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Whole-genome enzymatic DNA methylation sequencing and single-cell RNA sequencing data from nasal cells of COVID-19 patients

Nasal swabs were collected from COVID-19 patients during the acute phase of infection as well as 3 and 12-months post-infection. Cells isolated from nasal swabs were subjected to whole-genome enzymatic DNA methylation sequencing (n=33) and scRNA-seq (n=24). For n=12 former COVID-19 pateints, follow-up samples were collected at 3 and 12 months post-infection and subjected to scRNA-seq.

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Data access committee for the study "Whole-genome enzymatic DNA methylation sequencing and single-cell RNA sequencing data from nasal cells of COVID-19 patients"

Data Transfer Agreement between Charité - Universitätsmedizin Berlin Charitéplatz 1, 10117 Berlin Germany –hereinafter: „CHARITÉ" – [INSERT INSTITUTION DETAILS full legal name and address] –hereinafter: „RECIPIENT" – – individually referred to as "PARTY" and/or together referred to as "PARTIES" – Preamble This Data Transfer Agreement governs the terms on which access will be granted to the genotype data generated by CHARITÉ. 1.Definitions "Data" means all and any human genetic data obtained by the RECIPIENT from CHARITÉ. "Data Subject" means a person, to whom Data refers and who has been informed of the purpose for which the Data is held and has given her/his consent thereto. "Intellectual Property" means (i) patents, designs, trade marks and trade names (whether registered or unregistered), copyright and related rights, database rights, know-how and confidential information; (ii) all other intellectual property rights and similar or equivalent rights anywhere in the world which currently exist or are recognised in the future; and (iii) applications, extensions and renewals in relation to any such rights. "Publications" mean, without limitation, articles published in print journals, electronic journals, reviews, books, posters and other written and verbal presentation of research. "Registered User" means a researcher (or an individual conducting research under the supervision of a researcher) that is employed by the RECIPIENT and is bound by confidentiality and non-use obligations in respect of Data and who has signed this Agreement and has received acknowledgement of its acceptance. For the avoidance of doubt, "Registered User" may also include students, visiting academics, contractors, sub-contractors or independent consultants provided that any such individual is bound by confidentiality and non-use obligations no less onerous then those binding the RECIPIENT's employees. 2. Obligations of the RECIPIENT 2.1 Confidentiality The RECIPIENT agrees to preserve, at all times, the confidentiality of Data pertaining to identifiable Data Subjects. In particular, the RECIPIENT undertakes not to use, or attempt to use the Data to deliberately compromise or otherwise infringe the confidentiality of information on Data Subjects and their right to privacy. 2.2 Data Protection 2.2.1 The RECIPIENT agrees to use the Data solely for the approved purpose and project described in the RECIPIENT's application (Annex 1); use of the Data for a new purpose or project will require a new application and approval. 2.2.2 Data shall not be used for commercial purposes (e.g. diagnostic services). 