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Finding structural variation and functional consequences from the Skin fibroblast at the single-cell level

In this study, we aimed to identify somatic structural variation of Skin fibroblast at the single-cell level and investigate its direct consequence on the nucleosome occupancy using scNOVA approach. For this purpose, we performed strand-specific single-cell sequencing of skin fibroblast sample from male donor.

Request Access

This is the data access policy for the Single cell multi-omics (scNOVA) group for Skin fibroblast

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 Single cell multi-omics group for somatic structural variation in human blood lineages 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: Single cell multi-omics group for somatic structural variation in human blood lineages and the 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. 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. 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. 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 follow the Fort Lauderdale Guidelines (http://www.wellcome.ac.uk/stellent/groups/corporatesite/@policy_communications/documents/web_document/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. 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 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 ). 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 Single cell multi-omics group for somatic structural variation in human blood lineages within 30 days of any changes or departures of Authorised Personnel. 13. The User Institution will notify Single cell multi-omics group for somatic structural variation in human blood lineages prior to any significant changes to the protocol for the Project. 14. The User Institution will notify Single cell multi-omics group for somatic structural variation in human blood lineages as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. Single cell multi-omics group for somatic structural variation in human blood lineages 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 Single cell multi-omics group for somatic structural variation in human blood lineages. 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 XXXXX Signature: Name: Title: Date: APPENDIX I – DATASET DETAILS APPENDIX II ––PROJECT DETAILS APPENDIX III –– PUBLICATION POLICY APPENDIX I – DATASET DETAILS (to be completed by the data producer before passing to applicant) Dataset reference (EGA Study ID and Dataset Details) Name of project that created the dataset Names of other data producers/collaborators Specific limitations on areas of research 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. 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 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 Single cell multi-omics group for somatic structural variation in human blood lineages 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. Single cell multi-omics group for somatic structural variation in human blood lineages 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 XX months after these data were first made available on the relevant hosting database, unless Single cell multi-omics group for somatic structural variation in human blood lineages has provided written consent to earlier submission. 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, and acknowledge its use in a form agreed by the User Institution with Single cell multi-omics group for somatic structural variation in human blood lineages.

