to follow up the Research Participants fundamental rights in accordance to applicable privacy law. 4. The User Institution agrees to protect the confidentiality of Research Participants in any research papers or publications that they prepare by taking all reasonable and necessary steps to limit the possibility of identification. 5. 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. 6. 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. 7. 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. 8. 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. 9. 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. 10. 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. 11. 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 ). 12. 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. 13. The User Institution will notify OSBREAC within 30 days of any changes or departures of Authorised Personnel. 14. The User Institution will notify OSBREAC prior to any significant changes to the protocol for the Project. 15. The User Institution will notify OSBREAC as soon as it becomes aware of a breach of the terms or conditions of this agreement. 16. OSBREAC 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. 17. 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 OSBREAC. 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. 18. 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. 19. 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.

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
EGAS00001003631 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
EGAF00002452646 fastq.gz 992.4 MB
EGAF00002452647 fastq.gz 989.5 MB
EGAF00002452648 fastq.gz 1.0 GB
EGAF00002452649 fastq.gz 1.0 GB
EGAF00002452650 fastq.gz 1.2 GB
EGAF00002452651 fastq.gz 1.2 GB
EGAF00002452652 fastq.gz 1.3 GB
EGAF00002452653 fastq.gz 1.3 GB
EGAF00002452654 fastq.gz 1.2 GB
EGAF00002452655 fastq.gz 1.2 GB
EGAF00002452656 fastq.gz 1.2 GB
EGAF00002452657 fastq.gz 1.2 GB
EGAF00002452658 fastq.gz 1.2 GB
EGAF00002452659 fastq.gz 1.2 GB
EGAF00002452660 fastq.gz 1.4 GB
EGAF00002452661 fastq.gz 1.4 GB
EGAF00002452662 fastq.gz 939.4 MB
EGAF00002452663 fastq.gz 928.5 MB
EGAF00002452664 fastq.gz 1.1 GB
EGAF00002452665 fastq.gz 1.1 GB
EGAF00002452666 fastq.gz 1.6 GB
EGAF00002452667 fastq.gz 1.6 GB
EGAF00002452668 fastq.gz 198.1 MB
EGAF00002452669 fastq.gz 191.2 MB
EGAF00002452670 fastq.gz 989.9 MB
EGAF00002452671 fastq.gz 977.4 MB
EGAF00002452672 fastq.gz 1.4 GB
EGAF00002452673 fastq.gz 1.4 GB
EGAF00002452674 fastq.gz 796.2 MB
EGAF00002452675 fastq.gz 786.3 MB
EGAF00002452676 fastq.gz 617.3 MB
EGAF00002452677 fastq.gz 611.0 MB
