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

Area of Science:

• Molecular Biology
• Genomics
• Epigenetics

Background:

• Simultaneous analysis of epigenome and transcriptome is crucial for understanding cellular function.
• Limited cell numbers pose a challenge for traditional dual-omics profiling.
• Existing methods often require substantial starting material.

Purpose of the Study:

• To develop a simple, fast, and robust protocol for simultaneous ATAC-seq and mRNA-seq library generation.
• To enable dual-omics profiling from limited cell numbers.
• To facilitate joint epigenome and transcriptome analyses.

Main Methods:

• Coupling a simplified ATAC (Assay for Transposase-Accessible Chromatin) procedure using whole cells.
• A novel mRNA-seq approach with seamless on-bead processing.
• Direct mRNA isolation, solid-phase cDNA synthesis, and direct tagmentation of mRNA/cDNA hybrids.

Main Results:

• Successful generation of ATAC-seq and mRNA-seq libraries from the same cells.
• Demonstrated feasibility of dual-omics profiling with limited cell input.
• Protocol is simple, fast, and robust.

Conclusions:

• The low-input ATAC&mRNA-seq protocol enables efficient dual-omics profiling from scarce biological samples.
• This method is valuable for researchers needing to analyze both epigenome and transcriptome simultaneously.
• Provides a powerful tool for single-cell multi-omics studies.