High-throughput chromatin accessibility profiling at single-cell resolution.

Area of Science:

• Genomics
• Molecular Biology
• Cell Biology

Background:

• Assessing DNA accessibility is crucial for understanding gene regulation.
• Existing methods for single-cell chromatin accessibility have limitations in throughput and cost.

Purpose of the Study:

• To develop a high-throughput, cost-effective single-cell assay for measuring DNA accessibility.
• To demonstrate the utility of this method for analyzing cellular heterogeneity in complex tissues.

Main Methods:

• Development of a high-throughput single-cell assay for transposition of accessible chromatin (ATAC-seq).
• Integration of fluorescence imaging and addressable reagent deposition on a 5184 nano-well array.
• Application to peripheral blood mononuclear cells (PBMCs).

Main Results:

• Achieved a nearly 20-fold improvement in throughput compared to microfluidic methods (~1800 cells/chip).
• Reduced library preparation costs to approximately 81 cents per cell.
• Demonstrated robust, de novo clustering of single cells by hematopoietic cell type.

Conclusions:

• The developed high-throughput single-cell ATAC-seq method significantly enhances efficiency and reduces costs.
• This method provides a powerful tool for dissecting cellular heterogeneity and regulatory variation in complex biological systems.
• Enables precise identification of distinct cell populations within PBMCs based on chromatin accessibility profiles.