About file location

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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This dataset includes FASTQ for single-nucleus RNA-seq of normal controls, and multiple system atrophy (MSA) or Parkinson's disease (PD) patients.

The dataset includes more than 130k nuclei isolated using 10x Genomics Chromium Next GEM Single Cell 3' Reagent Kits v3.1. In total, 30 samples are included from 10 controls, 8 MSA (including one sample that was omitted during QC), or 12 PD patients. Samples were sequenced on Illumina Novaseq 6000 or NextSeq 550 instruments.

Request Access

Policy for Single-nucleus brain transcriptomics reveals microglia dysfunction in Multiple System Atrophy

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 Authorized Personnel: The individuals at the User Institution to whom the Data Access Committee 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 Authorized Personnel are set out in Appendix II. Data: The managed access datasets to which the User Institution has requested access. Data Producers: The individuals, listed in Appendix I, responsible for the development, organization, 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(s) that has requested access to the Data (detailed in Appendix II). Data Producers Institution(s): The Institution(s) that has produced the Data (detailed in Appendix I). Data Access Committee: The committee responsible for authorizing access to the data. Committee members are listed in Appendix I. 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 Authorized 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 (https://www.sanger.ac.uk/wp-content/uploads/fortlauderdalereport.pdf) and the Toronto Statement (http://www.nature.com/nature/journal/v461/n7261/full/461168a.html). This includes but is not limited to recognizing the contribution of the Data Producers and including a proper acknowledgment 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 analyzing 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.ott.nih.gov/sites/default/files/documents/pdfs/70fr18413.pdf) in conformity with the Organization for Economic Co-operation and Development Guidelines for the Licensing of the Genetic Inventions (2006) (https://www.oecd.org/sti/emerging-tech/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 the Data Access Committee within 30 days of any changes or departures of Authorized Personnel. 13. The User Institution will notify the Data Access Committee prior to any significant changes to the protocol for the Project. 14. The User Institution will notify the Data Access Committee as soon as it becomes aware of a breach of the terms or conditions of this agreement. 15. The Data Access Committee 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. 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 Authorized Personnel. The User Institution will procure that the Authorized 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 Denmark and shall be subject to the exclusive jurisdiction of the Danish courts. Agreed for User Institution (Name, Title, Date, Signature): Principal Investigator (Name, Title, Date, Signature): I confirm that I have read and understood this Agreement. Agreed for the Data Access Committee (Name, Title, Date, Signature): APPENDIX I – DATASET DETAILS & DATA ACCESS COMMITTEE APPENDIX II – PROJECT DETAILS APPENDIX III – PUBLICATION POLICY APPENDIX I – DATASET DETAILS & DATA ACCESS COMMITTEE Dataset reference (EGA Study ID, Dataset Accession Numbers and Dataset Details): Name of the project that created the dataset : Single-nucleus brain transcriptomics reveals microglia dysfunction in Multiple System Atrophy Data Producers Institution(s): Center for Neuroscience and Stereology, Bispebjerg-Frederiksberg Hospital, Nielsine Nielsens Vej 6B, entrance 11B, 2nd floor, DK-2400 Copenhagen NW, Denmark Names of other data producers/collaborators (Name, Email, Job Title): Specific limitations on areas of research: 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. Name of the Data Access Committee: DAC for study "Single-nucleus brain transcriptomics reveals microglia dysfunction in Multiple System Atrophy" Data Access Committee Members (Name, Email, Job Title): Principal Investigators Susana Aznar (susana.aznar.kleijn@regionh.dk) Konstantin Khodosevich (konstantin.khodosevich@bric.ku.dk) Data Manager Rasmus Rydbirk (rrydbirk@bmb.sdu.dk) Data Protection Officer Berit Schwartz (berit.schwartz.01@regionh.dk) 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): User Institution(s): All Individuals who the User Institution to be named as registered users (Name, Email, Job Title, Supervisor): All Individuals that should have an account created at the EGA (Name, Email, Job Title): APPENDIX III – PUBLICATION POLICY The Data Access Committee anticipates 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 the Data Access Committee have published their own global analysis or twelve (12) months after these data were first made available on the relevant hosting database, unless the Data Access Committee 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 (e.g., EGAS00000000029), and acknowledge its use in a form agreed by the User Institution with the Data Access Committee.

