Immune Cell Atlas of Environmental and Ancestral Diversity in Indonesia [scRNAseq]

DATA ACCESS POLICY Immune Cell Atlas of Environmental and Ancestral Diversity in Indonesia (Single-cell transcriptomic) 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 Immune Cell Atlas of Environmental and Ancestral Diversity in Indonesia committee 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 Immune Cell Atlas of Environmental and Ancestral Diversity in Indonesia committee and the collaborators listed in Appendix I are 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. Immune Cell Atlas of Environmental and Ancestral Diversity in Indonesia committee: The committee comprises the following members: Herawati Sudoyo, PhD, and Safarina G. Malik, PhD, from the Mochtar Riady Institute for Nanotechnology, Tangerang, Indonesia; Nicholas Banovich, PhD, from the Translational Genomics Research Institute (TGen), Arizona, USA; and Irene Gallego Romero, PhD, from St Vincent’s Institute for Medical Research, Melbourne, Australia. These members will retain their role, even if they relocate to other institutions. Membership of this committee may change over time. For legal purposes, the Indonesian committee members have precedence on all matters relating to this document. DATA ACCESS AGREEMENT 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 is not permitted to publish any findings, including in preprints or peer-reviewed journals, prior to the publication of the primary manuscript by the Immune Cell Atlas of Environmental and Ancestral Diversity in Indonesia committee. The User Institution will receive written notification from the committee upon the release of the formal publication of the Immune Cell Atlas of Environmental and Ancestral Diversity primary manuscript. 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 care 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 (https://www.wtccc.org.uk/wtccc/assets/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. 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 the Immune Cell Atlas of Environmental and Ancestral Diversity in Indonesia committee within 30 days of any changes or departures of Authorised Personnel. 14. The User Institution will notify the Immune Cell Atlas of Environmental and Ancestral Diversity in Indonesia committee prior to any significant changes to the protocol for the Project. 15. The User Institution will notify the Immune Cell Atlas of Environmental and Ancestral Diversity in Indonesia committee as soon as it becomes aware of a breach of the terms or conditions of this agreement. 16. The Immune Cell Atlas of Environmental and Ancestral Diversity in Indonesia committee 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 purposes 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 the Immune Cell Atlas of Environmental and Ancestral Diversity in Indonesia committee. 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 ensure that the Authorised Personnel comply with the terms of this agreement. 20. 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 Republic of Indonesia and shall be subject to the exclusive jurisdiction of Indonesian courts. AGREED FOR USER INSTITUTION Name: Title: Date: Signature: PRINCIPAL INVESTIGATOR I confirm that I have read and understood this Agreement Name: Title: Date: Signature: AGREED ON BEHALF OF THE IMMUNE CELL ATLAS OF ENVIRONMENTAL AND ANCESTRAL DIVERSITY IN INDONESIA COMMITTEE Name: Title: Date: Signature: =========================== APPENDIX I – DATASET DETAILS Single-cell immune profiles and multiomic sequences were collected to study the contributions of both genetic ancestry and environmental differences to immune cell variants. Indonesia has an extremely diverse population, with very different demographic histories and multiple genetic ancestries. To disentangle the contributions of environmental and lifestyle factors, this dataset reports single-cell RNA sequencing of 203 individuals from two different groups from each island: Balinese rural and urban, and Papuan highland and lowland. Contact person: Safarina G. Malik, PhD., Mochtar Riady Institute for Nanotechnology, Tangerang, Indonesia safarina.malik@mrinstitute.org The Immune Cell Atlas of Environmental and Ancestral Diversity in Indonesia project committee, which is a consortium comprising: Herawati Sudoyo, PhD., Mochtar Riady Institute for Nanotechnology, Tangerang, Indonesia Safarina G. Malik, PhD., Mochtar Riady Institute for Nanotechnology, Tangerang, Indonesia Nicholas Banovich, PhD., Translational Genomic Research, Arizona, USA Irene Gallego Romero, PhD., St Vincent’s Institute for Medical Research, Melbourne, Australia Names of other data producers/collaborators: St Vincent’s Institute for Medical Research, Melbourne, Australia: Muhamad Fachrul, PhD. Mochtar Riady Institute for Nanotechnology, Tangerang, Indonesia: Pradiptajati Kusuma, PhD. Massey University, New Zealand: Prof Murray P Cox Specific limitations on areas of research: The Users must be formally affiliated with an officially recognized Institution. The User can replicate existing studies published by the Immune Cell Atlas of Environmental and Ancestral Diversity in Indonesia research program, using similar techniques, approaches, and methods, to ensure that the published science is reproducible. Approval will be automatically granted for such use. The User cannot publicly release this data. All rights regarding data release remain with the Immune Cell Atlas of Environmental and Ancestral Diversity in Indonesia committee. The User cannot use Immune Cell Atlas of Environmental and Ancestral Diversity in Indonesia Project data for for-profit purposes. The User cannot undertake studies for personal use, such as family history research, or perform this research for others. The User cannot undertake studies of a medical or clinical nature without first seeking the approval of the Immune Cell Atlas of Environmental and Ancestral Diversity in Indonesia committee. Evidence of specific ethical approvals, including documentation from an Indonesian ethics board, will likely be necessary for approval to be granted. The User can undertake new studies, including studies focusing on the genetic and immune cell diversity, as long as this does not directly compete with ongoing studies by the Immune Cell Atlas of Environmental and Ancestral Diversity in Indonesia program. All research projects must be approved by the committee. Note that all uses of the data must have specific prior approval from the Immune Cell Atlas of Environmental and Ancestral Diversity in Indonesia committee. Evidence of ethical approvals, including documentation from an Indonesian ethics board, may be necessary for approval to be granted in some cases. Minimum protection measures required: Data can be held in unencrypted files on an institutional computer system behind a secure firewall, with Unix user group read/write access for one or more appropriate groups, but not Unix world read/write access. Laptops holding this data should have password-protected logins and screen locks (set to lock after 5 minutes of inactivity). If held on any kind of portable hard drive, the data must be encrypted. APPENDIX II – PROJECT DETAILS (to be completed by the Requestor) Brief, but detailed, 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 (repeat as needed) Name of Registered User: Job Title: Email: Supervisor: All Individuals that should have an account created at the EGA (repeat as needed) Name of Registered User: Job Title: Email: