Extended Data Fig. 5: Extended analysis of scRNAseq data generated by SMART-seq2.

a. UMAP visualization based on Fig. 1d highlighting the cells in this study (left panel), in Petropoulos et al.²⁰ (middle panel) and in Yan et al.²⁶ (right panel). P, passage; blast., blastocyst. All reference datasets used in this study are summarized in Supplementary Table 8. b. Hierarchical clustering diagram of sorted 8CLC (78 cells) and embryo E3/E4 cells showing the cell-to-cell similarity on the basis of Spearman correlation coefficients. Five closely correlated regions are defined: R1 and R2 include all E3 cells, 10 E4 cells and 31 sorted 8CLC (39.8%). R3 and R4 include E4, all late E4 cells and no sorted 8CLC. R5 includes 47 sorted 8CLC (60.2%) which share similarity with both E3 and E4. c–e. UMAP visualization based on Fig. 1d highlighting the expression of several totipotency genes (TPRX1, ZSCAN4, DUXA and ZSCAN5B) (c), the shared naïve pluripotency/8CLC genes DPPA3 and KLF17 (d) and the primed-enriched gene CD24 (e) as human ESC transition from a primed state to an 8CLC state. f. Pseudobulk correlation analysis of the in vitro culture data with the embryo data based on all the TE. The average linkage hierarchical clustering of the Pearson correlation is shown. g. Heatmap showing the embryonic stage-specific TE expression profiles in human E3 to E7, sorted 8CLC, 4CL-day 12 naïve ESC and primed ESC. The full list of stage-specific TE are included in Supplementary Table 2. h. GFP⁺ sorted 8CLC from e4CL-day 5 cells were cultured in 4CL for 24 h and subjected to FACS analysis. 48.8% remained GFP⁺ and 51.2% became GFP^- (exited from the 8CLC state) (upper panels). GFP^- cells were sorted from stepwise e4CL-day 5 and were cultured in e4CL for 24 h and subjected to FACS analysis. 5.76% became GFP⁺ (entered the 8CLC state) (lower panels). D, day.

Source data