2.2.3 The RECIPIENT, and her/his Registered Users, shall comply with the obligations contained in the applicable German and EU data protection laws and regulations as amended from time to time. 2.2.4 The RECIPIENT agrees that before they give any Registered User access to Data, they shall first show the Registered User a copy of this Agreement and shall inform the Registered User that he or she must comply with the obligations contained in this Agreement and sign up to the provisions of this Agreement in the form set out at the end of this Agreement (Annex 2). The RECIPIENT shall provide CHARITÉ with a copy of the Registered User's acceptance form within ten days of the date of acceptance by the Registered User. 2.2.5 The RECIPIENT agrees not to transfer or disclose the Data, in whole or in part, or any identifiable material derived from the Data, to others, except Registered Users. Should the RECIPIENT wish to share the Data with a collaborator out of the same institution, the third party must make a separate application for access to the Data. 2.2.6 The RECIPIENT agrees that she/he, and her/his Registered Users, shall not analyse or make any use of the Data in such a way that has the potential to: (i) lead to the re-identification of any Data Subject; or (ii) compromise the anonymity of any Data Subject in any way. 2.2.7 CHARITÉ reserves the right to request and inspect data security and management documentation to ensure the adequacy of data protection measures in countries that have no national laws comparable to that pertaining in the European Economic Area (EEA). 2.3 Data Security 2.3.1 The RECIPIENT agrees that she/he shall take all reasonable security precautions to keep the Data safe, such precautions to be no less onerous than in the applicable German and EU data protection laws and regulations. 2.3.2 The RECIPIENT shall adhere to the principle of IT-Security as set forth in Annex 3 hereto. 3. Provisions of cooperation 3.1 Errors The RECIPIENT agrees to notify CHARITÉ of any errors detected in the Data without undue delay. 3.2 Reissue of data The RECIPIENT accepts that CHARITÉ will reissue Data from time to time, with suitable versioning. If Data is reissued at the request of the Data Subject and/or as the result of other ethical scrutiny, the RECIPIENT agrees to destroy all earlier versions of the Data without undue delay once he has received such information. 3.3 Intellectual property 3.3.1 The RECIPIENT recognises that nothing in this Agreement shall operate to transfer to the RECIPIENT any intellectual property rights in or relating to the Data. 3.3.2 The RECIPIENT does not have the right to sublicense the Data. The RECEPIENT shall inform CHARITÉ about any third party requests for the Data. 3.3.3 The RECIPIENT shall have the right to develop intellectual property based on comparison with their own data. 3.3.4 CHARITÉ has no knowledge of any conflicting property rights of third parties regarding the provided Data. If CHARITÉ learns of potential conflicting property rights of third parties, CHARITÉ shall inform the RECIPIENT; however, no liability can be assumed for this. 3.4 Publications 3.4.1 The RECIPIENT agrees to acknowledge in any RECIPIENT's work based in whole or part on the Data, any publications which encompass and from which Data derive, the respective version of the Data obtained, and the role of CHARITÉ. The RECIPIENT is also entitled to release publications and, in doing so, agrees to acknowledge any of CHARITÉ's work based in whole or part on the Data in its publication. 3.4.2 The RECIPIENT will also declare in any such work that CHARITÉ and its employees bear no responsibility for the further analysis or interpretation of the Data by the RECIPIENT. 3.5 Liability 3.5.1 The RECIPIENT accepts that CHARITÉ, the original data creators, depositors or copyright holders, or the funders of the Data or any part of the Data supplied: (i) bear no legal responsibility for the accuracy or comprehensiveness of the Data; and (ii) accept no liability for indirect, consequential, or incidental, damages or losses arising rom use of the Data, or from the unavailability of, or break in access to, the Data for whatever reason, except for damages caused intentionally or by gross negligence. 