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16S sequencing of intestinal biopsies

Sequencing of V4 hypervariable region of 16S gene from microbiota present in intestinal biopsies of IBD patients

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Data Access Agreement for the 1000IBD Project

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 1000IBD, UMCG 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: 1000IBD, UMCG 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. 1000IBD, UMCG Dept. of Gastroenterology University Medical Center Groningen, University of Groningen P/O Box 30.001 9700 RB Groningen 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, the User Institution agrees 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 1000IBD, UMCG within 30 days of any changes or departures of Authorised Personnel. 13. The User Institution will notify 1000IBD, UMCG prior to any significant changes to the protocol for the Project. 14. The User Institution will notify 1000IBD, UMCG as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. 1000IBD, UMCG 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 1000IBD, UMCG. 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 Netherlands and shall be subject to the exclusive jurisdiction of the Dutch 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 1000IBD, UMCG 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: EGAS00001002702 Dataset files and description: 1. XXXX Description: Phenotype information on individuals in 1000IBD cohort, including gender, diagnosis, disease localization, extra-intestinal manifestations, and smoking status. 2. 16S microbiome data from feces 3. 16S microbiome data from biopsies 4. ImmunoChip genotyping data from germline DNA Name of project that created the dataset 1000IBD, UMCG Names of other data producers/collaborators Genomic Coordination Center, UMCG Specific limitations on areas of research Use of (part of) the 1000IBD dataset in any shape or form is limited to non-commercial biomedical research. The 1000IBD data cannot be used for biomedical research directly sponsored by a commercial entity (e.g. pharmaceutics), unless explicitly agreed otherwise with 1000IBD, UMCG. Minimum protection measures required Only persons involved in the project for which the 100IBD DAC has approved data use, should be allowed access to the data. Sharing of data beyond the original project group is not allowed under this DAA. 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), and an encrypted hard drive. If held on USB keys or other portable hard drives, the data must be encrypted. Data removal: After a project for which 1000IBD data is used has been published, the data has to be removed from all institutional compute systems, independent compute stations, laptops, external hard drives and USB keys within 6 months. 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 1000IBD, UMCG 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. 1000IBD, UMCG 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, unless 1000IBD, UMCG 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 1000IBD, UMCG.

