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Bulk-tissue RNA-sequencing paired nuclear and cytoplasmic fractions of anterior prefrontal cortex, cerebellar cortex and putamen tissues from 4 post-mortem neuropathologically-confirmed control individuals ( anterior prefrontal cortex & cerebellar cortex – 4 individuals, putamen- 3 individuals)

Profiling of paired nuclear and cytoplasmic fractions of anterior prefrontal cortex, cerebellar cortex and putamen samples by bulk-tissue RNA-sequencing. Samples were derived from 4 post-mortem neuropathologically-confirmed control individuals ( anterior prefrontal cortex – 4 individuals, cerebellar cortex – 4 individuals, putamen- 3 individuals). Paired-end FASTQ files for each of the human samples are provided. Fastp (v 0.20.0), a fast all-in-one FASTQ pre-processor, was used for adapter trimming, read filtering and base correction. Fastp default settings were used for quality filtering and base correction. Further details on parameters used are available here: https://github.com/RHReynolds/RNAseqProcessing .

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Policy describing terms and conditions for accessing data generated by University College London, Department of Genetics and Genomic Medicine.

University College London, Department of Genetics and Genomic Medicine (UCL GGM) 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 UCL GGM 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: UCL GGM 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 UCL GGM as soon as it becomes aware of a breach of the terms or conditions of this agreement. 13. UCL GGM 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. 14. 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 UCL GGM. 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. 15. 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. 16. 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. 17. 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 UCL GGM 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) EGAS00001006380 Profiling of paired nuclear and cytoplasmic fractions of anterior prefrontal cortex, cerebellar cortex and putamen samples by bulk-tissue RNA-sequencing. Samples were derived from 4 post-mortem neuropathologically-confirmed control individuals ( anterior prefrontal cortex – 4 individuals, cerebellar cortex – 4 individuals, putamen- 3 individuals). Paired-end FASTQ files for each of the human samples are provided. Fastp (v 0.20.0), a fast all-in-one FASTQ pre-processor, was used for adapter trimming, read filtering and base correction. Fastp default settings were used for quality filtering and base correction. Name of project that created the dataset Bulk-tissue RNA-sequencing paired nuclear and cytoplasmic fractions of anterior prefrontal cortex, cerebellar cortex and putamen tissues from 4 post-mortem neuropathologically-confirmed control individuals (anterior prefrontal cortex & cerebellar cortex – 4 individuals, putamen- 3 individuals) Names of other data producers/collaborators Karishma D’Sa Specific limitations on areas of research General research use (DUO:0000042) User-specific restriction (DUO:0000026) 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 UCL GGM 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. UCL GGM 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 6 months after these data were first made available on the relevant hosting database, unless UCL GGM 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., EGAS00001006380), and acknowledge its use in a form agreed by the User Institution with UCL GGM.

