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

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 isolated bone marrow CD34+ stem/progenitor cells, and isolated peripheral blood CD4+ T cells, CD8+ T cells, Monocytes, B cells and NK cells were were processed using the BioRad SureCell scATAC-seq platform across multiple channels in the instrument.