Fig. 5

Fig. 5 Transcriptional dynamics of NMPs during early development (A) Reprojection (UMAP) of the NMPs and adjacent clusters, color coded by annotated cell types. (B) Zoom in on the NMPs with color-coded cell types and superimposed RNA velocity streamlines. (C) Same projection but with cells color coded by their sox2/tbxta expression ratio; stronger yellow indicates higher sox2 and stronger magenta indicates higher tbxta. (D) Quantifying the proportion of cells in the NMP clusters relative to the total number of cells for each developmental stage. (E) Expression of sox2 (yellow) and tbxta (red) for segmented cells (12 hpf) derived by hybridization chain reaction (HCR). Cells co-expressing sox2 and tbxta, presumptive NMPs, have their boundary in white. (F) Same as (E) but at 16 hpf. (G) Quantification of presumptive NMPs (cells co-expressing sox2 and tbxta) obtained from the HCR image analysis. (H) Velocity trajectories are projected into a time series of aligned UMAPs centered around the NMPs and their adjacent clusters, colored by cell type. (I) Time-resolved quantification of the distribution of RNA velocity for NMPs along the neural-mesodermal axis. These are the normalized distributions of the magnitudes of individual RNA velocity vectors pointing toward either the neural or mesodermal tissues. (J) Pseudotime resolved scaled expression of genes involved in neural development (left axis) and mesodermal development (right axis). (K) Annotated cell-type visualized on the pseudotime axis rooted in the NMPs, recapitulating the neural (left) and the mesodermal (right) developmental transcriptomic trajectories. (L) Cell fraction from different developmental stages visualized along the pseudotime axis.