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

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: In a single experiment, we utilized 96 barcoded Tn5 to profile human bone marrow mononuclear cells from two donors before (untreated controls) and after stimulation. After the tagmentation reaction, all cells were pooled, washed and processed in 16 different channels (16 "samples") on the SureCell platform (thus, data from 16 samples should be collapsed for analysis)