A pipeline for single-cell chromatin accessibility data analysis

Area of Science:

• Genomics
• Epigenetics
• Computational Biology

Background:

• Single-cell chromatin accessibility analysis offers high-resolution insights into regulatory elements and gene regulation.
• Standardized and comprehensive analysis workflows for scATAC-seq data are currently limited.

Purpose of the Study:

• To present a streamlined and integrated pipeline for analyzing single-cell chromatin accessibility data.
• To enable robust exploration of epigenetic mechanisms and cellular heterogeneity.

Main Methods:

• Data preprocessing using scATAC-pro or Cell Ranger ATAC.
• Peak calling with MACS2 and differential accessibility analysis.
• Transcription factor activity inference with chromVAR, motif enrichment, and footprinting analysis.
• Reconstruction of transcriptional regulatory networks using SCENIC+.

Main Results:

• The pipeline effectively processes scATAC-seq data from preprocessing to network reconstruction.
• It facilitates the detection of open chromatin regions and differential accessibility between cell populations.
• The approach allows for in-depth exploration of epigenetic mechanisms at the single-cell level.

Conclusions:

• This integrative workflow provides a robust framework for analyzing single-cell chromatin accessibility data.
• It aids in decoding the regulatory landscape and understanding cellular heterogeneity in complex biological systems.