Extended Data Fig. 8: DNA methylation patterns during implantation.

a, Total number of embryos and cells collected at each stage (days 6–12) for single-cell Trio-seq analysis. b, t-SNE plot of cells based on the expression matrix. Each dot represents one cell and colours represent lineage types. For each lineage, we selected several individual cells for bisulfite sequencing. In total, 2,544 cells were included: EPI, n = 79 cells; PE, n = 136 cells; TE, n = 2,329 cells. c, Principal component analysis of cells based on the expression matrix. Only cells that were also used for bisulfite sequencing were used for the analysis. In total, 130 cells were used: EPI, n = 31 cells; PE, n = 45 cells; TE, n = 54 cells. d–f, The number of CpG sites detected with at least one-, three- and fivefold coverage across the single-cell samples. In total 2.7 Tb of sequencing data was generated, and on average 10 million CpG sites per cell were covered. Black line, median value. EPI, n = 31 cells; PE, n = 45 cells; TE, n = 54 cells. g, h, t-SNE analysis based on promoter methylation levels of genes. Each dot represents one cell and cells were coloured by culture day and lineage identity. EPI, n = 31 cells; PE, n = 45 cells; TE, n = 54 cells. i, Single-cell DNA methylation levels across gene bodies (from transcription start site (TSS) to transcription end site (TES)) and the 20-kb flanking regions of the transcription start and end sites. We found shared distribution patterns: genes were hypomethylated around the transcription start sites, evenly hypermethylated in the gene body regions and significant decrease in methylation after the transcription end sites.