Fig. 3
Global changes in accessible chromatin following oncogenic KrasG12D induction. a (i) ATAC-seq was used to measure chromatin accessibilities. Each point represents a region of accessible chromatin comparing KrasG12D off (0 hr) versus on (24 hrs). a (ii) Venn diagrams comparing the number of gene promoters gained or lost in differentially accessible regions at 24 hrs. a (iii) Pie graphs showing the genomic distribution of the significantly differentially accessible regions. b (i) Average profile plot of normalized reads ± 10 kb around gene transcription start sites (TSSs). Y-axis represents read count per million (RPM) mapped reads. Orange and green shaded areas represent the standard error of the mean. b (ii) Heatmap of normalized reads around the TSS for each gene for 0 and 24 hrs. c (i) Pathway enrichment and (ii) transcription factor enrichment analysis of genes annotated to accessible chromatin for 0 and 24 hrs. Color scale represents standardized −log10(FDR) values. The tags following the transcription factors in c (ii) represent the TRANSFAC database nomenclature, which indicates either a different motif and/or the quality of the data that was used to make the motif. d, e Normalized ATAC-seq read coverage tracks for: d Etv4 (upregulated RNA-seq gene) and e Cxcl15 (downregulated RNA-seq gene)