Need Help?

Genomics of enteropathy-associated T cell lymphoma (EATL)

Whole exome sequencing of enteropathy-associated T cell lymphoma (EATL) tumors and paired normals, as well as RNA-sequencing of EATL tumors: including (1) 69 exome capture, paired-end Illumina Hiseq sequencing, BAM files from EATL tumor samples, (2) 36 exome capture, paired-end Illumina Hiseq sequencing, BAM files from EATL paired normal samples, and (3) 32 RNAseq, paired-end Illumina Hiseq sequencing, BAM files from EATL tumor samples.

Request Access

Data access agreement for EATL

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 DAC for Dave Lab, Duke University 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: DAC for Dave Lab, Duke University 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 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. ? 1. The User Institution agrees to only use these Data for the purpose of the Project (described in Appendix II) and only for Non-Profit 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 (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 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) (https://www.icgc.org/files/daco/NIH_BestPracticesLicensingGenomicInventions_2005_en.pdf ) in conformity with the Organization 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 DAC for Dave Lab, Duke University within 30 days of any changes or departures of Authorized Personnel. 13. The User Institution will notify DAC for Dave Lab, Duke University prior to any significant changes to the protocol for the Project. 14. The User Institution will notify DAC for Dave Lab, Duke University as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. DAC for Dave Lab, Duke University 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. 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 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 England and Wales and shall be subject to the exclusive jurisdiction of the English 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 DAC for Dave Lab, Duke University Signature:   Name:   Title:   Date:   APPENDIX I – DATASET DETAILS APPENDIX II ––PROJECT DETAILS APPENDIX III –– PUBLICATION POLICY ?APPENDIX I – DATASET DETAILS Dataset reference (EGA Study ID and Dataset Details) Study ID: EGAS00001001954 Study title: Genomics of enteropathy associated T cell lymphoma (EATL) Dataset ID: EGAD00001003284 Name of project that created the dataset Genomics of enteropathy associated T cell lymphoma (EATL) Names of other data producers/collaborators N/A Specific limitations on areas of research Non-profit use only. Commercial entities are forbidden from access to the data. 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 screen locks (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 DAC for Dave Lab, Duke University 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. DAC for Dave Lab, Duke University 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 3 months after these data were first made available on the relevant hosting database. 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., EGAS00001001954), and acknowledge its use in a form agreed by the User Institution with DAC for Dave Lab, Duke University.

