Fig. 5: Single-cell transcriptomic profiling of EZH2i-treated naïve and primed cells.
a, UMAP projection reference annotation (TE: trophectoderm; Exe_Mes: extra-embryonic mesoderm). The colour of each data point represents the cell annotations retrieved for each publication. Light-grey-coloured data points represent cells in the multi-data integration that were not used to infer cell annotations. The shape of data points for the embryonic cells indicates the data source. b UMAP projection and cell identity annotations of single-cell transcriptome datasets obtained for EZH2i-treated naïve and primed cells at indicated timepoint, showing ELCs, TLCs, MeLCs, AMLCs and HLCs. Percentage of cells within major clusters are indicated in the maps. Bar chart (bottom) shows the percentage of cells per cluster at each time point. c, UMAP projection and cell identity annotations as in b for primed hESCs treated with EZH2i. In a–c, UMAP was generated from an extensive reference dataset, including data from human embryonic and PASE model (Extended Data Fig. 8a,b and Methods). d, Top ten significantly upregulated genes in MeLCs or TLCs, compared with ELC population. Bubble plot shows proportion of expressing cells and average expression per gene and condition. e, Single-cell expression of select TLC and MeLC markers mapped onto UMAP. log2 expression of selected genes overlaid on the UMAP. f, Selected genes differentially expressed within ELC population comparing 7-day-EZH2i-treated samples and untreated samples. Bubble plot shows proportion of expressing cells and average expression per gene and condition. g, Single-cell log2 expression of select factors mapped onto UMAP.
