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

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).