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
EGAS00001006380 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
EGAF00006772813 fastq.gz 1.5 GB
EGAF00006772814 fastq.gz 1.6 GB
EGAF00006772815 fastq.gz 1.4 GB
EGAF00006772816 fastq.gz 1.5 GB
EGAF00006772817 fastq.gz 675.4 MB
EGAF00006772818 fastq.gz 693.3 MB
EGAF00006772819 fastq.gz 636.0 MB
EGAF00006772820 fastq.gz 654.1 MB
EGAF00006772821 fastq.gz 1.7 GB
EGAF00006772822 fastq.gz 1.8 GB
EGAF00006772823 fastq.gz 374.4 MB
EGAF00006772824 fastq.gz 388.9 MB
EGAF00006772825 fastq.gz 352.4 MB
EGAF00006772826 fastq.gz 365.7 MB
EGAF00006772827 fastq.gz 1.8 GB
EGAF00006772828 fastq.gz 1.8 GB
EGAF00006772829 fastq.gz 2.6 GB
EGAF00006772830 fastq.gz 2.7 GB
EGAF00006772831 fastq.gz 2.5 GB
EGAF00006772832 fastq.gz 2.5 GB
EGAF00006772833 fastq.gz 1.5 GB
EGAF00006772834 fastq.gz 1.5 GB
EGAF00006772835 fastq.gz 1.4 GB
EGAF00006772836 fastq.gz 1.4 GB
EGAF00006772837 fastq.gz 1.6 GB
EGAF00006772838 fastq.gz 1.6 GB
EGAF00006772839 fastq.gz 1.5 GB
EGAF00006772840 fastq.gz 1.5 GB
EGAF00006772841 fastq.gz 1.4 GB
EGAF00006772842 fastq.gz 1.5 GB
EGAF00006772843 fastq.gz 1.4 GB
EGAF00006772844 fastq.gz 1.4 GB
EGAF00006772845 fastq.gz 1.1 GB
EGAF00006772846 fastq.gz 1.1 GB
EGAF00006772847 fastq.gz 993.3 MB
EGAF00006772848 fastq.gz 1.0 GB
EGAF00006772849 fastq.gz 841.5 MB
EGAF00006772850 fastq.gz 850.0 MB
EGAF00006772851 fastq.gz 1.1 GB
EGAF00006772852 fastq.gz 1.1 GB
EGAF00006772853 fastq.gz 999.9 MB
EGAF00006772854 fastq.gz 1.0 GB
EGAF00006772855 fastq.gz 1.4 GB
EGAF00006772856 fastq.gz 1.4 GB
EGAF00006772857 fastq.gz 1.8 GB
EGAF00006772858 fastq.gz 1.8 GB
EGAF00006772859 fastq.gz 1.6 GB
EGAF00006772860 fastq.gz 1.7 GB
EGAF00006772861 fastq.gz 558.7 MB
EGAF00006772862 fastq.gz 576.9 MB
EGAF00006772863 fastq.gz 524.6 MB
EGAF00006772864 fastq.gz 538.5 MB
EGAF00006772865 fastq.gz 2.0 GB
EGAF00006772866 fastq.gz 2.1 GB
EGAF00006772867 fastq.gz 728.7 MB
EGAF00006772868 fastq.gz 759.7 MB
EGAF00006772869 fastq.gz 688.1 MB
EGAF00006772870 fastq.gz 721.3 MB
EGAF00006772871 fastq.gz 521.0 MB
EGAF00006772872 fastq.gz 535.6 MB
EGAF00006772873 fastq.gz 490.4 MB
EGAF00006772874 fastq.gz 504.9 MB
EGAF00006772875 fastq.gz 1.7 GB
EGAF00006772876 fastq.gz 1.7 GB
EGAF00006772877 fastq.gz 1.2 GB
EGAF00006772878 fastq.gz 1.2 GB
EGAF00006772879 fastq.gz 1.1 GB
EGAF00006772880 fastq.gz 1.1 GB
EGAF00006772881 fastq.gz 391.7 MB
EGAF00006772882 fastq.gz 396.7 MB
EGAF00006772883 fastq.gz 923.9 MB
EGAF00006772884 fastq.gz 951.7 MB
EGAF00006772885 fastq.gz 869.4 MB
EGAF00006772886 fastq.gz 897.0 MB
EGAF00006772887 fastq.gz 1.4 GB
EGAF00006772888 fastq.gz 1.5 GB
EGAF00006772889 fastq.gz 1.5 GB