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
EGAS50000001406 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
EGAF50000497894 fastq.gz 342.1 MB
EGAF50000497895 fastq.gz 876.2 MB
EGAF50000497896 fastq.gz 2.9 GB
EGAF50000497897 fastq.gz 308.0 MB
EGAF50000497898 fastq.gz 777.6 MB
EGAF50000497899 fastq.gz 2.5 GB
EGAF50000497900 fastq.gz 393.4 MB
EGAF50000497901 fastq.gz 1.0 GB
EGAF50000497902 fastq.gz 3.4 GB
EGAF50000497903 fastq.gz 398.9 MB
EGAF50000497904 fastq.gz 1.1 GB
EGAF50000497905 fastq.gz 3.4 GB
EGAF50000497906 fastq.gz 465.5 MB
EGAF50000497907 fastq.gz 1.2 GB
EGAF50000497908 fastq.gz 4.0 GB
EGAF50000497909 fastq.gz 417.3 MB
EGAF50000497910 fastq.gz 1.1 GB
EGAF50000497911 fastq.gz 3.5 GB
EGAF50000497912 fastq.gz 529.8 MB
EGAF50000497913 fastq.gz 1.4 GB
EGAF50000497914 fastq.gz 4.7 GB
EGAF50000497915 fastq.gz 534.2 MB
EGAF50000497916 fastq.gz 1.4 GB
EGAF50000497917 fastq.gz 4.7 GB
EGAF50000497918 fastq.gz 515.4 MB
EGAF50000497919 fastq.gz 1.5 GB
EGAF50000497920 fastq.gz 4.6 GB
EGAF50000497921 fastq.gz 511.7 MB
EGAF50000497922 fastq.gz 1.5 GB
EGAF50000497923 fastq.gz 4.6 GB
EGAF50000497924 fastq.gz 516.3 MB
EGAF50000497925 fastq.gz 1.5 GB
EGAF50000497926 fastq.gz 4.7 GB
EGAF50000497927 fastq.gz 516.3 MB
EGAF50000497928 fastq.gz 1.5 GB
EGAF50000497929 fastq.gz 4.6 GB
EGAF50000497930 fastq.gz 878.5 MB
EGAF50000497931 fastq.gz 3.0 GB
EGAF50000497932 fastq.gz 5.5 GB
EGAF50000497933 fastq.gz 873.3 MB
EGAF50000497934 fastq.gz 2.9 GB
EGAF50000497935 fastq.gz 5.4 GB
EGAF50000497936 fastq.gz 875.9 MB
EGAF50000497937 fastq.gz 3.0 GB
EGAF50000497938 fastq.gz 6.8 GB
EGAF50000497939 fastq.gz 873.7 MB
EGAF50000497940 fastq.gz 2.9 GB
EGAF50000497941 fastq.gz 6.8 GB
EGAF50000497942 fastq.gz 1.2 GB
EGAF50000497943 fastq.gz 4.1 GB
EGAF50000497944 fastq.gz 8.4 GB
EGAF50000497945 fastq.gz 1.2 GB
EGAF50000497946 fastq.gz 4.1 GB
EGAF50000497947 fastq.gz 8.3 GB
EGAF50000497948 fastq.gz 1.3 GB
EGAF50000497949 fastq.gz 4.0 GB
EGAF50000497950 fastq.gz 9.4 GB
EGAF50000497951 fastq.gz 1.3 GB
EGAF50000497952 fastq.gz 4.0 GB
EGAF50000497953 fastq.gz 9.3 GB
EGAF50000497954 fastq.gz 840.6 MB
EGAF50000497955 fastq.gz 2.7 GB
EGAF50000497956 fastq.gz 6.1 GB
