ATAC-seq

[2] ATAC-seq requires no sonication or phenol-chloroform extraction like FAIRE-seq;[9] no antibodies like ChIP-seq;[10] and no sensitive enzymatic digestion like MNase-seq or DNase-seq.

[22] But combinatorial cellular indexing requires additional, custom-engineered equipment or a large quantity of custom, modified Tn5.

[23] Recently, a pooled barcode method called sci-CAR was developed, allowing joint profiling of chromatin accessibility and gene expression of single cells.

[24] Computational analysis of scATAC-seq is based on construction of a count matrix with number of reads per open chromatin regions.

Open chromatin regions can be defined, for example, by standard peak calling of pseudo bulk ATAC-seq data.

As with bulk ATAC-seq, scATAC-seq allows finding regulators like transcription factors controlling gene expression of cells.