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Targeted long-read snIso-Seq of the human brain in neurodegenerative diseases

Nuclei were extracted from postmortem human brain, and cDNA libraries were generated using the 10X Genomics 3' v3.1 kit. Prior to fragmentation, 75% of the library was reserved for long-read sequencing. This unfragmented library was used for target enrichment with a custom 50 gene probe panel from Twist Biosciences. The resulting amplified cDNA libraries were sequenced on a Sequel II. The files provided have undergone CCS generation, and we recommend following the guidelines in https://isoseq.how/ for further analysis starting with removal of primers using lima. The primer sequences that should be supplied are the Read 1 and TSO primers from the 10X Genomics kit.

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Chun Lab Human Data Access Policy

These terms and conditions govern access to the managed access 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 Chun Lab DAC grants access to the Data. This includes the User, the individuals listed on the Signature Page and any other individuals for whom the User Institution subsequently requests access to the Data. Details of the initial Authorized Personnel are listed in the Signature Page. Data: The managed access datasets to which the User Institution has requested access. Data Producers: The Chun Lab DAC and the collaborators listed in the publication author list 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 included on the Signature Page. 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. Chun Lab DAC: Data Access Committee, Laboratory of Jerold Chun, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California Terms 1. The User Institution agrees to only use these Data for the purpose of the Project (described on the Signature Page) 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 set in the Dataset Details. 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 the Dataset Details 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 Institutions agrees to recognize the contribution of the Data Producers by including a proper acknowledgement in all reports or publications resulting from the use of these Data. 7. 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. 8. The User Institution will notify the Chun Lab DAC within 30 days of any changes or departures of Authorized Personnel. 9. The User Institution will notify the Chun Lab DAC prior to any significant changes to the protocol for the Project. 10. The User Institution will notify the Chun Lab DAC as soon as it becomes aware of a breach of the terms or conditions of this agreement. 11. This agreement by written notice. 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. 12. 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 the Chun Lab DAC. 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. 13. 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.

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
EGAS50000000132 RNASeq

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
EGAF50000062136 bam 3.2 GB
EGAF50000062137 bam 2.7 GB
EGAF50000062138 bam 2.2 GB
EGAF50000062139 bam 2.4 GB
EGAF50000062140 bam 2.4 GB
EGAF50000062141 bam 2.5 GB
EGAF50000062142 bam 2.2 GB
EGAF50000062143 bam 2.5 GB
EGAF50000062144 bam 2.9 GB
EGAF50000062145 bam 2.7 GB
EGAF50000062146 bam 2.4 GB
EGAF50000062147 bam 2.3 GB
EGAF50000062148 bam 2.0 GB
EGAF50000062149 bam 2.7 GB
14 Files (35.1 GB)