Determining genome-wide binding of ETS2 by CUT&RUN in primary human macrophages

This dataset consists of sequencing data from an ETS2 CUT&RUN experiment in primary inflammatory (TPP) macrophages (n = 2). Raw data are provided as 100 bp paired-end Illumina reads. Library preparation was performed according to a protocols.IO protocol (dx.doi.org/10.17504/protocols.io.bagaibse) using the NEBNext Ultra II DNA Library Prep Kit. Size selection was performed using AMPure XP beads (Beckman Coulter) and fragment sizes were determined using an Agilent 2100 Bioanalyzer (High Sensitivity DNA kit). Equimolar pools of indexed libraries were sequenced on an Illumina NovaSeq 6000 (100bp PE reads).

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. 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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. 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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 sequencing data from an ETS2 CUT&RUN experiment in primary inflammatory (TPP) macrophages (n = 2). Raw data are provided as 100 bp paired-end Illumina reads. Library preparation was performed according to a protocols.IO protocol (dx.doi.org/10.17504/protocols.io.bagaibse) using the NEBNext Ultra II DNA Library Prep Kit. Size selection was performed using AMPure XP beads (Beckman Coulter) and fragment sizes were determined using an Agilent 2100 Bioanalyzer (High Sensitivity DNA kit). Equimolar pools of indexed libraries were sequenced on an Illumina NovaSeq 6000 (100bp PE reads). 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.