Figure 2.
Lineage Segregation of Cells into Inner Cell Mass, Trophectoderm, Epiblast, and Primitive Endoderm
(A) t-SNE plot of all cells, as in Figure 1E, showing ICM and TE assignment of cells. Cells from E5 are highlighted in the lower left insert. The ICM-TE cell classification was done using PAM clustering in a PCA dimensionality-reduced sub-space (Figure 2B and Supplemental Experimental Procedures).
(B) PCA biplot showing ICM and TE classification of cells from E5. Cells were classified as ICM or TE using PAM clustering in the PCA dimensionality-reduced space with the 250 most variable genes across all non-pre-lineage E5 cells as input (Supplemental Experimental Procedures). Cells in embryos with a pseudo-time <12.5 were assigned as pre-lineage. Genes with high PC loadings are shown. Colors indicate the weighted mean of the expression of previously known lineage markers using weights −1 and 1 for ICM and TE genes, respectively.
(C) Heatmap of E5 cells and the top 500 differentially expressed genes between ICM and TE E5 cells (top 250 genes from each lineage). Upper colored bar indicates embryo membership, lower bar indicates lineage. Right-hand-side bars indicate the log2 fold-change of the TE divided by ICM mean-expression level for each gene and embryonic day (E5–E7).
(D) PCA biplot showing EPI and PE classification of ICM cells from E5. Cells were classified as EPI or PE using PAM clustering in the PCA dimensionality-reduced space with the 250 most variable genes across all ICM cells that belonged to the right-most hierarchical cell-cluster in Figure 2C (Supplemental Experimental Procedures). Genes with high PC loadings are shown. Colors indicate the weighted mean of the expression of known lineage markers using weights −1 and 1 for EPI and PE genes, respectively.
(E) Heatmap of E5 cells and the top 200 differentially expressed genes between EPI and PE E5 cells (top 100 genes from each lineage). Upper colored bar indicates embryo membership, lower bar indicates lineage. Right-hand-side bars indicate the log2 fold-change of the PE divided with EPI mean-expression level for each gene and embryonic day (E5–E7).
(F) Number of cells (upper table) and lineage-specific genes (lower table) per embryonic day (E5–E7) and lineage. TE, trophectoderm; EPI, epiblast; PE, primitive endoderm.