Simple oligonucleotide-based multiplexing of single-cell chromatin accessibility.

Area of Science:

• Genomics
• Epigenetics
• Molecular Biology

Background:

• Microdroplet single-cell ATAC-seq (scATAC-seq) is crucial for studying chromatin accessibility.
• Existing methods lack scalable and simple sample multiplexing procedures.
• Multiplexing is essential for increasing throughput and reducing costs in single-cell genomics.

Purpose of the Study:

• To introduce SNuBar-ATAC, a novel transposome-assisted single nucleus barcoding approach for ATAC-seq.
• To provide a simple, accurate, and scalable method for multiplexing scATAC-seq experiments.
• To demonstrate the utility of SNuBar-ATAC in diverse biological applications, including multi-omics.

Main Methods:

• Developed SNuBar-ATAC using a single oligonucleotide adaptor for sample multiplexing during the tagmentation step.
• Validated SNuBar-ATAC accuracy and scalability using cell line mixture experiments.
• Applied SNuBar-ATAC to analyze chromatin accessibility in mouse lung tumors and human breast tissue, and for multi-omic assays.

Main Results:

• SNuBar-ATAC demonstrated high accuracy and scalability in cell line mixtures.
• Successfully investigated treatment-induced chromatin accessibility dynamics in 28 mice with lung tumors.
• Revealed spatial epigenetic heterogeneity in 32 regions of human breast tissue.
• Showcased SNuBar's capability to multiplex single-cell ATAC and RNA assays.

Conclusions:

• SNuBar-ATAC is a highly accurate, user-friendly, and scalable system for multiplexing scATAC-seq experiments.
• The method facilitates the study of chromatin accessibility dynamics and spatial epigenetics.
• SNuBar enables efficient multi-omic analyses, combining ATAC and RNA assays.