Fig. 5

Uncovering coordinated changes between the transcriptome and DNA methylation within an embryonic stem cell differentiation trajectory. a Comparisons of principal component analyses (PCA) of scRNA-seq data, single-cell DNA methylation data, and aggregated single-cell DNA methylation data learned by scAI. Cells are colored based on the cell subpopulations identified using scAI. Marker shapes denote the culture conditions. b Heatmap of the expression level and methylation level of cluster-specific marker genes (left), loci (middle), and loci within 500 kb of the TSS of marker genes (right) in the three cell clusters. c Genes and loci are ranked based on their enrichment scores in each factor. Labeled genes (top) are known pluripotency markers or differentiation markers. Labeled loci (bottom), including CpG sites, enhancers, and promoters, are located within 500 kb of the TSS of marker genes in each factor. d VscAI visualization of cells and known pluripotency markers and differentiation markers derived from transcriptome (top) and DNA methylation (bottom) data