Extended Data Fig. 5: Molecular basis for VE-InterVE-DE transition.

(a) Heatmap representing DEGs in the InterVE cluster. Gene expression in this heatmap includes both DE-expressed genes (first part of the heatmap) and VE-expressed genes (the second part of heatmap), which are co-expressed in the InterVE cluster. Genes are hierarchically clustered. (b) Cumulative gene expression of Smoothened GO-FC. Boxplots show median value, bordered by upper/lower (75/25) percentile, whiskers showing max/min value in 1.5 * IQR (interquartile range) and outliers as black dots. Two-sided Mann-Whitney U test was used to determine the significance between AVE and InterVE as well as DE2 and InterVE; *=<0.05; **=<0.01; ***=<0.001; ns=non-significant. (c) CAT networks representing examples of GO-FC, where InterVE is fully separated from VE-lineages and aligned with DE-lineages. The VE-lineages are in yellow, DE-lineages in blue, InterVE in green, and other lineages in pink. (d) CAT networks representing examples of GO-FC, where InterVE is aligned with VE-lineages and separated from DE-lineages. The VE-lineages are in yellow, DE-lineages in blue, InterVE in green, and other lineages in pink. AVE – anterior visceral endoderm, DE1- early definitive endoderm, DE2 – later definitive endoderm, EmVE – embryonic visceral endoderm, ExVE – extra-embryonic endoderm, FG – foregut, FP – floorplate, HG – hindgut, InterVE – intermediate visceral endoderm, LIV – liver, MG – midgut, NOTO – notochord, PE – parietal endoderm, PS1 – early primitive streak, PS2 – later primitive streak.