High-throughput combinatorial indexing enables scalable single-cell chromatin accessibility profiling [PBMC]. High-throughput combinatorial indexing enables scalable single-cell chromatin accessibility profiling [PBMC]

While recent technical advancements have facilitated the mapping of epigenomes at the single-cell resolution, the throughput and quality of these methods have limited the widespread application of these technologies. Here, we describe a high-throughput platform for single-cell assay for transposase accessible chromatin (scATAC-seq) using droplet microfluidics that yields essential qualities for high-throughput profiling, including improvements in per-cell library complexity and throughput. This approach enables robust cell-typing of complex tissues and reveals a de novo atlas of cellular and epigenomic diversity across many cell types and cell stages. Overall design: Human peripheral blood mononuclear cells from 2 donors were processed using the BioRad SureCell scATAC-seq platform across multiple channels in the instrument.