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As the EGA is co-managed by the EMBL-EBI and CRG, files could be located in the UK and/or Spain, as indicated by their respective flags.

Alternatively, files could be located in one of the international Federated EGA nodes, as indicated next to the node's flag.
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CRISPR_perturbations_IRF4_PRDM1_Bcells

CRISPR perturbations of IRF4, PRDM1, and AAVS1 (within PPP1R12C gene) in activated B cells

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B cell activation time course - Data Access Policy

DATA ACCESS AGREEMENT to access the data on which the results of a scientific research project carried out by Fondazione Human Tecnhopole are based, for the purpose of their verification 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. By entering into this agreement, the User Institution agrees to be bound by these terms and conditions. Definitions Authorised Personnel: The individuals at the User Institution who are granted access to the Data. This consists of the Users listed in Appendix II. Data: The managed access datasets to which the User Institution has requested and expressly obtained access. Data Producers: the organizations listed in Appendix I that collected the samples and/or generated any associated analyses of the Personal Data and that are responsible for the development, organization, and oversight of these Data. Research Participant: An individual whose data form part of these Data. User: The individual at the User Institution who will access the Data. User Institution: The Institution that has requested access to the Data. HUMAN TECHNOPOLE: Fondazione Human Technopole, tax code 97821360159, Viale Rita Levi-Montalcini, 1 - Area MIND – Cargo 6 - 20157 Milano, Italy. 1. The User Institution agrees to only use these Data for the purpose of verifying the results of the scientific research project described in Appendix I carried out by HUMAN TECHNOPOLE. 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 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 its own Authorised Personnel and not to transfer nor disclose the Data to any other individual within its organization nor any third party. 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 User Institution that may arise (whether directly or indirectly) in any way whatsoever from the User Institution’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 Data consist in genetic, phenotypic, health-related and other information regarding natural persons collected for / used within a scientific research project. Said Data are de-identified and do not include direct identifiers of said individuals. Regardless of the foregoing, the User Institution shall comply with any and all applicable rules and provisions under the Regulation (EU) 2016/679 (GDPR), as well as under any other applicable data protection laws and regulations, including those regarding the legal basis for data processing. For the avoidance of doubt, HUMAN TECHNOPOLE and any other Data Producer assume no liability for any possible violation of the abovementioned rules and provisions. Should the User Institution be based outside the European Union, the transfer of the Data could happen solely if the conditions under art. 44 – 50 of the GDPR are meet at HUMAN TECHNOPOLE’s sole discretion. The data are made accessible solely to verified and qualified research institutions, at HUMAN TECHNOPOLE’s sole discretion. 