Droplet-based combinatorial indexing for massive-scale single-cell chromatin accessibility

Area of Science:

• Epigenomics and Single-Cell Biology
• Genomics and Bioinformatics
• Molecular Biology and Genetics

Background:

• Current single-cell epigenome mapping methods face limitations in throughput and data quality, hindering broad application.
• Efficiently profiling chromatin accessibility at single-cell resolution is crucial for understanding cellular heterogeneity and regulatory mechanisms.

Purpose of the Study:

• To introduce a high-quality, droplet-microfluidics-based method for single-cell chromatin accessibility profiling.
• To demonstrate the scalability and flexibility of this droplet-based platform for large-scale epigenomic studies.

Main Methods:

• Development of droplet single-cell assay for transposase-accessible chromatin using sequencing (dscATAC-seq) for high-throughput profiling.
• Integration of dscATAC-seq with combinatorial indexing (dsciATAC-seq) to further enhance throughput for massive-scale single-cell studies.
• Application of the platform to assay over 510,000 single-cell profiles from mouse brain and human bone marrow cells.

Main Results:

• Successfully profiled chromatin accessibility in 46,653 mouse brain cells, enabling unbiased discovery of cell types and regulatory elements.
• Analyzed 136,463 human bone marrow cells, revealing dynamic changes in cis- and trans-regulatory landscapes under different conditions.
• Demonstrated the platform's capacity to generate over 510,000 single-cell epigenomic profiles.

Conclusions:

• The droplet-based dscATAC-seq and dsciATAC-seq platforms offer a scalable and flexible solution for single-cell epigenome profiling.
• This technology facilitates large-scale discovery of cell types, regulatory elements, and dynamic regulatory changes at single-cell resolution.
• The method significantly advances the capacity for comprehensive epigenomic studies across diverse biological systems and conditions.