Fig. 2

ATAC-seq quality control (QC). a Millions of unique and duplicated reads sequenced on each replicate, rounded, and stranded. b Fragment length distribution of ATAC-seq reads from a representative sample (MDA-MB-231 WT R1). Most of the reads fall into the nucleosome-free region or mono-nucleosome peak. c HOMER peak annotation of genome ontologies from MACS2 called peaks for each replicate. d Distance matrix of replicates after DESeq2 processing. e Enrichment of ATAC-seq signal around transcription start sites (TSS) in a representative sample (MDA-MB-231 WT R1). Top: aggregated enrichment around all TSSs. Bottom enrichment around individual TSS