Overview
The BD Rhapsody™ Assay for Transposase-Accessible Chromatin assay (ATAC-seq) enables you to either reproducibly generate standalone open chromatin profiling data or perform a multiomic analysis of open chromatin accessibility and transcriptome of single cells in one experiment on the BD Rhapsody™ Single-Cell Analysis System.
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.
Why Choose BD Rhapsody™ ATAC-Seq?
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.