8. Omissis 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. Omissis 11. The User Institution agrees to destroy/discard the Data held, once it is no longer used for the purposes under this agreement. 12. The User Institution will notify HUMAN TECHNOPOLE within 30 days of any changes or departures of Authorised Personnel. 13. Omissis 14. The User Institution will notify HUMAN TECHNOPOLE as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. HUMAN TECHNOPOLE 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. As an example, this may include specific provisions relating to the Data required by Data Producers other than HUMAN TECHNOPOLE. 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 undertakes 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 Italy and shall be subject to the exclusive jurisdiction of the Court of Milan, Italy. Agreed for User Institution Signature: Name: Title: Date: User I confirm that I have read and understood this Agreement. Signature: Name: Title: Date: Agreed for HUMAN TECHNOPOLE Signature: Name: Title: Director of HUMAN TECHNOPOLE Date: APPENDIX I – DATASET DETAILS APPENDIX II – USER(S) APPENDIX I – DATASET DETAILS [to be completed by the data producer before passing to applicant] Dataset reference (EGA Study ID and Dataset Details) To investigate the gene programs involved in B cell activation and antibody switching, we performed scRNA-seq and BCR-seq of human naive and memory B cells at resting and one, three and six days following activation. We also knocked out IRF4 and PRDM1 and performed scRNA-seq. Finally, we assessed the clonal structure of B cells. Name of project that created the dataset Competing gene regulatory networks drive naive and memory B cell differentiation Names of other data producers/collaborators Dr Blagoje Soskic, Research Group Leader, Human Technopole, Milan Professor Luca Valenti, luca.valenti@policlinico.mi.it, Ospedale Maggiore Policlinico, Milan Specific limitations The Data are made available solely for the purposes of verifying the results of the scientific research project described in the present Appendix I carried out by HUMAN TECHNOPOLE. Minimum protection measures required Access Control: 1. Data can be held in unencrypted files on an institutional computer system if disk encryption is present, role base access control should be in place, for instance with Unix user group read/write access for one or more appropriate groups without having everyone accessing it 2. The device which manages access (e.g.: the storage cluster) must be behind a firewall, following the least privilege principle 3. Laptops holding these data should have password protected logins and screenlocks (set to lock after 5 min of inactivity) 4. If held on USB keys or other portable hard drives, the data must be encrypted (e.g.: using AES-256 algorithm). 5. Multi-Factor authentication must be used for granting access to genomic data handling systems Data Protection & Storage: 1. Data in transit should use at least TLSv1.2 , in case no encryption protocol is used, files should be encrypted using at least AES-256 or equivalent 2. Encrypted backups must be maintained, testing restoration regularly Monitoring & Incident Management: 1. Access to data must be logged for having appropriate accountability 2. Regular logs review must be done for detecting for anomalies 3. A documented incident response plan must be present Training & Awareness: Regular Data protection training should be delivered to all personnel handling genomic data APPENDIX II – USER(S) All Individuals shall have an account created at the EGA Name of Registered User Email Job Title

