Fig. 2

DNA methylome and transcriptome analysis of SHC-MSCs (a, b) Volcano plot (a) and numbers (b) of hyper-methylated and hypo-methylated CpG sites in SHC-MSCs versus naïve MSCs. The numbers of hypo-methylated CpG sites in each DNA element are indicated in the right panel. UTR, untranslated region; TSS, transcription start site. c The 10 most highly enriched Pathway Maps and Process Networks in MetaCore analysis. d, e Number of genes differentially expressed between naïve MSCs and SHC-MSCs (d) and a representative PLK1 and DHRS3-associated gene network (e) identified via MetaCore analysis. Gene networks are illustrated by overlaying experimental values as fold changes in SHC-MSCs versus naïve MSCs. Up- and down-regulated genes are indicated in red and blue, respectively. f Real-time qPCR analysis of genes in the PLK1-associated, DHRS3-associated, ZNF143-associated networks. g, h Venn diagram (g) and heat-map (h) of 68 genes that were hypo-methylated and whose expression was increased (≥1.5-fold) in SHC-MSCs compared with naïve MSCs. i, j Real-time qPCR (i) and western blot (j) analyses of a subset of these 68 genes. In western blots, molecular weight (M.W.) marker sizes are shown on the left. β-actin was used as a loading control. Quantitative data show the fold change of expression in SHC-MSCs compared with that in naïve MSCs (set to 1; denoted by the red dotted line) (n = 4). *p < 0.05, **p < 0.01, ***p < 0.001, one-way ANOVA with the Bonferroni post-hoc test