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
EGAS00001001954 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
EGAF00001513987 bam 10.9 GB
EGAF00001513988 bam 15.6 GB
EGAF00001513989 bam 15.5 GB
EGAF00001513990 bam 12.2 GB
EGAF00001513991 bam 8.0 GB
EGAF00001513992 bam 15.0 GB
EGAF00001513993 bam 26.5 GB
EGAF00001513994 bam 1.5 GB
EGAF00001513995 bam 4.6 GB
EGAF00001513996 bam 5.1 GB
EGAF00001513997 bam 5.8 GB
EGAF00001513998 bam 26.1 GB
EGAF00001513999 bam 19.6 GB
EGAF00001514000 bam 807.0 MB
EGAF00001514001 bam 2.7 GB
EGAF00001514002 bam 1.2 GB
EGAF00001514003 bam 5.9 GB
EGAF00001514004 bam 6.5 GB
EGAF00001514005 bam 9.1 GB
EGAF00001514006 bam 11.1 GB
EGAF00001514007 bam 2.4 GB
EGAF00001514008 bam 5.6 GB
EGAF00001514009 bam 5.7 GB
EGAF00001514010 bam 13.2 GB
EGAF00001514011 bam 9.9 GB
EGAF00001514012 bam 11.4 GB
EGAF00001514013 bam 3.7 GB
EGAF00001514014 bam 9.9 GB
EGAF00001514015 bam 7.1 GB
EGAF00001514016 bam 7.4 GB
EGAF00001514017 bam 662.2 MB
EGAF00001514018 bam 4.3 GB
EGAF00001514019 bam 14.7 GB
EGAF00001514020 bam 13.7 GB
EGAF00001514021 bam 9.3 GB
EGAF00001514022 bam 11.0 GB
EGAF00001514023 bam 10.6 GB
EGAF00001514024 bam 8.5 GB
EGAF00001514025 bam 9.4 GB
EGAF00001514026 bam 17.0 GB
EGAF00001514027 bam 11.4 GB
EGAF00001514028 bam 13.6 GB
EGAF00001514029 bam 3.1 GB
EGAF00001514030 bam 11.5 GB
EGAF00001514031 bam 8.9 GB
EGAF00001514032 bam 9.8 GB
EGAF00001514033 bam 4.1 GB
EGAF00001514034 bam 3.9 GB
EGAF00001514035 bam 2.6 GB
EGAF00001514036 bam 6.6 GB
EGAF00001514037 bam 3.7 GB
EGAF00001514038 bam 3.3 GB
EGAF00001514039 bam 18.9 GB
EGAF00001514040 bam 4.8 GB
EGAF00001514041 bam 1.3 GB
EGAF00001514042 bam 6.3 GB
EGAF00001514043 bam 4.6 GB
EGAF00001514044 bam 2.5 GB
EGAF00001514045 bam 3.4 GB
EGAF00001514046 bam 10.2 GB
EGAF00001514047 bam 3.8 GB
EGAF00001514048 bam 3.9 GB
EGAF00001514049 bam 3.2 GB
EGAF00001514050 bam 9.1 GB
EGAF00001514051 bam 7.1 GB
EGAF00001514052 bam 1.8 GB
EGAF00001514053 bam 3.5 GB
EGAF00001514054 bam 13.9 GB
EGAF00001514055 bam 5.1 GB
EGAF00001514056 bam 10.2 GB
EGAF00001514057 bam 17.9 GB
EGAF00001514058 bam 3.0 GB
EGAF00001514059 bam 7.4 GB
EGAF00001514060 bam 1.6 GB
EGAF00001514061 bam 2.6 GB
EGAF00001514062 bam 810.4 MB
EGAF00001514063 bam 8.6 GB
EGAF00001514064 bam 23.7 GB
EGAF00001514065 bam 10.9 GB
EGAF00001514066 bam 7.3 GB
EGAF00001514067 bam 6.9 GB
EGAF00001514068 bam 9.8 GB
EGAF00001514069 bam 2.9 GB
EGAF00001514070 bam 264.4 MB
EGAF00001514071 bam 13.0 GB
EGAF00001514072 bam 5.7 GB
EGAF00001514073 bam 375.2 MB
EGAF00001514074 bam 953.1 MB
EGAF00001514075 bam 24.7 GB
EGAF00001514076 bam 3.2 GB
EGAF00001514077 bam 456.5 MB
EGAF00001514078 bam 9.4 GB
EGAF00001514079 bam 442.7 MB
EGAF00001514080 bam 9.4 GB
EGAF00001514081 bam 10.5 GB
EGAF00001514082 bam 5.9 GB
EGAF00001514083 bam 7.3 GB
EGAF00001514084 bam 15.9 GB
EGAF00001514085 bam 4.8 GB
EGAF00001514086 bam 100.1 MB
EGAF00001514087 bam 7.0 GB
EGAF00001514088 bam 1.2 GB
EGAF00001514089 bam 13.3 GB
EGAF00001514090 bam 11.4 GB
EGAF00001514091 bam 5.4 GB
EGAF00001514092 bam 143.0 MB
EGAF00001514093 bam 254.8 MB
EGAF00001514094 bam 840.8 MB
EGAF00001514095 bam 182.4 MB
EGAF00001514096 bam 903.2 MB
EGAF00001514097 bam 1.7 GB
EGAF00001514098 bam 560.1 MB
EGAF00001514099 bam 1.4 GB
EGAF00001514100 bam 1.6 GB
EGAF00001514101 bam 100.9 MB
EGAF00001514102 bam 1.1 GB
EGAF00001514103 bam 258.8 MB
EGAF00001514104 bam 818.8 MB
EGAF00001514105 bam 3.7 GB
EGAF00001514106 bam 774.0 MB
EGAF00001514107 bam 596.4 MB
EGAF00001514108 bam 59.8 MB
EGAF00001514109 bam 75.6 MB
EGAF00001514110 bam 220.7 MB
EGAF00001514111 bam 1.2 GB
EGAF00001514112 bam 736.3 MB
EGAF00001514113 bam 1.9 GB
EGAF00001514114 bam 102.5 MB
EGAF00001514115 bam 1.4 GB
EGAF00001514116 bam 498.4 MB
EGAF00001514117 bam 115.1 MB
EGAF00001514118 bam 107.9 MB
EGAF00001514119 bam 547.6 MB
EGAF00001514120 bam 204.8 MB
EGAF00001514121 bam 79.5 MB
EGAF00001514122 bam 89.1 MB
EGAF00001514123 bam 306.3 MB
137 Files (852.1 GB)