Protocol for single-nucleus ATAC sequencing and bioinformatic analysis in frozen human brain tissue
Zechuan Shi, Sudeshna Das, Samuel Morabito, Emily Miyoshi, Vivek Swarup
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).
Topics & Concepts
Protocol (science)Pipeline (software)Computer scienceComputational biologyBrain tissueNucleusBiologyNeuroscienceMedicineProgramming languagePathologyAlternative medicineRNA modifications and cancerSingle-cell and spatial transcriptomicsAdvanced biosensing and bioanalysis techniques