EGAF50000497957 fastq.gz 837.2 MB
EGAF50000497958 fastq.gz 2.6 GB
EGAF50000497959 fastq.gz 6.0 GB
EGAF50000497960 fastq.gz 976.9 MB
EGAF50000497961 fastq.gz 3.1 GB
EGAF50000497962 fastq.gz 7.1 GB
EGAF50000497963 fastq.gz 967.6 MB
EGAF50000497964 fastq.gz 3.0 GB
EGAF50000497965 fastq.gz 7.0 GB
EGAF50000497966 fastq.gz 1.1 GB
EGAF50000497967 fastq.gz 3.7 GB
EGAF50000497968 fastq.gz 8.8 GB
EGAF50000497969 fastq.gz 1.1 GB
EGAF50000497970 fastq.gz 3.7 GB
EGAF50000497971 fastq.gz 8.7 GB
EGAF50000497972 fastq.gz 1.2 GB
EGAF50000497973 fastq.gz 3.8 GB
EGAF50000497974 fastq.gz 8.6 GB
EGAF50000497975 fastq.gz 1.2 GB
EGAF50000497976 fastq.gz 3.7 GB
EGAF50000497977 fastq.gz 8.6 GB
EGAF50000497978 fastq.gz 812.3 MB
EGAF50000497979 fastq.gz 2.7 GB
EGAF50000497980 fastq.gz 6.0 GB
EGAF50000497981 fastq.gz 806.5 MB
EGAF50000497982 fastq.gz 2.6 GB
EGAF50000497983 fastq.gz 5.9 GB
EGAF50000497984 fastq.gz 1.1 GB
EGAF50000497985 fastq.gz 3.7 GB
EGAF50000497986 fastq.gz 7.8 GB
EGAF50000497987 fastq.gz 1.1 GB
EGAF50000497988 fastq.gz 3.7 GB
EGAF50000497989 fastq.gz 7.7 GB
EGAF50000497990 fastq.gz 1.3 GB
EGAF50000497991 fastq.gz 4.2 GB
EGAF50000497992 fastq.gz 9.6 GB
EGAF50000497993 fastq.gz 1.3 GB
EGAF50000497994 fastq.gz 4.1 GB
EGAF50000497995 fastq.gz 9.5 GB
EGAF50000497996 fastq.gz 1.0 GB
EGAF50000497997 fastq.gz 3.2 GB
EGAF50000497998 fastq.gz 7.1 GB
EGAF50000497999 fastq.gz 1.0 GB
EGAF50000498000 fastq.gz 3.1 GB
EGAF50000498001 fastq.gz 7.0 GB
EGAF50000498002 fastq.gz 1.2 GB
EGAF50000498003 fastq.gz 3.9 GB
EGAF50000498004 fastq.gz 8.8 GB
EGAF50000498005 fastq.gz 1.2 GB
EGAF50000498006 fastq.gz 3.9 GB
EGAF50000498007 fastq.gz 8.7 GB
EGAF50000498008 fastq.gz 1.1 GB
EGAF50000498009 fastq.gz 3.5 GB
EGAF50000498010 fastq.gz 6.9 GB
EGAF50000498011 fastq.gz 1.1 GB
EGAF50000498012 fastq.gz 3.5 GB
EGAF50000498013 fastq.gz 6.8 GB
EGAF50000498014 fastq.gz 1.3 GB
EGAF50000498015 fastq.gz 4.1 GB
EGAF50000498016 fastq.gz 9.4 GB
EGAF50000498017 fastq.gz 1.3 GB
EGAF50000498018 fastq.gz 4.0 GB
EGAF50000498019 fastq.gz 9.3 GB
EGAF50000498020 fastq.gz 941.3 MB
EGAF50000498021 fastq.gz 3.1 GB
EGAF50000498022 fastq.gz 7.1 GB
EGAF50000498023 fastq.gz 942.4 MB
EGAF50000498024 fastq.gz 3.1 GB
