Fig. 1

scCAT-seq provides an accurate genome-wide measure of both chromatin accessibility and gene expression. a Overview of the scCAT-seq protocol. b Top panel: chromatin accessibility read enrichment around the transcription start site (TSS). Bottom panel: coverage of mRNA reads along the body of transcripts. Titration series (one single-cell, 5 cells, 50 cells, 500 cells) were marked by the indicated colors. All profiles were generated using the scCAT-seq protocol with the indicated number of cells as input. c A representative region showing a consistent pattern of chromatin accessibility and gene expression across datasets generated using different number of input cells. The bulk ATAC-seq track was generated using 50,000 K562 cells. The DNase-seq and bulk RNA-seq data of K562 cells were downloaded from ENCODE. The scCAT-seq tracks are chromatin accessibility (upper) and gene expression read density (bottom) from a total of 74 K562 single cells. d Top panel: mean chromatin accessibility read density around regions that are enriched by the indicated individual or combined histone modifications. Bottom panel: mean expression level of genes associated with regions that are enriched by the indicated individual or combined histone modifications. e Top panel: mean chromatin accessibility read density within regions that are bound by the indicated transcription factors. Bottom panel: mean expression level of genes associated with regions that are bound by the indicated transcription factors