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
EGAS00001006498 Other

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
EGAF00006785057 txt.gz 78.5 MB
EGAF00006785058 txt.gz 77.2 MB
EGAF00006785059 txt.gz 41.4 MB
EGAF00006785060 txt.gz 40.6 MB
EGAF00006785061 txt.gz 92.2 MB
EGAF00006785062 txt.gz 91.1 MB
EGAF00006785063 txt.gz 83.3 MB
EGAF00006785064 txt.gz 82.2 MB
EGAF00006785065 txt.gz 74.9 MB
EGAF00006785066 txt.gz 73.8 MB
EGAF00006785067 txt.gz 78.4 MB
EGAF00006785068 txt.gz 77.1 MB
EGAF00006785069 txt.gz 66.6 MB
EGAF00006785070 txt.gz 65.7 MB
EGAF00006785071 txt.gz 1.7 MB
EGAF00006785072 txt.gz 1.8 MB
EGAF00006785073 txt.gz 71.9 MB
EGAF00006785074 txt.gz 70.5 MB
EGAF00006785075 txt.gz 60.7 MB
EGAF00006785076 txt.gz 59.7 MB
EGAF00006807717 txt.gz 44.0 MB
EGAF00006807718 txt.gz 43.2 MB
EGAF00006807719 txt.gz 83.7 MB
EGAF00006807720 txt.gz 82.1 MB
EGAF00006807721 txt.gz 93.7 MB
EGAF00006807722 txt.gz 92.6 MB
EGAF00006807723 txt.gz 83.6 MB
EGAF00006807724 txt.gz 82.0 MB
EGAF00006807725 txt.gz 65.2 MB
EGAF00006807726 txt.gz 64.4 MB
EGAF00006807727 txt.gz 92.4 MB
EGAF00006807728 txt.gz 91.0 MB
EGAF00006807729 txt.gz 122.0 MB
EGAF00006807730 txt.gz 119.6 MB
EGAF00006807731 txt.gz 100.0 MB
EGAF00006807732 txt.gz 98.1 MB
EGAF00006807733 txt.gz 103.2 MB
EGAF00006807734 txt.gz 101.7 MB
EGAF00006807735 txt.gz 43.4 MB
EGAF00006807736 txt.gz 42.7 MB
EGAF00006807737 txt.gz 141.4 MB
EGAF00006807738 txt.gz 138.8 MB
EGAF00006807739 txt.gz 12.1 MB
EGAF00006807740 txt.gz 11.9 MB
EGAF00006807741 txt.gz 53.9 MB
EGAF00006807742 txt.gz 52.7 MB
EGAF00006807743 txt.gz 57.8 MB
EGAF00006807744 txt.gz 56.7 MB
EGAF00006807745 txt.gz 117.3 MB
EGAF00006807746 txt.gz 114.8 MB
EGAF00006807747 txt.gz 72.8 MB
EGAF00006807748 txt.gz 72.1 MB
EGAF00006807749 txt.gz 105.9 MB
EGAF00006807750 txt.gz 103.8 MB
EGAF00006807751 txt.gz 106.7 MB
EGAF00006807752 txt.gz 104.6 MB
EGAF00006807753 txt.gz 140.8 MB
EGAF00006807754 txt.gz 138.4 MB
EGAF00006807755 txt.gz 84.9 MB
EGAF00006807756 txt.gz 83.3 MB
EGAF00006807757 txt.gz 42.2 MB
EGAF00006807758 txt.gz 41.4 MB
EGAF00006807759 txt.gz 70.2 MB
EGAF00006807760 txt.gz 69.1 MB
EGAF00006807761 txt.gz 100.4 MB
EGAF00006807762 txt.gz 98.5 MB
EGAF00006807763 txt.gz 63.6 MB
EGAF00006807764 txt.gz 62.4 MB
EGAF00006807765 txt.gz 95.8 MB
EGAF00006807766 txt.gz 93.9 MB
EGAF00006807767 txt.gz 92.9 MB
EGAF00006807768 txt.gz 90.9 MB
EGAF00006807769 txt.gz 101.5 MB
EGAF00006807770 txt.gz 99.9 MB
EGAF00006807771 txt.gz 37.9 MB
EGAF00006807772 txt.gz 37.2 MB
EGAF00006807773 txt.gz 63.9 MB
EGAF00006807774 txt.gz 62.7 MB
EGAF00006807775 txt.gz 87.5 MB
EGAF00006807776 txt.gz 85.9 MB
EGAF00006807777 txt.gz 127.4 MB
EGAF00006807778 txt.gz 125.0 MB
EGAF00006807779 txt.gz 38.1 MB
EGAF00006807780 txt.gz 37.6 MB
EGAF00006807781 txt.gz 40.7 MB
EGAF00006807782 txt.gz 40.1 MB
EGAF00006807783 txt.gz 79.8 MB
EGAF00006807784 txt.gz 78.2 MB
EGAF00006807785 txt.gz 138.6 MB
EGAF00006807786 txt.gz 136.0 MB
EGAF00006807787 txt.gz 33.0 MB
EGAF00006807788 txt.gz 32.2 MB
EGAF00006807789 txt.gz 42.1 MB
