Low-input ATAC&mRNA-seq protocol for simultaneous profiling of chromatin accessibility and gene expression

STAR Protoc. 2021 Aug 27;2(3):100764. doi: 10.1016/j.xpro.2021.100764. eCollection 2021 Sep 17.

Abstract

We present a simple, fast, and robust protocol (low-input ATAC&mRNA-seq) to simultaneously generate ATAC-seq and mRNA-seq libraries from the same cells in limited cell numbers by coupling a simplified ATAC procedure using whole cells with a novel mRNA-seq approach that features a seamless on-bead process including direct mRNA isolation from the cell lysate, solid-phase cDNA synthesis, and direct tagmentation of mRNA/cDNA hybrids for library preparation. It enables dual-omics profiling from limited material when joint epigenome and transcriptome analyses are needed. For complete details on the use and execution of this protocol, please refer to Li et al. (2021).

Keywords: Genomics; High Throughput Screening; Molecular Biology.

Publication types

  • Research Support, N.I.H., Intramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Chromatin / genetics*
  • DNA, Complementary / chemical synthesis
  • Gene Expression Profiling / instrumentation
  • Gene Expression Profiling / methods*
  • High-Throughput Nucleotide Sequencing / methods
  • Mice
  • Mouse Embryonic Stem Cells / physiology
  • Polymerase Chain Reaction / methods
  • RNA, Messenger / genetics*
  • Sequence Analysis, RNA / instrumentation
  • Sequence Analysis, RNA / methods*
  • Solid-Phase Synthesis Techniques

Substances

  • Chromatin
  • DNA, Complementary
  • RNA, Messenger