a, Global methylation levels on different genomic elements for different cell lineages. EPI, n = 31 cells; PE, n = 45 cells; TE, n = 54 cells. b, The average DNA methylation levels of promoter regions (250 bp upstream to 250 bp downstream of the transcription start site) for each lineage at different developmental stages. Only promoters for which methylation levels were less than 0.1 at day 6 and more than 0.35 at days 10, 12 and 14 are shown in the heat map. Colours from blue to red represent methylation levels from low to high. EPI, n = 31 cells, PE, n = 45 cells; TE, n = 54 cells. c, DNA methylation levels of represent loci for lineage-specific genes at promoter regions. Each column represents one read. Red represents a methylated CpG site, blue represents an unmethylated CpG site and white represents an undetected site. Only reads that covered at least five CpG sites are shown in the heat map.