Fig. 3

Changes in chromatin accessibility during in vitro culture and association between expression levels and chromatin accessibility. A Number of differentially accessible regions between different states (FDR <  = 0.05). B Bar plot for the enrichment of the regions with significantly differential accessibility in promoter (< = 3 kb), intron, distal intergenic, exon, downstream and 5’/3’ UTR regions. The enrichment score represents the log2-transformed observed overlapping peaks / the expected overlapping peaks. C GO-BP enrichment analysis of increased promoter accessibility in HepLPC-P3 versus PHC (left) and HepLPC-P10 versus HepLPC-P3 (right) indicated that processes involved in cell growth and proliferation were enriched in HepLPC-P3 and processes involved in inflammatory response were enriched in HepLPC-P10. D Correlation of the RNA expression and promoter accessibility changes in HepLPC-P3 versus PHC (left) and HepLPC-P10 versus HepLPC-P3 (right) showed that the transcriptomic changes were positively correlated with the changes in promoter accessibility. E IGV shows peaks located in the promoter regions of proliferation-related (KRT19, MST1R, WNT7B, KRT7 and ESRP2) and inflammatory-related (ICAM1, LBP, and TNIP3) genes