3.5.2 Nothing in this Agreement limits or excludes either Party's liability for (i) product liability claims, (ii) death or personal injury resulting from negligence or any fraud or (iii) or in case of breaches of so called "material contractual obligations (Kardinalpflichten)". Material contractual obligations (Kardinalpflichten) are obligations which principally enable the fulfilment of the proper enforcement of the contract and on which the contractual partner can trust and is allowed to trust for compliance (iiii) for any sort of other liability which by law cannot be limited or excluded according to applicable law. 4. General provisions 4.1 Termination of Agreement 4.1.1 This Agreement shall expire automatically three years after its signature by both PARTIES. 4.1.2 This Agreement will terminate immediately upon any breach of the provisions of this Agreement by the RECIPIENT. 4.1.3 The RECIPIENT accepts that the changing ethical framework of human genetic research may lead to: (i) alteration to the provisions of this Agreement, in which case the RECIPIENT may accept such alterations or terminate this Agreement; or (ii) the withdrawal of this Agreement in extreme circumstances. 4.1.4 The notification of either PARTY to terminate this Agreement shall be made in writing with 4 weeks' notice. 4.1.5 In the event that this Agreement is expired or terminated in accordance with this Clause 4.1 the RECIPIENT shall destroy all Data at the direction of CHARITÉ. This shall not apply to the extent that Data is saved in automatic back-up systems for which destruction shall follow the regular process of such back-up system, however, such Data shall be eliminated within a period of 90 days after the date of termination. Upon request of CHARITÉ, the RECIPIENT will certify the destruction of the Data. 4.2 Applicable Law 4.2.1 This Agreement shall be governed, construed and interpreted in accordance with the substantive laws of Germany. This Agreement shall be in the English language and the English version of this Agreement shall be deemed the official and governing instrument, notwithstanding any translations thereof. 4.2.2 The PARTIES agree to submit to the exclusive jurisdiction of the courts of Berlin, Germany, as regards any disputes, claims or matter arising under this Agreement. Annexes Annex 1 Application for Access to Genotype Data Annex 2 Declaration of commitment Annex 3 Data Security SIGNATURES for CHARITÉ ______________________ ______________________ Place, date, Anne Großkopff, Business Director Faculty for RECIPIENT ______________________ Place, date, _____________________ [Name ... ] Annex 1 Application for Access to Genotype Data Name of RECIPIENT and registered USERS, including affiliations and contact details. Enter the primary correspondence email address you would like to use: Please ensure that a full postal and email address is included for the RECIPIENT and each registered USER. Title of Project (in less than 30 words) Data Request Research Question Please provide a clear description of the project and its specific aims in no more than 750 words. This should include specific details of what you plan to do with the data and include key references. Feasibility Please describe fully your experience and expertise, and that of your collaborators, and how this will be applied to the proposed study. Please send completed forms to: Charité - Universitätsmedizin Berlin BIH Digital Health Center, Molecular Epidemiology Unit Dr. rer. nat. Saskia Trump Kapelle-Ufer 2 10117 Berlin Germany Email: saskia.trump@bih-charite.de Annex 2 Declaration of Commitment I, __________________________________, declare that I will comply with the requirements of the Data Transfer Agreement as agreed upon between CHARITÉ and the RECIPIENT, including but not limited to the requirements of the applicable data protection regulations. With my signature I confirm the receipt of a copy of this agreement. ______________________ ______________________ Place, date, name Please send signed form to: