Fig. 6

Transcriptome by RNA-seq and DNA Demethylation by Base-Resolution BS-Seq Analysis of Each Group and in vivo Data Sets. A tSNE plot of RNA-seq data. Color codes indicate the cell types, and shapes for cell states; B PCA plot of WGBS data, color codes for the cell types are indicated; C Pseudotime trajectory (Monocle analysis) of the cells. Cells are colored based on the predicted pseudotime; D Heat map of top 20 DEGs in each subpopulation estimated by ROTS. The GO functional terms and representative genes included are shown for each gene cluster; E Violin plots showing the distribution of CpG methylation levels in overlapped 1 kb genomic tiles of each sample, the white point indicates median; F Averaged CpG methylation level profiles of all genes from -5 kb upstream of the transcription start sites (TSS), through scaled gene bodies to + 5 kb downstream of transcription end sites (TES); (G) Methylation distribution according to the different segments defined by the MethylSeekR approach; n = 2 independent experiments. Data are presented as means ± s.d. Statistical analysis was performed by Student’s t-test (two-sided): * represent compared to hESCs group p < 0.05