Overview
Mapping open chromatin regions at the single-cell level elucidates cell-to-cell variability in gene regulatory landscapes that drives cell fate decisions and responses to stimuli. Assay for transposase-accessible chromatin using sequencing (ATAC-seq) excels at this by providing an unbiased, genome-wide readout of chromatin accessibility with higher sensitivity than its predecessors. When combined with single-cell transcriptomic data from the same cells, the resulting multi-layer view enables direct associations of the gene regulatory chromatin state with gene expression output in each cell, affording even deeper mechanistic understanding of cell state in different conditions.
The BD Rhapsody™ ATAC-Seq Assays enable you to either generate highly reproducible open chromatin profiling data from single cells or perform a multiomic analysis of open chromatin accessibility and transcriptome of single cells in one experiment using the BD Rhapsody™ Single-Cell Analysis System.
Learn more from the BD Rhapsody™ ATAC-Seq Assay Brochure.
Features
Validated on the new BD Rhapsody™ Enhanced Cell Capture Beads V3, BD Rhapsody™ ATAC-Seq Assays generate consistent, high-quality data across different samples and users and a wide range of cell inputs. Key features include:
- High sensitivity and specificity across different experimental conditions
- Capable of accommodating a wide range of cell inputs
- Integrated epigenomic and transcriptomic characterization on the same cells
- Compatibility with Custom BD® Nuclear Antibody-Oligonucleotide Conjugates
Applications
In this study, the BD Rhapsody™ Single-Cell Multiomic ATAC-Seq Assay was used to analyze 2,190 nuclei from human peripheral blood mononuclear cells (PBMCs). A joint whole transcriptome analysis (WTA) and ATAC-seq dimensionality reduction was performed by Uniform Manifold Approximation and Projection (UMAP) and cells were annotated as members of distinct cell types using the WTA data from a PBMC reference atlas.
The heat map shows normalized enrichment scores of cell type–specific transcription factor motifs. Motif scores were calculated using a binomial distribution, determining the relative enrichment of each motif in differentially accessible regions of a given cell type compared to GC-matched background regions. The scores were then normalized across cell types per motif on a 0–1 scale, where 0 indicates least enrichment and 1 indicates highest enrichment of each motif.
A. Read density across each ATAC-seq cluster at the transcription start sites of cell type marker genes.
B. Violin plots showing cell type-specific gene expression in WTA data.
This heatmap shows Pearson’s correlation coefficients between ATAC-seq gene activity scores and gene expression values in PBMCs, with each row representing a cell type in WTA data and each column a cell type in ATAC-seq data.
