Supplementary Figure 4: MS275 treatment only minimally mimics SNA.

(A-B) Cropped western blot (A) and quantification (B) of H3K9ac and H3K27ac expression following intraperitoneal MS275 injection after DCA. Uncropped version of the western blot is in Supplementary Fig. 11. In B, the levels of H3K9ac and H3K27ac have been normalized to total H3 and expressed as percentage vs vehicle, which is represented by the dotted red line (mean+s.e.m. of N=5 independent experiments; 1-way Anova, Dunnett’s multiple comparisons test; full statistics in Supplementary Data 15). (C) Bar plot of the number of genes with differential TSS accessibility (TSS+/−1Kb) (left) and differential expression (right) upon intraperitoneal MS275 injection after DCA injury vs vehicle (N=3 independent samples; Pvalue<0.05). (D) Odds ratio analysis of gene enrichment associated with a higher or lower chromatin accessibility at the TSS for upregulated, downregulated or non-DE genes upon MS275 treatment; the numbers represent the Pvalue, two-sided Fisher’s exact test (ns= not significant). (E) Bar chart showing the top ranked GO categories in the upregulated (red) and downregulated (blue) genes upon MS275 treatment (BP: Biological Process and MF: Molecular Function, Modified Fisher Exact Pvalue<0.01). (F-G) BaGfoot plots of the ΔFA (differential flanking accessibility) and ΔFPD (differential footprint depth) values of the motifs upon MS275 treatment at the level of TSS (TSS+/−1Kb) (F) and enhancers (G). The population median is marked in orange; the bag area (dark blue) represents the region where 50% of the motifs are located; the fence area (light blue) is the region where the remaining non-outlier motifs are located. The plots are divided in 4 quadrants (I-IV), and the red squares depict the statistically significant motifs outside the fence (Pvalue<0.05).