EGAF50000498025 fastq.gz 7.1 GB
EGAF50000498026 fastq.gz 1.0 GB
EGAF50000498027 fastq.gz 3.3 GB
EGAF50000498028 fastq.gz 7.7 GB
EGAF50000498029 fastq.gz 1.0 GB
EGAF50000498030 fastq.gz 3.4 GB
EGAF50000498031 fastq.gz 7.7 GB
EGAF50000498032 fastq.gz 920.2 MB
EGAF50000498033 fastq.gz 2.9 GB
EGAF50000498034 fastq.gz 6.7 GB
EGAF50000498035 fastq.gz 917.2 MB
EGAF50000498036 fastq.gz 2.9 GB
EGAF50000498037 fastq.gz 6.8 GB
EGAF50000498038 fastq.gz 936.6 MB
EGAF50000498039 fastq.gz 3.1 GB
EGAF50000498040 fastq.gz 7.2 GB
EGAF50000498041 fastq.gz 935.8 MB
EGAF50000498042 fastq.gz 3.1 GB
EGAF50000498043 fastq.gz 7.2 GB
EGAF50000498044 fastq.gz 1.1 GB
EGAF50000498045 fastq.gz 3.4 GB
EGAF50000498046 fastq.gz 7.8 GB
EGAF50000498047 fastq.gz 1.1 GB
EGAF50000498048 fastq.gz 3.4 GB
EGAF50000498049 fastq.gz 7.8 GB
EGAF50000498050 fastq.gz 1.2 GB
EGAF50000498051 fastq.gz 4.1 GB
EGAF50000498052 fastq.gz 9.5 GB
EGAF50000498053 fastq.gz 1.2 GB
EGAF50000498054 fastq.gz 4.1 GB
EGAF50000498055 fastq.gz 9.5 GB
EGAF50000498056 fastq.gz 1.2 GB
EGAF50000498057 fastq.gz 3.9 GB
EGAF50000498058 fastq.gz 9.1 GB
EGAF50000498059 fastq.gz 1.2 GB
EGAF50000498060 fastq.gz 4.0 GB
EGAF50000498061 fastq.gz 9.2 GB
EGAF50000498062 fastq.gz 1.2 GB
EGAF50000498063 fastq.gz 4.1 GB
EGAF50000498064 fastq.gz 9.4 GB
EGAF50000498065 fastq.gz 1.2 GB
EGAF50000498066 fastq.gz 4.1 GB
EGAF50000498067 fastq.gz 9.5 GB
EGAF50000498068 fastq.gz 1.1 GB
EGAF50000498069 fastq.gz 3.8 GB
EGAF50000498070 fastq.gz 8.4 GB
EGAF50000498071 fastq.gz 1.1 GB
EGAF50000498072 fastq.gz 3.8 GB
EGAF50000498073 fastq.gz 8.4 GB
EGAF50000498074 fastq.gz 1.2 GB
EGAF50000498075 fastq.gz 3.8 GB
EGAF50000498076 fastq.gz 8.9 GB
EGAF50000498077 fastq.gz 1.1 GB
EGAF50000498078 fastq.gz 3.8 GB
EGAF50000498079 fastq.gz 8.9 GB
EGAF50000498080 fastq.gz 1.2 GB
EGAF50000498081 fastq.gz 4.1 GB
EGAF50000498082 fastq.gz 9.6 GB
EGAF50000498083 fastq.gz 1.2 GB
EGAF50000498084 fastq.gz 4.1 GB
EGAF50000498085 fastq.gz 9.6 GB
EGAF50000498086 fastq.gz 1.2 GB
EGAF50000498087 fastq.gz 3.7 GB
EGAF50000498088 fastq.gz 8.6 GB
EGAF50000498089 fastq.gz 1.2 GB
EGAF50000498090 fastq.gz 3.7 GB
EGAF50000498091 fastq.gz 8.6 GB
198 Files (749.2 GB)