Fig 2: Cell composition and differentiation trajectory of developing RPA. Integrated UMAP plot of cell clusters from RP. B. Median scaled ln-normalized gene expression of selected DEGs for RP cell clusters from (A). Cell type-enriched genes are listed on the right and labeled in the same colors as corresponding cell types. C. Bifurcation of the 381 top RP DEGs along two branches clustered hierarchically into five modules in a pseudo-temporal order. Development trajectories of RP cells are shown on the right and left, respectively. Red arrow indicates the pseudo-time of cell fate 1 (HEC); blue arrow indicates the pseudo-time of cell fate 2 (OB). Representative genes are shown on the right. D. RNA velocity recapitulating the dynamics of the RP cell differentiation. The arrows indicate the position of the future state. E. Expression pattern (left), unspliced–spliced phase portrait (middle; cells colored according to D), and u residual (right) of the RP cells are shown for CD248, CD34, COL1A1, and MATN1. RP, rib primordium.

Fig 3: Angiogenesis network construction and cell type-specific marker immunofluorescence analysis of developing TLV and RPA. Module visualization of the network connections and associated functions using CD34 as a hub gene. Gene-connected intra-modular degree is simultaneously indicated by spot size and color intensity. The hub gene CD34 is indicated in yellow. B. and C. Immunofluorescence analysis of CD93, CD248, and CD34 in TV and RP (B) and in LV (C). Green, white, and red indicate fluorescence signals of CD93, CD248, and CD34, respectively. White, yellow, and blue triangles indicate CD93+, CD248+, and CD34+ cells. White, blue, and red dashed lines in (B and C) indicate the regions of TV, LV, and RP, respectively. Scale bar, 400 µm.