Fig. 2: Transcriptomic landscape during early trophoblast development.

a UMAP plot showing the integrative clustering and annotation of bin50 from the labyrinth and JZ; E7.5 S1, E7.5 S2, E8.5 S1, E8.5 S2, and E9.5 S1 sections were used for this analysis. b E7.5 S1, E8.5 S1, and E9.5 S1 uterine sections are shown with (top) and without (bottom) trophoblast structures. c Bubble plot showing the expression profiles of representative marker genes. Gene labels are displayed in the left panel, and corresponding clusters are annotated and colored in the top and right panels. Colors from black to yellow indicate low to high gene expression levels. d Multicolor display of representative markers and magnified images of the ectoplacental cone regions in section E8.5 S1. e Top: spatial visualization of deconvoluted cell types in the sections in b. Bottom: magnified images showing the cellular composition in the regions in the square of the upper panel. f Heatmap showing scaled proportions of the cell types in each cluster in section E8.5. S1. g Left: spatial RNA velocity streamlines visualization of the directional flows. Right: RNA velocity PAGA graph predicting the developmental trajectory of the ectoplacental cone and P-TGCs in section E8.5 S1. Bins are colored by cluster identity, as in a. h Transcript expression of Hand1 in each cluster across early stages and its median regulon activity score (RAS) among all the clusters.