Fig. 3: Ent treatment restricts chromatin opening during PSC activation.

a Numbers and percentages of accessible sites detected by ATAC-seq and their genomic annotations in pre-activated PSCs (D1) and PSCs at D3 under Veh (D3V) or Ent treatment (D3E, 5 μM). n = 2 independent samples. b Venn diagrams showing the distributions of accessible sites among PSC samples with the percentages relative to the total detected sites. c Numbers of sites with significantly increased or decreased accessibility (FC > 2, FDR q < 0.05) and those without significant changes (others) post-activation (D3V vs D1) and under Ent treatment (D3E vs D3V), along with the percentages relative to D3V. d Scatter plot showing the accessibility changes post-activation (y-axis) and under Ent treatment (x-axis) at genomic sites (22,879) with accessibility significantly increased in PSC activation (FC > 2, FDR q < 0.05) and changed by Ent (FDR q < 0.05), including sites at selected PSC activation markers and TFs. Dotted lines, FC of 2 (D3E vs D3V). e, f Heatmap showing the normalized ATAC-seq read counts (e) and histogram showing average normalized read counts (f) for genomic sites (55,422) showing significantly increased accessibility post-activation in individual replicates (Rep.) of PSC samples. g GSEA plots showing genes upregulated post-activation are enriched in genes with genomic sites showing highly increased accessibility. h–j Genome browser tracks for selected myofibroblast (h), proliferation (i) and TF (j) gene loci in representative PSC samples with genomic sites displaying differential accessibility highlighted (box). Scale bar, 10 kb. k Venn diagram showing the distribution of genomic sites with significantly increased accessibility post-activation (FC > 2, FDR q < 0.05) and those with significantly reduced accessibility under Ent (FC > 2, FDR q < 0.05). l Representative enriched ontology terms for genes with sites showing accessibility highly increased post-activation (FC > 4, FDR q < 0.05) and highly reduced by Ent (FC > 4, FDR q < 0.05). GO analysis, one-sided Fisher’s exact test. Source data are provided as a Source Data file.