Fig. 8

Transcriptome and epigenome reprogramming events during differentiation. a Principal component analysis plot illustrating differential expression patterns before and after induction of differentiation in each cell line. b Heatmap showing relative enrichment for the top canonical pathways in the uniquely up- and downregulated genes in each cell type in response to differentiation. Color migrating from light yellow to red indicates increased enrichment. The left two columns show pathway enrichment level for down- and upregulated genes in GSCs. Right two columns show the same data for NSCs. c, d Bar graphs depicting the feature enrichment of differential 5mC (c) and 5hmC (d) events in GSC and NSC, after normalizing to the total number of CpGs associated with the feature and total number of hyper- (positive) or hypo- (negative) events. X-axis indicates the genomic feature. Y-axis indicates the enrichment level. e ChromHMM model illustrating the co-localization of DNA modification changes induced by differentiation related to enhancer marks in the corresponding cell line in its undifferentiated state. Green denotes events in NSC, red events in GSC. DNA mark switching is denoted as follows: 0, no change; +, gain; −, loss. f Bar graph showing the biological processes associated with genes gaining methylation during NSC differentiation at state 16 in box 2