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Chromatin accessibility profiling by ATAC-seq
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DOI：10.1038/s41596-022-00692-9.png)
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Abstract
En 中文
The assay for transposase-accessible chromatin using sequencing (ATAC-seq) provides a simple and scalable way to detect the unique chromatin landscape associated with a cell type and how it may be altered by perturbation or disease. ATAC-seq requires a relatively small number of input cells and does not require a priori knowledge of the epigenetic marks or transcription factors governing the dynamics of the system. Here we describe an updated and optimized protocol for ATAC-seq, called Omni-ATAC, that is applicable across a broad range of cell and tissue types. The ATAC-seq workflow has five main steps: sample preparation, transposition, library preparation, sequencing and data analysis. This protocol details the steps to generate and sequence ATAC-seq libraries, with recommendations for sample preparation and downstream bioinformatic analysis. ATAC-seq libraries for roughly 12 samples can be generated in 10 h by someone familiar with basic molecular biology, and downstream sequencing analysis can be implemented using benchmarked pipelines by someone with basic bioinformatics skills and with access to a high-performance computing environment. A protocol for generating chromatin accessibility profiles from a broad variety of cell and tissue types, including a step-by-step workflow for library preparation and guidelines for data processing and downstream analysis.
Keywords:
GENE-EXPRESSION
SINGLE CELLS
R/BIOCONDUCTOR PACKAGE
HYPERSENSITIVE SITES
REGULATORY ELEMENTS
READ ALIGNMENT
SEQUENCE BIAS
CHIP-SEQ
IN-VIVO
GENOME
