Simultaneous profiling of gene expression and chromatin accessibility in single cells

Area of Science:

• Single-cell multi-omics
• Genomics
• Transcriptomics
• Epigenomics

Background:

• Multi-omic profiling in single cells reveals biological insights beyond mono-omic data.
• Existing multi-omic methods are often costly and complex, limiting widespread adoption.
• Simultaneous analysis of gene expression and chromatin accessibility is crucial for understanding cellular function.

Purpose of the Study:

• To present a simplified method for joint profiling of gene expression and chromatin accessibility in single cells.
• To evaluate the quality and utility of this new multi-omic approach.
• To demonstrate its potential for improved cell state classification and hypothesis generation.

Main Methods:

• Developed a straightforward protocol for simultaneous single-cell RNA-seq and ATAC-seq.
• Assessed data quality across three cell types.
• Investigated the correlation between chromatin accessibility and gene expression at specific loci (CD3G, FTH1) in human T cells and monocytes.
• Compared clustering accuracy using mono-omic versus combined data.

Main Results:

• The new method yields high-quality single-cell ATAC-seq and RNA-seq data.
• Established a link between chromatin accessibility and gene expression at selected loci.
• Demonstrated that combined multi-omic data improves clustering accuracy compared to mono-omic data.
• The protocol is accessible to standard biological laboratories.

Conclusions:

• This simplified multi-omic technique facilitates joint profiling of gene expression and chromatin accessibility.
• It offers a more accessible and cost-effective alternative to existing methods.
• Enables enhanced cell state classification and mechanistic hypothesis generation in biological research.