Fig. 3: The IFE Differentiation program is already established at E14.5.

a UMAP showing distribution of cell states as defined in the P0 IFE (Fig. 1) in the developing IFE (E14.5, E16.5, and P0). We observe two transition populations, IFEE.T1 and IFE.T2, at E14.5 and E16.5. IFE.T2 cells are proliferating transition cells. b Pie charts showing the proportion of major cell states at each developmental time point. IFE.B and IFE.TD decrease and increase, respectively, across development. c The expression of the indicated differentiation and proliferation markers projected onto the combined UMAP for all three developmental time points in a. d PHATE maps of cell populations defined in a, showing pseudotime progression at each developmental stage. The gray circle emphasizes the extension of terminal differentiation at P0. e Expression of the indicated differentiation and proliferation markers onto the combined PHATE maps from d. f Left panel, expression heatmap and expression pattern of 2801 pseudotime-dependent genes from the combined PHATE maps from d; these cluster into six gene modules. Right panel, expression heatmap of 149 pseudotime-dependent transcription factor (TF) genes from the combined PHATE maps from c. Representative TFs from each gene modules are color-coded and indicated on the left. Gene lists in Supplementary Data 1. g Gene ontology categories of genes differentially expressed at each developmental stage in all IFE cells. Gene lists in Supplementary Data 1. h Gene ontology categories of genes differentially expressed at E16.5 and P0 in IFE.B1 and IFE.B2 cells. Gene lists in Supplementary Data 1. i Gene ontology categories of genes differentially expressed at E16.5 and P0 in IFE.D and IFE.TD cells. Gene lists in Supplementary Data 1.