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
EGAS50000001468 Transcriptome Sequencing

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 Quality Report
Located in
i
EGAF50000508762 fastq.gz 73.6 MB
EGAF50000508763 fastq.gz 73.3 MB
EGAF50000508764 fastq.gz 75.8 MB
EGAF50000508765 fastq.gz 76.9 MB
EGAF50000508766 fastq.gz 79.1 MB
EGAF50000508767 fastq.gz 80.1 MB
EGAF50000508768 fastq.gz 113.7 MB
EGAF50000508769 fastq.gz 123.6 MB
EGAF50000508770 fastq.gz 112.5 MB
EGAF50000508771 fastq.gz 112.5 MB
EGAF50000508772 fastq.gz 124.2 MB
EGAF50000508773 fastq.gz 124.1 MB
EGAF50000508774 fastq.gz 125.0 MB
EGAF50000508775 fastq.gz 125.3 MB
EGAF50000508776 fastq.gz 128.8 MB
EGAF50000508777 fastq.gz 130.3 MB
EGAF50000508778 fastq.gz 130.0 MB
EGAF50000508779 fastq.gz 124.3 MB
EGAF50000508780 fastq.gz 143.1 MB
EGAF50000508781 fastq.gz 141.9 MB
EGAF50000508782 fastq.gz 126.6 MB
EGAF50000508783 fastq.gz 123.8 MB
EGAF50000508784 fastq.gz 205.8 MB
EGAF50000508785 fastq.gz 207.2 MB
EGAF50000508786 fastq.gz 127.9 MB
EGAF50000508787 fastq.gz 129.2 MB
EGAF50000508788 fastq.gz 196.7 MB
EGAF50000508789 fastq.gz 129.9 MB
EGAF50000508790 fastq.gz 222.2 MB
EGAF50000508791 fastq.gz 204.5 MB
EGAF50000508792 fastq.gz 143.1 MB
EGAF50000508793 fastq.gz 223.5 MB
EGAF50000508794 fastq.gz 222.6 MB
EGAF50000508795 fastq.gz 221.9 MB
EGAF50000508796 fastq.gz 226.9 MB
EGAF50000508797 fastq.gz 227.1 MB
EGAF50000508798 fastq.gz 229.4 MB
EGAF50000508799 fastq.gz 322.3 MB
EGAF50000508800 fastq.gz 319.2 MB
EGAF50000508801 fastq.gz 323.6 MB
EGAF50000508802 fastq.gz 329.1 MB
EGAF50000508803 fastq.gz 328.0 MB
EGAF50000508804 fastq.gz 398.6 MB
EGAF50000508805 fastq.gz 396.9 MB
EGAF50000508806 fastq.gz 399.1 MB
EGAF50000508807 fastq.gz 380.9 MB
EGAF50000508808 fastq.gz 383.9 MB
EGAF50000508809 fastq.gz 383.7 MB
EGAF50000508810 fastq.gz 381.7 MB
EGAF50000508811 fastq.gz 446.4 MB
EGAF50000508812 fastq.gz 444.1 MB
EGAF50000508813 fastq.gz 520.1 MB
EGAF50000508814 fastq.gz 440.1 MB
EGAF50000508815 fastq.gz 522.9 MB
EGAF50000508816 fastq.gz 515.8 MB
EGAF50000508817 fastq.gz 523.5 MB
EGAF50000508818 fastq.gz 634.3 MB
EGAF50000508819 fastq.gz 638.6 MB
EGAF50000508820 fastq.gz 769.5 MB
EGAF50000508821 fastq.gz 777.4 MB
EGAF50000508822 fastq.gz 766.6 MB
EGAF50000508823 fastq.gz 766.6 MB
EGAF50000508824 fastq.gz 1.1 GB
EGAF50000508825 fastq.gz 1.1 GB
EGAF50000508826 fastq.gz 1.1 GB
EGAF50000508827 fastq.gz 1.1 GB
EGAF50000508828 fastq.gz 1.0 GB
EGAF50000508829 fastq.gz 1.1 GB
EGAF50000508830 fastq.gz 1.1 GB
EGAF50000508831 fastq.gz 1.1 GB
EGAF50000508832 fastq.gz 1.0 GB
EGAF50000508833 fastq.gz 1.1 GB
EGAF50000508834 fastq.gz 1.1 GB
EGAF50000508835 fastq.gz 1.1 GB
EGAF50000508836 fastq.gz 1.1 GB
EGAF50000508837 fastq.gz 1.1 GB
EGAF50000508838 fastq.gz 1.1 GB
EGAF50000508839 fastq.gz 1.1 GB
EGAF50000508840 fastq.gz 1.1 GB
EGAF50000508841 fastq.gz 1.1 GB
EGAF50000508842 fastq.gz 1.1 GB
EGAF50000508843 fastq.gz 1.2 GB
EGAF50000508844 fastq.gz 1.2 GB
EGAF50000508845 fastq.gz 1.2 GB
EGAF50000508846 fastq.gz 1.2 GB
EGAF50000508847 fastq.gz 1.2 GB
EGAF50000508848 fastq.gz 1.2 GB
EGAF50000508849 fastq.gz 1.2 GB
