Extended Data Fig. 12: Embryoid bodies recapitulate the transcriptional, methylation and accessibility dynamics of the embryo.

a, Embryoid bodies show high transcriptional similarity to gastrulation-stage embryos. Top left, UMAP projection of RNA expression for the embryoid body dataset (n = 775). Cells are coloured by lineage assignment and shaped by genotype (WT or Tet TKO). Bottom left, UMAP projection of stages E6.5 to E8.5 of the atlas dataset (no extra-embryonic cells) with the nearest neighbours that were used to assign cell type labels to the scNMT-seq embryoid body dataset coloured in red (WT) or blue (Tet TKO). Middle, UMAP projection of embryoid body cells coloured by the relative RNA expression of marker genes. Right, scatter plot of the differential gene expression (log₂ normalized counts) between different assigned lineages for embryoid bodies (x axis) versus embryos (y axis). Each dot represents one gene. Pearson correlation coefficient with corresponding P value (two-sided) are displayed. Lines show the linear regression fit. The top-four genes with the largest differential expression are highlighted in red. b, Global DNA methylation and chromatin accessibility levels during embryoid body differentiation. Top, box plots showing the distribution of genome-wide CpG methylation (left) or GpC accessibility levels (right) per time point and lineage (compare with Extended Data Fig. 3). Each dot represents a single cell (only wild-type cells are used). Box plots show median levels and the first and third quartile, whiskers show 1.5× the interquartile range. Bottom, heat map of DNA methylation (left) or chromatin accessibility (right) levels per time point and genomic context (compare with Fig. 1e, f). c, Ectoderm enhancers are more methylated in Tet TKO compared with wild-type epiblast cells in vivo. Bar plots show the mean (bulk) DNA methylation levels for ectoderm (left), endoderm (middle) and mesoderm (right) enhancers in E6.5 epiblast cells²⁵. For each genotype, two replicates are shown. d, Profiles of DNA methylation (red) and chromatin accessibility (blue) at lineage-defining enhancers quantified over different lineages across embryoid body differentiation (only wild-type cells). Running averages in 50-bp windows around the centre of the ChIP–seq peaks (2 kb upstream and downstream) are shown. Solid lines display the mean across cells and shading displays the corresponding s.d. Dashed horizontal lines represent genome-wide background levels for methylation (red) and accessibility (blue).