A Simple, Cost-Effective, High-Throughput Method for Measuring Chromatin Accessibility and Gene Expression in Single...

Area of Science:

• Molecular Biology
• Genomics
• Biotechnology

Background:

• Single-nucleus epigenomic profiling is crucial for understanding cellular heterogeneity.
• Existing methods often rely on microfluidics, which can be complex and costly.
• There is a need for accessible and efficient techniques for large-scale epigenomic analysis.

Purpose of the Study:

• To introduce novel microfluidic-free, droplet-based assays for single-nucleus epigenomic profiling.
• To present Particle-templated Instant Partition single-nucleus assay for transposase-accessible chromatin using sequencing (PIP-ATAC-seq) and its multiomic counterpart (PIP-Multiome-seq).
• To evaluate the performance and utility of these new assays.

Main Methods:

• Development of droplet-based, microfluidic-free assays: PIP-ATAC-seq and PIP-Multiome-seq.
• Generation of large-scale datasets from thousands of nuclei using cell lines and mouse brains.
• Benchmarking and comparison against established single-nucleus epigenomic measurement techniques.

Main Results:

• PIP-ATAC-seq and PIP-Multiome-seq successfully generated high-quality epigenomic data from thousands of nuclei.
• The assays demonstrated straightforward implementation and affordability.
• Performance was comparable to existing, more complex methods.

Conclusions:

• PIP-ATAC-seq and PIP-Multiome-seq are valuable, cost-effective additions to the single-cell molecular measurement toolkit.
• These methods provide accessible approaches for high-throughput single-nucleus epigenomic and multiomic profiling.
• The microfluidic-free design enhances the practicality and scalability of these assays.