Extended Data Fig. 8: Characterization of ten major developmental trajectories present during mouse organogenesis.

a, Heat map showing the proportion of cells from each of the 38 major cell types assigned to each of the 12 PAGA algorithm-identified groups. We merged 2 groups corresponding to sensory neurons (12 and 3) and another 2 groups corresponding to blood cells (6 and 7) as each pair was closely located in UMAP space upon visual inspection, yielding the 10 supergroups shown in a similar heat map in Fig. 4b. b, Same as Fig. 4a, but with colours corresponding to the 38 major cell clusters. c, Area plot showing the estimated proportion (top) and estimated absolute number (bottom) of cells per embryo derived from each of the ten major cell trajectories from E9.5 to E13.5. Although the estimated number of cells per embryo in each of these supergroups increases exponentially, their proportions remain relatively stable, with the exception of hepatocytes which expand their contribution by nearly tenfold during this developmental window (from 0.3% at E9.5 to 2.8% at E13.5). d, UMAP 3D visualization of epithelial subtrajectories (as in Fig. 4c), coloured as per the epithelial subtypes shown in Fig. 3a.