EGAF50000508850 fastq.gz 1.4 GB
EGAF50000508851 fastq.gz 1.4 GB
EGAF50000508852 fastq.gz 1.4 GB
EGAF50000508853 fastq.gz 1.4 GB
EGAF50000508854 fastq.gz 1.5 GB
EGAF50000508855 fastq.gz 1.5 GB
EGAF50000508856 fastq.gz 1.5 GB
EGAF50000508857 fastq.gz 1.5 GB
EGAF50000508858 fastq.gz 1.5 GB
EGAF50000508859 fastq.gz 1.6 GB
EGAF50000508860 fastq.gz 1.5 GB
EGAF50000508861 fastq.gz 1.6 GB
EGAF50000508862 fastq.gz 1.6 GB
EGAF50000508863 fastq.gz 1.6 GB
EGAF50000508864 fastq.gz 1.6 GB
EGAF50000508867 fastq.gz 3.3 GB
EGAF50000508868 fastq.gz 3.4 GB
EGAF50000508869 fastq.gz 3.6 GB
EGAF50000508870 fastq.gz 3.6 GB
EGAF50000508871 fastq.gz 3.6 GB
EGAF50000508872 fastq.gz 3.6 GB
EGAF50000508873 fastq.gz 3.6 GB
EGAF50000508874 fastq.gz 3.6 GB
EGAF50000508878 fastq.gz 4.6 GB
EGAF50000508879 fastq.gz 4.6 GB
EGAF50000508880 fastq.gz 4.6 GB
EGAF50000508882 fastq.gz 5.2 GB
EGAF50000508883 fastq.gz 5.1 GB
EGAF50000508884 fastq.gz 5.2 GB
EGAF50000508885 fastq.gz 5.7 GB
EGAF50000508886 fastq.gz 5.7 GB
EGAF50000508887 fastq.gz 7.9 GB
EGAF50000508888 fastq.gz 8.0 GB
EGAF50000508889 fastq.gz 8.1 GB
EGAF50000508890 fastq.gz 8.0 GB
EGAF50000508891 fastq.gz 8.5 GB
EGAF50000508892 fastq.gz 8.5 GB
EGAF50000508893 fastq.gz 8.4 GB
EGAF50000508894 fastq.gz 8.4 GB
EGAF50000508895 fastq.gz 8.6 GB
EGAF50000508896 fastq.gz 8.5 GB
EGAF50000508897 fastq.gz 8.6 GB
EGAF50000508898 fastq.gz 11.3 GB
EGAF50000508899 fastq.gz 11.1 GB
EGAF50000508900 fastq.gz 12.6 GB
EGAF50000508901 fastq.gz 12.4 GB
EGAF50000508905 fastq.gz 11.2 GB
EGAF50000508906 fastq.gz 12.5 GB
EGAF50000508907 fastq.gz 12.3 GB
EGAF50000508908 fastq.gz 13.5 GB
EGAF50000508909 fastq.gz 13.7 GB
EGAF50000508914 fastq.gz 73.1 MB
EGAF50000508915 fastq.gz 80.5 MB
EGAF50000508916 fastq.gz 73.7 MB
EGAF50000508917 fastq.gz 81.2 MB
EGAF50000508918 fastq.gz 81.1 MB
EGAF50000508919 fastq.gz 76.4 MB
EGAF50000508920 fastq.gz 112.6 MB
EGAF50000508921 fastq.gz 76.5 MB
EGAF50000508922 fastq.gz 124.6 MB
EGAF50000508923 fastq.gz 197.8 MB
EGAF50000508924 fastq.gz 127.4 MB
EGAF50000508925 fastq.gz 140.2 MB
EGAF50000508926 fastq.gz 198.0 MB
EGAF50000508927 fastq.gz 196.3 MB
EGAF50000508928 fastq.gz 206.0 MB
EGAF50000508929 fastq.gz 403.1 MB
EGAF50000508930 fastq.gz 326.9 MB
EGAF50000508931 fastq.gz 320.7 MB
EGAF50000508932 fastq.gz 632.5 MB
EGAF50000508933 fastq.gz 657.8 MB
EGAF50000508934 fastq.gz 660.1 MB
EGAF50000508935 fastq.gz 671.6 MB
EGAF50000508936 fastq.gz 663.8 MB
EGAF50000508937 fastq.gz 1.1 GB
EGAF50000508938 fastq.gz 1.2 GB
EGAF50000508939 fastq.gz 1.5 GB
EGAF50000508940 fastq.gz 1.4 GB
EGAF50000508941 fastq.gz 1.6 GB
EGAF50000508942 fastq.gz 1.4 GB
EGAF50000508943 fastq.gz 1.6 GB
EGAF50000508944 fastq.gz 1.4 GB
EGAF50000508945 fastq.gz 1.4 GB
EGAF50000508946 fastq.gz 3.4 GB
EGAF50000508947 fastq.gz 4.5 GB
EGAF50000508948 fastq.gz 3.5 GB
EGAF50000508949 fastq.gz 3.4 GB
EGAF50000508954 fastq.gz 5.2 GB
EGAF50000508956 fastq.gz 11.0 GB
EGAF50000508959 fastq.gz 13.5 GB
EGAF50000508960 fastq.gz 80.6 MB
EGAF50000508961 fastq.gz 79.7 MB
EGAF50000508962 fastq.gz 80.7 MB
EGAF50000508963 fastq.gz 228.2 MB
EGAF50000508964 fastq.gz 325.5 MB
EGAF50000508965 fastq.gz 441.0 MB
EGAF50000508966 fastq.gz 648.3 MB
EGAF50000508967 fastq.gz 1.6 GB
EGAF50000508968 fastq.gz 1.6 GB
EGAF50000508969 fastq.gz 3.5 GB
EGAF50000508971 fastq.gz 5.6 GB
EGAF50000508972 fastq.gz 5.6 GB
EGAF50000508973 fastq.gz 8.4 GB
EGAF50000508974 fastq.gz 13.6 GB
192 Files (445.4 GB)