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
EGAS00001002702 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
EGAF00001816759 fq.gz 1.7 MB
EGAF00001816760 fq.gz 1.4 MB
EGAF00001816761 fq.gz 487.9 kB
EGAF00001816762 fq.gz 931.9 kB
EGAF00001816763 fq.gz 2.5 MB
EGAF00001816764 fq.gz 4.1 MB
EGAF00001816765 fq.gz 3.2 MB
EGAF00001816766 fq.gz 2.3 MB
EGAF00001816775 fq.gz 2.9 MB
EGAF00001816776 fq.gz 1.5 MB
EGAF00001816777 fq.gz 419.9 kB
EGAF00001816778 fq.gz 624.8 kB
EGAF00001816779 fq.gz 3.5 MB
EGAF00001816780 fq.gz 2.9 MB
EGAF00001816781 fq.gz 2.5 MB
EGAF00001816782 fq.gz 1.3 MB
EGAF00001816783 fq.gz 3.2 MB
EGAF00001816784 fq.gz 2.2 MB
EGAF00001816785 fq.gz 3.3 MB
EGAF00001816786 fq.gz 3.9 MB
EGAF00001816787 fq.gz 1.8 MB
EGAF00001816788 fq.gz 2.2 MB
EGAF00001816789 fq.gz 2.1 MB
EGAF00001816790 fq.gz 1.8 MB
EGAF00001816791 fq.gz 2.1 MB
EGAF00001816792 fq.gz 308.0 kB
EGAF00001816793 fq.gz 1.9 MB
EGAF00001816794 fq.gz 2.0 MB
EGAF00001816795 fq.gz 2.5 MB
EGAF00001816817 fq.gz 2.2 MB
EGAF00001816818 fq.gz 1.8 MB
EGAF00001816819 fq.gz 1.7 MB
EGAF00001816820 fq.gz 1.6 MB
EGAF00001816821 fq.gz 1.6 MB
EGAF00001816822 fq.gz 778.2 kB
EGAF00001816823 fq.gz 4.0 MB
EGAF00001816824 fq.gz 2.2 MB
EGAF00001816825 fq.gz 2.2 MB
EGAF00001816826 fq.gz 866.8 kB
EGAF00001816827 fq.gz 2.2 MB
EGAF00001816828 fq.gz 1.5 MB
EGAF00001816829 fq.gz 2.0 MB
EGAF00001816830 fq.gz 1.8 MB
EGAF00001816831 fq.gz 1.7 MB
EGAF00001816832 fq.gz 2.1 MB
EGAF00001816833 fq.gz 3.1 MB
EGAF00001816834 fq.gz 1.9 MB
EGAF00001816835 fq.gz 2.9 MB
EGAF00001816836 fq.gz 1.4 MB
EGAF00001816837 fq.gz 2.3 MB
EGAF00001816859 fq.gz 742.5 kB
EGAF00001816860 fq.gz 1.6 MB
EGAF00001816861 fq.gz 544.0 kB
EGAF00001816862 fq.gz 2.6 MB
EGAF00001816863 fq.gz 2.9 MB
EGAF00001816864 fq.gz 4.4 MB
EGAF00001816865 fq.gz 3.2 MB
EGAF00001816866 fq.gz 2.3 MB
EGAF00001816867 fq.gz 1.7 MB
EGAF00001816868 fq.gz 2.0 MB
EGAF00001816869 fq.gz 3.0 MB
EGAF00001816870 fq.gz 1.2 MB
EGAF00001816871 fq.gz 2.0 MB
EGAF00001816872 fq.gz 1.2 MB
EGAF00001816873 fq.gz 379.7 kB
EGAF00001816874 fq.gz 2.1 MB
EGAF00001816875 fq.gz 3.2 MB
EGAF00001816876 fq.gz 1.9 MB
EGAF00001816877 fq.gz 2.0 MB
EGAF00001816878 fq.gz 1.1 MB
EGAF00001816879 fq.gz 503.6 kB
EGAF00001816901 fq.gz 1.2 MB
EGAF00001816902 fq.gz 3.2 MB
EGAF00001816903 fq.gz 1.9 MB
EGAF00001816904 fq.gz 3.0 MB
EGAF00001816905 fq.gz 2.4 MB
EGAF00001816906 fq.gz 66.2 kB
EGAF00001816907 fq.gz 2.0 MB
EGAF00001816908 fq.gz 3.1 MB
EGAF00001816909 fq.gz 768.8 kB
EGAF00001816910 fq.gz 1.6 MB
EGAF00001816911 fq.gz 457.3 kB
EGAF00001816912 fq.gz 625.6 kB
EGAF00001816913 fq.gz 2.2 MB
EGAF00001816914 fq.gz 2.4 MB
EGAF00001816915 fq.gz 1.4 MB
EGAF00001816916 fq.gz 2.5 MB
EGAF00001816917 fq.gz 5.4 MB
EGAF00001816918 fq.gz 1.6 MB
EGAF00001816919 fq.gz 277.9 kB
EGAF00001816920 fq.gz 475.2 kB
EGAF00001816921 fq.gz 3.6 MB
EGAF00001816943 fq.gz 3.0 MB
EGAF00001816944 fq.gz 500.1 kB
EGAF00001816945 fq.gz 1.5 MB
EGAF00001816946 fq.gz 147.8 kB
EGAF00001816947 fq.gz 2.6 MB
EGAF00001816948 fq.gz 1.9 MB
EGAF00001816949 fq.gz 454.9 kB
EGAF00001816950 fq.gz 2.4 MB
EGAF00001816951 fq.gz 2.2 MB
EGAF00001816952 fq.gz 549.7 kB
EGAF00001816953 fq.gz 2.3 MB
EGAF00001816954 fq.gz 2.5 MB
EGAF00001816955 fq.gz 3.2 MB
EGAF00001816956 fq.gz 2.8 MB
EGAF00001816957 fq.gz 429.5 kB
107 Files (210.4 MB)