Fig. 2

BROCKMAN identifies cell types, drug treatments, cycling cells, and experimental artifacts in scATAC-seq data. a Identification of cell types. t-SNE two dimensional projection of the 131 significant PCs for all cells. Cells are colored by pre-annotated type (legend) and major cell type clusters are encircled. GM = GM12878 (LCLs), rep = replicate, Imat = Imatinib (BCR-ABL inhibition), CDKi = CDK4/6 inhibition, JNKi = JNK inhibition, TNFa = TNFa treatment. b Detection of outliers. Shown are the cell indices (position on C1 chip) for cells from K562-replicate 3, with outlier K562 cells (as in a) marked in black. The outlier cells have consecutive indices suggesting a shared location on the chip. White: cells filtered out prior to analysis. c Cell cycle phases. t-SNE projection as in a, but with color indicating cell cycle stage as determined by the ATAC reads falling within replication domains, showing that the “mixed” population from a are comprised primarily of replicating cells