Using single-cell chromatin accessibility sequencing to characterize CD4+ T cells from murine tissues

Area of Science:

• Genomics
• Immunology
• Molecular Biology

Background:

• Chromatin accessibility is crucial for understanding gene regulation.
• Single-cell Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq) offers high-resolution insights into cellular heterogeneity.
• Characterizing T cell regulatory programs requires robust methodologies.

Purpose of the Study:

• To provide a complete workflow for generating and analyzing single-cell ATAC-seq data from murine T cells.
• To detail methods for isolating scATAC-seq-ready CD4+ T cells from various tissues.
• To establish a bioinformatic pipeline for scATAC-seq data pre-processing and downstream analysis.

Main Methods:

• Isolation of CD4+ T cells from murine tissues (visceral adipose tissue, skin, colon, spleen).
• Nuclei preparation and quality control for scATAC-seq library construction.
• Bioinformatic analysis using the R-based ArchR framework for scATAC-seq data.

Main Results:

• Established protocols for scATAC-seq library preparation from diverse murine T cell populations.
• Developed and validated a step-by-step bioinformatic pipeline for scATAC-seq data analysis.
• Demonstrated the utility of the workflow for characterizing chromatin accessibility landscapes in T cells.

Conclusions:

• The described workflow provides a comprehensive resource for researchers studying T cell epigenomes.
• This integrated approach facilitates the investigation of cell type-specific gene regulatory programs.
• The methodology enables detailed analysis of chromatin accessibility at the single-cell level.