Extended Data Fig. 4: Emergence of cell-type heterogeneity from gastrulation to neurulation.

a, Scheme of tissue sampling between E7 and E8.5. b, t-SNE from Fig. 1 overlaid with cells sampled E7–E8.5 and belonging to dendrogram clades 1–4. c, t-SNE overlaid with expression of lineage-specific marker genes. d, Uniform manifold approximation and projection (UMAP) of the mouse gastrulation single-cell atlas from ref. ¹⁷. e, Cells from b projected onto the embedding in d¹⁷. f, Pairwise correlation between neurulation-stage clusters of this Article and those of ref. ¹⁷. g–i, UMAP embedding of cells of the first (g), second (h) and third (i) cluster clade of the dendrogram. Cells are coloured and labelled by cluster identity. J–l, Heat map showing genes enriched in of the first (j), second (k) and third (l) cluster clade. m, UMAP embedding of subclustered neuroepithelial cells obtained from time points E7–E8.5. Cells are coloured by cluster. n, Heat map displaying expression of genes enriched in each of the neuroepithelial populations. o, Expression of broad neuroepithelial markers overlaid on the UMAP in m. p, Bar plot reporting the number of E7–E8.5 cells that clustered with the indicated neuroblast clusters. Clusters are sorted by number of cells. Bars are coloured as in l. q, Bar plots showing the dissection origins of the cells belonging to the clusters in p. r, UMAP representation of the E8.5 cells belonging to clusters no. 377, no. 366 and no. 338 (top left), and overlaid with expression of enriched transcription factors.