EGAF00002452678 fastq.gz 906.1 MB
EGAF00002452679 fastq.gz 899.3 MB
EGAF00002452680 fastq.gz 822.3 MB
EGAF00002452681 fastq.gz 815.1 MB
EGAF00002452682 fastq.gz 1.3 GB
EGAF00002452683 fastq.gz 1.3 GB
EGAF00002452684 fastq.gz 1.2 GB
EGAF00002452685 fastq.gz 1.2 GB
EGAF00002452686 fastq.gz 1.1 GB
EGAF00002452687 fastq.gz 1.1 GB
EGAF00002452688 fastq.gz 1.5 GB
EGAF00002452689 fastq.gz 1.5 GB
EGAF00002452690 fastq.gz 1.3 GB
EGAF00002452691 fastq.gz 1.3 GB
EGAF00002452692 fastq.gz 910.4 MB
EGAF00002452693 fastq.gz 910.9 MB
EGAF00002452694 fastq.gz 1.4 GB
EGAF00002452695 fastq.gz 1.4 GB
EGAF00002452696 fastq.gz 1.5 GB
EGAF00002452697 fastq.gz 1.5 GB
EGAF00002452698 fastq.gz 1.1 GB
EGAF00002452699 fastq.gz 1.1 GB
EGAF00002452700 fastq.gz 1.2 GB
EGAF00002452701 fastq.gz 1.2 GB
EGAF00002452702 fastq.gz 1.2 GB
EGAF00002452703 fastq.gz 1.3 GB
EGAF00002452704 fastq.gz 1.3 GB
EGAF00002452705 fastq.gz 1.2 GB
EGAF00002452706 fastq.gz 1.2 GB
EGAF00002452707 fastq.gz 1.2 GB
EGAF00002452708 fastq.gz 1.3 GB
EGAF00002452709 fastq.gz 1.3 GB
EGAF00002452710 fastq.gz 1.3 GB
EGAF00002452711 fastq.gz 1.3 GB
EGAF00002452712 fastq.gz 1.1 GB
EGAF00002452713 fastq.gz 1.1 GB
EGAF00002452714 fastq.gz 1.2 GB
EGAF00002452715 fastq.gz 1.2 GB
EGAF00002452716 fastq.gz 1.1 GB
EGAF00002452717 fastq.gz 1.1 GB
EGAF00002452718 fastq.gz 1.3 GB
EGAF00002452719 fastq.gz 1.3 GB
EGAF00002452720 fastq.gz 1.2 GB
EGAF00002452721 fastq.gz 1.2 GB
EGAF00002452722 fastq.gz 1.4 GB
EGAF00002452723 fastq.gz 1.4 GB
EGAF00002452724 fastq.gz 834.0 MB
EGAF00002452725 fastq.gz 820.2 MB
EGAF00002452726 fastq.gz 1.2 GB
EGAF00002452727 fastq.gz 1.1 GB
EGAF00002452728 fastq.gz 1.0 GB
EGAF00002452729 fastq.gz 1.0 GB
EGAF00002452730 fastq.gz 971.6 MB
EGAF00002452731 fastq.gz 966.6 MB
EGAF00002452732 fastq.gz 1.1 GB
EGAF00002452733 fastq.gz 1.1 GB
EGAF00002452734 fastq.gz 1.1 GB
EGAF00002452735 fastq.gz 1.1 GB
EGAF00002452736 fastq.gz 1.1 GB
EGAF00002452737 fastq.gz 1.1 GB
EGAF00002452738 fastq.gz 1.0 GB
EGAF00002452739 fastq.gz 1.0 GB
EGAF00002452740 fastq.gz 1.0 GB
EGAF00002452741 fastq.gz 1.0 GB
EGAF00002452742 fastq.gz 1.1 GB
EGAF00002452743 fastq.gz 1.1 GB
EGAF00002452744 fastq.gz 979.1 MB
EGAF00002452745 fastq.gz 979.4 MB
EGAF00002452746 fastq.gz 1.1 GB
EGAF00002452747 fastq.gz 1.1 GB
EGAF00002452748 fastq.gz 1.2 GB
EGAF00002452749 fastq.gz 1.2 GB
EGAF00002452750 fastq.gz 1.1 GB
EGAF00002452751 fastq.gz 1.1 GB
EGAF00002452752 fastq.gz 1.0 GB
EGAF00002452753 fastq.gz 1.0 GB
EGAF00002452754 fastq.gz 1.2 GB
EGAF00002452755 fastq.gz 1.1 GB
EGAF00002452756 fastq.gz 1.1 GB
EGAF00002452757 fastq.gz 1.1 GB
EGAF00002452758 fastq.gz 1.0 GB
