RNA sequencing in primary human macrophages overexpressing ETS2

Data Access Agreement for access to raw RNAseq data (FASTQs) from ETS2 overexpression experiment in M0 macrophages. Controlled overexpression of ETS2 mRNA or control mRNA (an equivalent amount of mRNA encoding the reverse complement of ETS2 – thereby controlling for the quantity, length and purine/pyrimidine composition of the transfected RNA but with a transcript that would not be translated) was induced in resting, non-activated (M0) macrophages by transfecting predefined amounts of in vitro transcribed mRNA. To minimise non-specific activation due to the transfected RNA, in vitro transcription was performed using co-transcriptional capping (to minimise uncapped products), and incorporating modified, minimally immunogenic nucleotides (replacing uridine with N1-methyl-pseudouridine and cytidine with methylcytidine). After 18 hours, transfected cells were were activated with low dose LPS and harvested for RNA-sequencing 6 hours later. Raw data are provided as 100 bp paired-end Illumina reads from n = 8 donors.

GENOMIC 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 Crick 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. Crick: The Francis Crick Institute Limited, a registered charity in England and Wales (no. 1140062) and a company registered in England and Wales (no. 06885462), whose address is at 1 Midland Road, London, NW1 1AT Data: The managed access datasets to which the User Institution has requested access. Data Producers: The Crick and any 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. 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, and always in accordance with all applicable laws, regulations and ethical requirements, including without limitation applicable laws on data protection. 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. If the employment/ affiliation of any Authorised Personnel with the User Institution ends, or the Authorised Personnel’s professional responsibilities no longer require access to the Data, or the scope of required access changes, the User Institution shall ensure that such Authorised Personnel Data access is revoked or changed appropriately. If such access is not changed in a timely manner, the User Institution shall notify the Crick immediately. Should the User Institution wish to share these Data with an External Collaborator, the External Collaborator must complete and send to the Crick 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 publish in accordance with Appendix III. 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. Where Crick data is unpublished, the Crick retains the right of first publication of its Data (or any part of the Data) and the User Institution agrees to delay any publication until the earlier of one (1) year from the date of this agreement or the Crick primary publication. 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 applicable laws of the Data Producer. 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 Crick within 30 days of any changes or departures of Authorised Personnel. 13. The User Institution will notify the Crick prior to any significant changes to the protocol for the Project. 14. The User Institution will notify the Crick as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. The Crick 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 the Crick. 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 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 THE FRANCIS CRICK INSTITUTE LIMITED 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) EGADxxx This dataset consists of RNA sequencing data from an ETS2 overexpression experiment in M0 macrophages. Controlled overexpression of ETS2 mRNA or control mRNA (an equivalent amount of mRNA encoding the reverse complement of ETS2 – thereby controlling for the quantity, length and purine/pyrimidine composition of the transfected RNA but with a transcript that would not be translated) was induced in resting, non-activated (M0) macrophages by transfecting predefined amounts of in vitro transcribed mRNA. To minimise non-specific activation due to the transfected RNA, in vitro transcription was performed using co-transcriptional capping (to minimise uncapped products), and incorporating modified, minimally immunogenic nucleotides (replacing uridine with N1-methyl-pseudouridine and cytidine with methylcytidine). After 18 hours, transfected cells were were activated with low dose LPS and harvested for RNA-sequencing 6 hours later. Sequencing libraries were prepared from 10ng RNA using the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara) following the manufacturer’s instructions. The quality and molarity of all libraries was assessed using a BioAnalyzer 2100 and the libraries were sequenced on a NovaSeq6000. Raw data are provided as 100 bp paired-end Illumina reads from n = 8 donors. Name of project that created the dataset “Mechanisms of Autoimmunity: Genes, Pathways and Immunological Effects” REC 21/LO/0682 London Brent Research Ethics Committee Names of other data producers/collaborators Data custodian: Dr James Lee Format in which Data will be supplied Access through the European Genome-Phenome Archive (EGA). 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 screenlocks (set to lock after 5 min of inactivity). If held on USB keys or other portable hard drives, the data must be encrypted. The User Institution shall store the Data only in the original encrypted form from EGA. The User Institution agrees and warrants that Data shall only be decrypted when necessary and only during the performance of the Project. At the end of the Project, the User Institution shall delete any decrypted files, including additional copies, any computer records or files containing Data that have been created by the User Institution’s automatic archiving and back-up procedures. The User Institution agrees and warrants that Data shall not be accessed: a) outside the User Institution’s network, including non-User Institution email systems; b) using unauthorized devices, including personal devices; c) via mobile and wireless devices, and devices on networks with wireless access points. Data shall not be stored on any portable device (laptop, smartphone, etc.) unless absolutely necessary and always strongly encrypted, and the portable devices shall always have password protected logins and screen locks, set to lock after maximum five (5) minutes of inactivity. Data written to removable storage media shall be automatically encrypted without the User Institution intervention. 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 wants 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 The Data Producers 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. The Data Producers 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 12 months after these data were first made available on the relevant hosting database, unless the Data Producers have provided written consent to earlier submission. 7.1 The User Institution may only publish Data if: (a) the publication comprises only parts of the Data and not all of the Data; (b) it is not possible to establish the identity of any data subject from, or using, the Data contained in the publication; and (c) the publication complies with Clause 7.2. 7.2 The User Institution shall ensure that each work based in whole or part on the Data that is authored by an Authorised Personnel acknowledges the published paper from which the Data derives, the version of the Data, and the role of the Crick source project and its funders in its distribution in accordance with customary scientific and academic practice. Further, the User Institution shall ensure that any publication which contains, in any way, any of the patentable Intellectual Property shall be submitted to the Crick for review at least sixty (60) days prior to the intended publication. The Crick shall have thirty (30) days following receipt of the proposed publication to review such publication and determine, if in the Crick’s reasonable opinion, a delay of the publication is necessary in order to protect its Intellectual Property (such delay not to exceed a period of six (6) months from the date of the Crick’s notice to the Recipient pursuant to this clause). 7.3 Further, authors utilizing the Data for any permitted publication agree to discuss with Dr James Lee, the principal investigator, whether authorship is appropriate based on actual intellectual contribution made. Decisions regarding authorship will be determined in accordance with usual academic practice. Irrespective of authorship decisions, the Francis Crick Institute shall be acknowledged in a manner consistent with the usual conventions in the field of research involved. 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 the Crick.