(A–C) UMAP plots for cells collected at HH7 (1 somite stage), ss4 (4 somite stage), and ss8 (8 somite stage). Cell clusters are coloured and labelled based on their semi-unbiased cell state classifications (binary knowledge matrix available in Supplementary file 1). (D) Dot plots displaying the average expression of key marker genes across cell states at HH7, ss4, and ss8. The size of the dots represents the number of cells expressing a given gene within each cell population. (E) Feature plots revealing the expression of the pioneer factor Tfap2a and lineage restricted expression of neural (Sox21), placodal (Six1, Dlx5,), and neural crest (Pax7, Tfap2b) markers. (F–G) UMAP plots for ss4 and ss8 overlaid with RNA velocity vectors depicting the predicted directionality of transcriptional change. Cells are coloured by cell state classification (shown in B and C). Schematics summarise the key fate segregation events taking place at these stages predicted by RNA velocity analysis.