EGAF00002452759 fastq.gz 1.0 GB
EGAF00002452760 fastq.gz 898.0 MB
EGAF00002452761 fastq.gz 895.0 MB
EGAF00002452762 fastq.gz 979.1 MB
EGAF00002452763 fastq.gz 984.1 MB
EGAF00002452764 fastq.gz 1.1 GB
EGAF00002452765 fastq.gz 1.1 GB
EGAF00002452766 fastq.gz 1.1 GB
EGAF00002452767 fastq.gz 1.1 GB
EGAF00002452768 fastq.gz 1.1 GB
EGAF00002452769 fastq.gz 1.1 GB
EGAF00002452770 fastq.gz 1.1 GB
EGAF00002452771 fastq.gz 1.1 GB
EGAF00002452772 fastq.gz 1.1 GB
EGAF00002452773 fastq.gz 1.1 GB
EGAF00002452774 fastq.gz 1.0 GB
EGAF00002452775 fastq.gz 1.0 GB
EGAF00002452776 fastq.gz 1.2 GB
EGAF00002452777 fastq.gz 1.2 GB
EGAF00002452778 fastq.gz 658.6 MB
EGAF00002452779 fastq.gz 657.3 MB
EGAF00002452780 fastq.gz 1.3 GB
EGAF00002452781 fastq.gz 1.3 GB
EGAF00002452782 fastq.gz 1.3 GB
EGAF00002452783 fastq.gz 1.3 GB
EGAF00002452784 fastq.gz 1.3 GB
EGAF00002452785 fastq.gz 1.3 GB
EGAF00002452786 fastq.gz 1.1 GB
EGAF00002452787 fastq.gz 1.1 GB
EGAF00002452788 fastq.gz 1.2 GB
EGAF00002452789 fastq.gz 1.2 GB
EGAF00002452790 fastq.gz 1.3 GB
EGAF00002452791 fastq.gz 1.3 GB
EGAF00002452792 fastq.gz 1.1 GB
EGAF00002452793 fastq.gz 1.1 GB
EGAF00002452794 fastq.gz 1.2 GB
EGAF00002452795 fastq.gz 1.2 GB
EGAF00002452796 fastq.gz 1.0 GB
EGAF00002452797 fastq.gz 1.0 GB
EGAF00002452798 fastq.gz 1.2 GB
EGAF00002452799 fastq.gz 1.2 GB
EGAF00002452800 fastq.gz 1.1 GB
EGAF00002452801 fastq.gz 1.1 GB
EGAF00002452802 fastq.gz 1.2 GB
EGAF00002452803 fastq.gz 1.2 GB
EGAF00002452804 fastq.gz 1.2 GB
EGAF00002452805 fastq.gz 1.2 GB
EGAF00002452806 fastq.gz 1.2 GB
EGAF00002452807 fastq.gz 1.2 GB
EGAF00002452808 fastq.gz 1.1 GB
EGAF00002452809 fastq.gz 1.1 GB
EGAF00002452810 fastq.gz 1.6 GB
EGAF00002452811 fastq.gz 1.6 GB
EGAF00002452812 fastq.gz 1.3 GB
EGAF00002452813 fastq.gz 1.3 GB
EGAF00002452814 fastq.gz 1.2 GB
EGAF00002452815 fastq.gz 1.2 GB
EGAF00002452816 fastq.gz 1.2 GB
EGAF00002452817 fastq.gz 1.2 GB
EGAF00002452818 fastq.gz 1.1 GB
EGAF00002452819 fastq.gz 1.1 GB
EGAF00002452820 fastq.gz 1.4 GB
EGAF00002452821 fastq.gz 1.4 GB
EGAF00002452822 fastq.gz 1.4 GB
EGAF00002452823 fastq.gz 1.4 GB
EGAF00002452824 fastq.gz 1.5 GB
EGAF00002452825 fastq.gz 1.5 GB
EGAF00002452826 fastq.gz 1.3 GB
EGAF00002452827 fastq.gz 1.3 GB
EGAF00002452828 fastq.gz 998.2 MB
EGAF00002452829 fastq.gz 999.5 MB
EGAF00002452830 fastq.gz 1.1 GB
EGAF00002452831 fastq.gz 1.1 GB
EGAF00002452832 fastq.gz 1.2 GB
EGAF00002452833 fastq.gz 1.2 GB
EGAF00002452834 fastq.gz 1.0 GB
EGAF00002452835 fastq.gz 1.0 GB
EGAF00002452836 fastq.gz 1.3 GB
EGAF00002452837 fastq.gz 1.3 GB
EGAF00002452838 fastq.gz 1.2 GB
EGAF00002452839 fastq.gz 1.1 GB
194 Files (222.2 GB)