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Protocol for single-nucleus ATAC sequencing and bioinformatic analysis in frozen human brain tissue.

ABSTRACT: Single-nucleus ATAC sequencing (snATAC-seq) employs a hyperactive Tn5 transposase to gain precise information about the cis-regulatory elements in specific cell types. However, the standard protocol of snATAC-seq is not optimized for all tissues, including the brain. Here, we present a modified protocol for single-nuclei isolation from postmortem frozen human brain tissue, followed by snATAC-seq library preparation and sequencing. We also describe an integrated bioinformatics analysis pipeline using an R package (ArchRtoSignac) to robustly analyze snATAC-seq data. For complete details on the use and execution of this protocol, please refer to Morabito et al. (2021).

SUBMITTER: Shi Z

PROVIDER: S-EPMC9218237 | biostudies-literature | 2022 Sep

REPOSITORIES: biostudies-literature

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Protocol for single-nucleus ATAC sequencing and bioinformatic analysis in frozen human brain tissue.

Shi Zechuan Z Das Sudeshna S Morabito Samuel S Miyoshi Emily E Swarup Vivek V

STAR protocols 20220617 3

Single-nucleus ATAC sequencing (snATAC-seq) employs a hyperactive Tn5 transposase to gain precise information about the cis-regulatory elements in specific cell types. However, the standard protocol of snATAC-seq is not optimized for all tissues, including the brain. Here, we present a modified protocol for single-nuclei isolation from postmortem frozen human brain tissue, followed by snATAC-seq library preparation and sequencing. We also describe an integrated bioinformatics analysis pipeline u ...[more]

PMID: 35755130

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