Charité - Universitätsmedizin Berlin BIH Digital Health Center, Molecular Epidemiology Unit Dr. rer. nat. Saskia Trump Kapelle-Ufer 2 10117 Berlin Germany Email: saskia.trump@bih-charite.de Annex 3 Principle of IT-Security An appropriate level of data protection shall be ensured through appropriate technical and organisational measures: Guarantee of confidentiality Admission control No unauthorised access to data processing equipment, e.g: magnetic or chip cards, keys, electric door openers, plant security or gatekeepers, alarm systems, video systems Access control No unauthorized system use, e.g: (secure) passwords, automatic locking mechanisms, two-factor authentication, encryption of data carriers No unauthorized reading, copying, modification or removal within the system, e.g: authorization concepts and need-based access rights, logging of accesses Guarantee of integrity Transmission control No unauthorized reading, copying, modification or removal during electronic transmission or transport, e.g: encryption, Virtual Private Networks (VPN), electronic signature Input control Determination whether and by whom personal data have been entered, modified or removed from data processing systems, e.g: logging, document management Guarantee of the availability and resilience of the system Availability control Protection against accidental or deliberate destruction or loss, e.g: Backup strategy (online/offline; on-site/off-site), uninterruptible power supply (UPS), virus protection, firewall, reporting channels and emergency plans Rapid recoverability Procedures for regular review, assessment and evaluation Data protection management Incident response management Privacy friendly default settings The implementation shall take into account the state of the art, implementation costs and the nature, scale and purposes of the processing, as well as the varying degrees of probability and seriousness of the risk to the rights and freedoms of natural persons. The technical and organisational measures are subject to technical progress and further development.

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
EGAS50000000273 Epigenetics

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
EGAF50000094687 fastq.gz 2.8 GB
EGAF50000094688 fastq.gz 2.7 GB
EGAF50000094689 fastq.gz 6.5 GB
EGAF50000094690 fastq.gz 4.9 GB
EGAF50000094691 fastq.gz 1.9 GB
EGAF50000094692 fastq.gz 5.0 GB
EGAF50000094693 fastq.gz 4.8 GB
EGAF50000094694 fastq.gz 2.9 GB
EGAF50000094695 fastq.gz 4.5 GB
EGAF50000094696 fastq.gz 2.9 GB
EGAF50000094697 fastq.gz 7.8 GB
EGAF50000094698 fastq.gz 7.7 GB
EGAF50000094699 fastq.gz 3.4 GB
EGAF50000094700 fastq.gz 1.8 GB
EGAF50000094701 fastq.gz 1.9 GB
EGAF50000094702 fastq.gz 1.6 GB
EGAF50000094703 fastq.gz 1.7 GB
EGAF50000094704 fastq.gz 3.7 GB
EGAF50000094705 fastq.gz 3.9 GB
EGAF50000094706 fastq.gz 4.8 GB
EGAF50000094707 fastq.gz 10.2 GB
EGAF50000094708 fastq.gz 4.7 GB
EGAF50000094709 fastq.gz 3.3 GB
EGAF50000094710 fastq.gz 10.1 GB
EGAF50000094711 fastq.gz 3.4 GB
EGAF50000094712 fastq.gz 7.9 GB
EGAF50000094713 fastq.gz 7.8 GB
EGAF50000094714 fastq.gz 2.0 GB
EGAF50000094715 fastq.gz 4.5 GB
EGAF50000094716 fastq.gz 1.7 GB
EGAF50000094717 fastq.gz 8.2 GB
EGAF50000094718 fastq.gz 3.7 GB
EGAF50000094719 fastq.gz 3.6 GB
EGAF50000094720 fastq.gz 3.6 GB
EGAF50000094721 fastq.gz 3.7 GB
EGAF50000094722 fastq.gz 7.2 GB
EGAF50000094723 fastq.gz 7.4 GB
EGAF50000094724 fastq.gz 4.0 GB
EGAF50000094725 fastq.gz 8.5 GB
EGAF50000094726 fastq.gz 2.9 GB
EGAF50000094727 fastq.gz 6.5 GB
EGAF50000094728 fastq.gz 8.5 GB
EGAF50000094729 fastq.gz 8.4 GB
EGAF50000094730 fastq.gz 8.4 GB
EGAF50000094731 fastq.gz 5.7 GB
EGAF50000094732 fastq.gz 2.8 GB
EGAF50000094733 fastq.gz 2.7 GB
EGAF50000094734 fastq.gz 5.8 GB
EGAF50000094735 fastq.gz 5.7 GB
EGAF50000094736 fastq.gz 2.5 GB
EGAF50000094737 fastq.gz 5.5 GB
EGAF50000094738 fastq.gz 2.6 GB
EGAF50000094739 fastq.gz 5.7 GB
