Figure 4.

Temporal dynamics during epiblast, primitive streak, and nascent mesoderm commitment

(A) Vein plots describe the continuous transition of cell types to their direct descendants (represented by diagonal flows spanning time points), and the dynamic relative frequencies of these cell types in the embryo over time (vein width on the y axis). This panel shows transitions emanating from the epiblast to the primitive streak (PS) and definitive ectoderm (DEc). Vein connection width represents flow flux at each time point. Dashed arrow represents a link to a subsequent panel (here, F).

(B) Bars represent the composition of direct differentiation targets of epiblast cells at each time group.

(C) Row-normalized heatmaps of expression in the epiblast per time. Genes with homogeneous expression are shown on the left, clusters of variable expression, on right.

(D) Gene-flow plots in which nodes represent MCs, and edges link each MC to the source MC with the highest contributing flow in the network. MC level expression versus MC mean time is depicted for Eomes, Tdgf1, and Irx5 genes. Only MCs from Epiblast and related cell types are shown.

(E) Expression of members of TGF-β superfamily signaling modulators over time. Line graphs represent total transcript levels for the entire endoderm or mesoderm for each age group.

(F) Vein plot (as in A) describing the flow model emanating from PS to its predicted direct descendants.

(G) Predicted fate composition of early/late NM cells at each age group. Columns represent fraction of cells committing to each of the mesoderm fates, separated into hematoendothelial and extraembryonic lineages (negative values), and embryonic mesoderm (positive values).

(H and I) Vein plots illustrating the flow emanating from early and late NM (respectively) and gene-flow plots for key NM markers.

See also Figure S4.