EGAF00006772890 fastq.gz 1.6 GB
EGAF00006772891 fastq.gz 1.4 GB
EGAF00006772892 fastq.gz 1.5 GB
EGAF00006772893 fastq.gz 1.4 GB
EGAF00006772894 fastq.gz 1.5 GB
EGAF00006772895 fastq.gz 1.4 GB
EGAF00006772896 fastq.gz 1.4 GB
EGAF00006772897 fastq.gz 1.2 GB
EGAF00006772898 fastq.gz 1.2 GB
EGAF00006772899 fastq.gz 1.1 GB
EGAF00006772900 fastq.gz 1.1 GB
EGAF00006772901 fastq.gz 418.2 MB
EGAF00006772902 fastq.gz 431.2 MB
EGAF00006772903 fastq.gz 1.2 GB
EGAF00006772904 fastq.gz 1.2 GB
EGAF00006772905 fastq.gz 1.1 GB
EGAF00006772906 fastq.gz 1.1 GB
EGAF00006772907 fastq.gz 729.6 MB
EGAF00006772908 fastq.gz 745.0 MB
EGAF00006772909 fastq.gz 1.5 GB
EGAF00006772910 fastq.gz 1.5 GB
EGAF00006772911 fastq.gz 1.4 GB
EGAF00006772912 fastq.gz 1.4 GB
EGAF00006772913 fastq.gz 995.6 MB
EGAF00006772914 fastq.gz 1.0 GB
EGAF00006772915 fastq.gz 932.2 MB
EGAF00006772916 fastq.gz 946.9 MB
EGAF00006772917 fastq.gz 1.7 GB
EGAF00006772918 fastq.gz 1.7 GB
EGAF00006772919 fastq.gz 1.0 GB
EGAF00006772920 fastq.gz 1.1 GB
EGAF00006772921 fastq.gz 965.3 MB
EGAF00006772922 fastq.gz 990.7 MB
EGAF00006772923 fastq.gz 910.8 MB
EGAF00006772924 fastq.gz 927.4 MB
EGAF00006772925 fastq.gz 2.0 GB
EGAF00006772926 fastq.gz 2.0 GB
EGAF00006772927 fastq.gz 4.1 GB
EGAF00006772928 fastq.gz 4.2 GB
EGAF00006772929 fastq.gz 2.3 GB
EGAF00006772930 fastq.gz 2.3 GB
EGAF00006772931 fastq.gz 3.7 GB
EGAF00006772932 fastq.gz 3.8 GB
EGAF00006772933 fastq.gz 2.0 GB
EGAF00006772934 fastq.gz 2.0 GB
EGAF00006772935 fastq.gz 3.5 GB
EGAF00006772936 fastq.gz 3.3 GB
EGAF00006772937 fastq.gz 2.2 GB
EGAF00006772938 fastq.gz 2.2 GB
EGAF00006772939 fastq.gz 3.3 GB
EGAF00006772940 fastq.gz 3.2 GB
EGAF00006772941 fastq.gz 3.0 GB
EGAF00006772942 fastq.gz 3.1 GB
EGAF00006772943 fastq.gz 1.9 GB
EGAF00006772944 fastq.gz 1.9 GB
EGAF00006772945 fastq.gz 3.8 GB
EGAF00006772946 fastq.gz 3.8 GB
EGAF00006772947 fastq.gz 2.1 GB
EGAF00006772948 fastq.gz 2.1 GB
EGAF00006772949 fastq.gz 3.6 GB
EGAF00006772950 fastq.gz 3.7 GB
EGAF00006772951 fastq.gz 1.9 GB
EGAF00006772952 fastq.gz 1.9 GB
EGAF00006772953 fastq.gz 3.4 GB
EGAF00006772954 fastq.gz 3.4 GB
EGAF00006772955 fastq.gz 2.1 GB
EGAF00006772956 fastq.gz 2.1 GB
EGAF00006772957 fastq.gz 3.8 GB
EGAF00006772958 fastq.gz 3.9 GB
EGAF00006772959 fastq.gz 1.8 GB
EGAF00006772960 fastq.gz 1.8 GB
EGAF00006772961 fastq.gz 3.6 GB
EGAF00006772962 fastq.gz 3.7 GB
EGAF00006772963 fastq.gz 1.9 GB
EGAF00006772964 fastq.gz 1.9 GB
EGAF00006772965 fastq.gz 4.2 GB
EGAF00006772966 fastq.gz 4.3 GB
EGAF00006772967 fastq.gz 4.4 GB
EGAF00006772968 fastq.gz 4.4 GB
EGAF00006772969 fastq.gz 3.9 GB
EGAF00006772970 fastq.gz 4.0 GB
158 Files (271.2 GB)