EGAF50000094740 fastq.gz 2.3 GB
EGAF50000094741 fastq.gz 2.4 GB
EGAF50000094742 fastq.gz 5.2 GB
EGAF50000094743 fastq.gz 2.0 GB
EGAF50000094744 fastq.gz 4.3 GB
EGAF50000094745 fastq.gz 7.8 GB
EGAF50000094746 fastq.gz 3.4 GB
EGAF50000094747 fastq.gz 7.7 GB
EGAF50000094748 fastq.gz 2.1 GB
EGAF50000094749 fastq.gz 2.2 GB
EGAF50000094750 fastq.gz 6.5 GB
EGAF50000094751 fastq.gz 6.4 GB
EGAF50000094752 fastq.gz 3.5 GB
EGAF50000094753 fastq.gz 3.4 GB
EGAF50000094754 fastq.gz 3.3 GB
EGAF50000094755 fastq.gz 4.1 GB
EGAF50000094756 fastq.gz 4.2 GB
EGAF50000094757 fastq.gz 3.4 GB
EGAF50000094758 fastq.gz 7.9 GB
EGAF50000094759 fastq.gz 7.9 GB
EGAF50000094760 fastq.gz 4.4 GB
EGAF50000094761 fastq.gz 12.3 GB
EGAF50000094762 fastq.gz 5.3 GB
EGAF50000094763 fastq.gz 12.2 GB
EGAF50000094764 tsv 826.3 MB
EGAF50000094765 fastq.gz 4.8 GB
EGAF50000094766 fastq.gz 1.8 GB
EGAF50000094767 fastq.gz 4.0 GB
EGAF50000094768 fastq.gz 9.6 GB
EGAF50000094769 fastq.gz 3.9 GB
EGAF50000094770 fastq.gz 4.2 GB
EGAF50000094771 fastq.gz 4.3 GB
EGAF50000094772 fastq.gz 4.3 GB
EGAF50000094773 fastq.gz 9.6 GB
EGAF50000094774 fastq.gz 3.0 GB
EGAF50000094775 fastq.gz 3.6 GB
EGAF50000094776 fastq.gz 3.6 GB
EGAF50000094777 fastq.gz 3.0 GB
EGAF50000094778 fastq.gz 6.6 GB
EGAF50000094779 fastq.gz 8.3 GB
EGAF50000094780 fastq.gz 3.7 GB
EGAF50000094781 fastq.gz 1.7 GB
EGAF50000094782 fastq.gz 4.0 GB
EGAF50000094783 fastq.gz 1.7 GB
EGAF50000094784 fastq.gz 1.9 GB
EGAF50000094785 fastq.gz 1.9 GB
EGAF50000094786 fastq.gz 4.2 GB
EGAF50000094787 fastq.gz 4.1 GB
EGAF50000094788 fastq.gz 4.5 GB
EGAF50000094789 fastq.gz 4.6 GB
EGAF50000094790 fastq.gz 10.1 GB
EGAF50000094791 fastq.gz 4.6 GB
EGAF50000094792 fastq.gz 10.2 GB
EGAF50000094793 fastq.gz 3.9 GB
EGAF50000094794 fastq.gz 3.8 GB
EGAF50000094795 fastq.gz 8.3 GB
EGAF50000094796 fastq.gz 8.2 GB
EGAF50000094797 fastq.gz 7.4 GB
EGAF50000094798 fastq.gz 3.9 GB
EGAF50000094799 fastq.gz 3.9 GB
EGAF50000094800 fastq.gz 3.7 GB
EGAF50000094801 fastq.gz 7.9 GB
EGAF50000094802 fastq.gz 5.3 GB
EGAF50000094803 fastq.gz 4.6 GB
EGAF50000094804 fastq.gz 10.3 GB
EGAF50000094805 fastq.gz 2.0 GB
EGAF50000094806 fastq.gz 5.2 GB
EGAF50000094807 fastq.gz 2.0 GB
EGAF50000094808 fastq.gz 2.0 GB
EGAF50000094809 fastq.gz 4.5 GB
EGAF50000094810 fastq.gz 4.4 GB
EGAF50000094811 fastq.gz 4.4 GB
EGAF50000094812 fastq.gz 2.0 GB
EGAF50000094813 fastq.gz 7.7 GB
EGAF50000094814 fastq.gz 7.5 GB
EGAF50000094815 fastq.gz 12.0 GB
EGAF50000094816 fastq.gz 12.1 GB
EGAF50000094817 fastq.gz 5.4 GB
EGAF50000094818 fastq.gz 2.1 GB
EGAF50000094819 fastq.gz 3.7 GB
EGAF50000094820 fastq.gz 7.7 GB
EGAF50000094821 fastq.gz 3.7 GB
EGAF50000094822 fastq.gz 6.6 GB
EGAF50000094823 fastq.gz 7.4 GB
EGAF50000094824 fastq.gz 5.6 GB
EGAF50000094825 fastq.gz 2.7 GB
EGAF50000094826 fastq.gz 10.3 GB
EGAF50000094827 fastq.gz 3.8 GB
EGAF50000094828 fastq.gz 8.1 GB
EGAF50000094829 fastq.gz 4.0 GB
EGAF50000094830 fastq.gz 8.4 GB
EGAF50000094831 fastq.gz 4.0 GB
EGAF50000094832 tsv 825.6 MB
EGAF50000094833 tsv 825.5 MB
EGAF50000094834 tsv 825.6 MB
EGAF50000094835 tsv 825.6 MB
EGAF50000094836 tsv 825.5 MB
EGAF50000094837 tsv 825.3 MB
EGAF50000094838 tsv 825.6 MB
EGAF50000094839 tsv 825.4 MB
EGAF50000094840 tsv 825.3 MB
EGAF50000094841 tsv 825.6 MB
EGAF50000094842 tsv 825.7 MB
EGAF50000094843 tsv 825.4 MB
EGAF50000094844 tsv 826.0 MB
EGAF50000094845 tsv 825.9 MB
EGAF50000094846 tsv 824.8 MB
EGAF50000094847 tsv 824.6 MB
EGAF50000094848 tsv 827.9 MB
EGAF50000094849 tsv 825.0 MB
EGAF50000094850 tsv 824.6 MB
EGAF50000094851 tsv 824.7 MB
EGAF50000094852 tsv 825.3 MB
EGAF50000094853 tsv 825.5 MB
EGAF50000094854 tsv 826.3 MB
EGAF50000094855 tsv 825.3 MB
EGAF50000094856 tsv 826.2 MB
EGAF50000094857 tsv 826.4 MB
EGAF50000094858 tsv 824.8 MB
EGAF50000094859 tsv 823.7 MB
EGAF50000094860 tsv 826.2 MB
EGAF50000094861 tsv 824.7 MB
EGAF50000094862 tsv 826.2 MB
EGAF50000094863 tsv 825.8 MB
177 Files (760.4 GB)