Fig. 2: Analysis of transcriptional profiles by scRNA-Seq.

a Schematic representation of assay performed for SMART-seq2 analysis. b UMAP representation of scRNA-seq results, showing 3 distinct transcriptomic clusters. c Dot Plots showing expression of stem-cell-specific marker genes (Amn, Dkk1, Gata4, Sox17 = VE-like cells; Pou5f1/Oct4, Nanog, Gdf3, Tdgf1 = Epi-like cells; Cdx2, Elf5, Eomes, Tfap2c = ExE-like cells). d GO term enrichment analysis of top 100 differentially expressed genes (log-fold change 1.5; FDR p < 0.05). Statistical test: GO terms were selected from the top sorting by adjusted P-value (p adjusted < 0.05, one-tailed hypergeometric test with Benjamini–Hochberg correction). Bars depict fold enrichment for terms with p < 0.05. e AUCell-based enrichment scores (AUC scores) showing similarity of gene expression signatures of the three clusters compared to their respective natural counterparts as assessed by Cheng et al.²³. f UMAP of four integrated reference datasets tracking cells during developmental stages from morula to E7.5 gastrulation in murine embryonic and extraembryonic lineages, in comparison to RtL-embryoid VE-, Epi-, and ExE-like cells. g AUCell-based enrichment scores comparing gene signatures of 2D mono-culture and 3D co-culture induced ESCs, TSCs, and XEN cells to natural murine embryo cell clusters from f. Source data of d are provided as a Source Data file.