Comparative analysis of human brain tissue preprocessing methods for single-nucleus chromatin accessibility profiling

ABSTRACT: The ability to analyze chromatin accessibility at the single-nucleus level is a critical step towards capturing the highly complex mechanisms that regulate gene expression in the human brain, and to functionally characterize the genetic architecture of neuropsychiatric traits. The assay for transposase accessible chromatin (ATAC-seq) has rapidly established itself as a robust means of studying epigenome regulation in bulk tissues and, more recently, at the single-cell level. To facilitate optimal preparation of frozen archival human brain tissue samples for single-nuclear ATAC-seq (snATAC-seq), we assessed the impact of different sample preparation approaches on the quality of snATAC-seq libraries. We tested six conditions, including different fluorescent activated nuclear sorting (FANS) strategies, from nuclei isolated from a sample of human cortical tissue. Using an unbiased computational approach, we were able to identify major cell populations in all snATAC-seq libraries, including those not subjected to FANS. When FANS was used, we observed that the choice of DNA stain impacts the quality of ATAC-seq libraries. Staining samples with DAPI can lead to insufficient detection of open chromatin regions, whereas 7aad provides improved identification of some nuclear sub-populations. We also observed that use of fluorescent dyes (in particular, DAPI) can lead to under-sampling of excitatory neurons. Our work provides guidelines on the trade-offs associated with different nuclear isolation strategies when preparing samples for snATAC-seq.

ORGANISM(S): Homo sapiens

PROVIDER: GSE166016 | GEO | 2022/01/29

REPOSITORIES: GEO