Figure 3: Genomic distribution of RPKM normalized signal for PRO-seq and ChIP-exo targets (Pol II, H2A.Z, H3K4me3, H3K4me2, H3K4me1, H3K27ac, H3K9ac, H3K27me3, H4K20me1, and CTCF).
From: Epigenetic and transcriptional profiling of triple negative breast cancer
(a) Row-linked heatmaps show RPKM normalized number of reads across a 4 kb genomic interval in 40 bp bins relative to the TSS. Heatmaps were generated from merged biological replicate pairs for each data set. Regions are sorted in descending order based on average row tag density for Pol II. Each row represents a gene, with 18,793 genes displayed. Red and blue reflect high and low read densities, respectively. (b) Composite plots below each heatmap quantify the normalized tag density. The central trace denotes the average tag density for each 40 bp bin and the orange fill reflects the standard deviation. (c) Genome browser view of PRO-seq and ChIP-exo signal for the indicated targets in HCC1806 cells shown at the MYC gene. Tag distributions were smoothed and RPKM normalized using deepTOOLS. Traces were generated from merged biological replicate pairs.
