Nanowell-based single-cell combinatorial indexed ATAC-seq

Here we present advancements in single-cell combinatorial indexed ATAC-seq (sciATAC) to measure chromatin accessibility that leverage nanowell chips to achieve atlas-scale cell throughput (>105) at low cost. Our optimized techniques also achieve a high fraction of reads that fall within called peaks (>80%) and low cell doublet rates. We also demonstrate an alternative workflow that achieves high cell coverage while retaining exceptional enrichment for open chromatin regions, enabling the assessment of >70,000 unique accessible loci per cell. Overall design: Single-cell combinatorial indexed ATAC-seq using nanowell-based compartmentalization for the second tier of cell indexing (PCR)