EGAF00006807790 txt.gz 41.4 MB
EGAF00006807791 txt.gz 93.6 MB
EGAF00006807792 txt.gz 91.8 MB
EGAF00006807793 txt.gz 127.9 MB
EGAF00006807794 txt.gz 125.3 MB
EGAF00006807795 txt.gz 94.3 MB
EGAF00006807796 txt.gz 92.7 MB
EGAF00006807797 txt.gz 104.3 MB
EGAF00006807798 txt.gz 102.2 MB
EGAF00006807799 txt.gz 102.6 MB
EGAF00006807800 txt.gz 100.5 MB
EGAF00006807801 txt.gz 128.9 MB
EGAF00006807802 txt.gz 126.6 MB
EGAF00006807803 txt.gz 163.3 MB
EGAF00006807804 txt.gz 159.9 MB
EGAF00006807805 txt.gz 56.4 MB
EGAF00006807806 txt.gz 55.2 MB
EGAF00006807807 txt.gz 77.2 MB
EGAF00006807808 txt.gz 76.3 MB
EGAF00006807809 txt.gz 70.3 MB
EGAF00006807810 txt.gz 68.9 MB
EGAF00006807811 txt.gz 72.7 MB
EGAF00006807812 txt.gz 71.8 MB
EGAF00006807813 txt.gz 97.0 MB
EGAF00006807814 txt.gz 95.0 MB
EGAF00006807815 txt.gz 81.4 MB
EGAF00006807816 txt.gz 79.9 MB
EGAF00006807817 txt.gz 91.5 MB
EGAF00006807818 txt.gz 89.5 MB
EGAF00006807819 txt.gz 126.1 MB
EGAF00006807820 txt.gz 123.9 MB
EGAF00006807821 txt.gz 43.5 MB
EGAF00006807822 txt.gz 42.6 MB
EGAF00006807823 txt.gz 32.6 MB
EGAF00006807824 txt.gz 32.2 MB
EGAF00006807825 txt.gz 85.1 MB
EGAF00006807826 txt.gz 83.5 MB
EGAF00006807827 txt.gz 58.3 MB
EGAF00006807828 txt.gz 57.2 MB
EGAF00006807829 txt.gz 88.7 MB
EGAF00006807830 txt.gz 86.9 MB
EGAF00006807831 txt.gz 20.0 MB
EGAF00006807832 txt.gz 19.7 MB
EGAF00006807833 txt.gz 51.4 MB
EGAF00006807834 txt.gz 50.4 MB
EGAF00006807835 txt.gz 68.1 MB
EGAF00006807836 txt.gz 67.0 MB
EGAF00006807837 txt.gz 73.3 MB
EGAF00006807838 txt.gz 71.9 MB
EGAF00006807839 txt.gz 81.3 MB
EGAF00006807840 txt.gz 79.5 MB
EGAF00006807841 txt.gz 44.4 MB
EGAF00006807842 txt.gz 43.4 MB
EGAF00006807843 txt.gz 70.7 MB
EGAF00006807844 txt.gz 69.4 MB
EGAF00006807845 txt.gz 43.3 MB
EGAF00006807846 txt.gz 42.5 MB
EGAF00006807847 txt.gz 46.3 MB
EGAF00006807848 txt.gz 45.5 MB
EGAF00006807849 txt.gz 53.9 MB
EGAF00006807850 txt.gz 53.0 MB
EGAF00006816698 txt.gz 81.8 MB
EGAF00006816699 txt.gz 80.2 MB
EGAF00006816700 txt.gz 106.5 MB
EGAF00006816701 txt.gz 104.5 MB
EGAF00006816704 txt.gz 60.6 MB
EGAF00006816705 txt.gz 59.6 MB
EGAF00006816706 txt.gz 72.0 MB
EGAF00006816707 txt.gz 71.3 MB
EGAF00006816708 txt.gz 111.3 MB
EGAF00006816709 txt.gz 109.3 MB
EGAF00006816710 txt.gz 105.5 MB
EGAF00006816711 txt.gz 103.7 MB
EGAF00006816712 txt.gz 78.2 MB
EGAF00006816713 txt.gz 76.8 MB
EGAF00006816714 txt.gz 114.0 MB
EGAF00006816715 txt.gz 112.0 MB
EGAF00006816716 txt.gz 63.0 MB
EGAF00006816717 txt.gz 61.6 MB
EGAF00006816718 txt.gz 59.3 MB
EGAF00006816719 txt.gz 58.0 MB
EGAF00006816720 txt.gz 91.8 MB
EGAF00006816721 txt.gz 90.3 MB
EGAF00006816722 txt.gz 53.3 MB
EGAF00006816723 txt.gz 52.2 MB
EGAF00006816724 txt.gz 164.6 kB
EGAF00006816725 txt.gz 167.0 kB
EGAF00006816726 txt.gz 36.4 MB
EGAF00006816727 txt.gz 35.7 MB
EGAF00006816728 txt.gz 39.2 MB
EGAF00006816729 txt.gz 38.5 MB
EGAF00006816730 txt.gz 62.7 MB
EGAF00006816731 txt.gz 61.7 MB
EGAF00006816732 txt.gz 112.1 MB
EGAF00006816733 txt.gz 110.1 MB
EGAF00006816734 txt.gz 7.7 MB
EGAF00006816735 txt.gz 7.7 MB
190 Files (14.3 GB)