Extended Data Fig. 5: Analysis of E14 snRNA-seq data reveals differentiating neurons and progenitor cells.

(a) UMAP of E14 cells colored according to assigned cell cycle phase, based on cell cycle marker expression. (b) Expression of progenitor cell markers Hes5, Sox9, and Ascl1, and mature neuronal marker Snap25. (c) UMAP of E14 excitatory and inhibitory neurons colored by mapped cell type (colors match legend in Fig. 1c). Compare to Extended Data Fig. 2h. (d) Mapping of E14 onto P65 clusters using canonical correlation analysis, for excitatory neurons. Prediction score is averaged across cells within a cluster. Note weaker on-diagonal elements and stronger off-diagonal elements compared to E16, shown in Fig. 1d. Boxed areas point out regions of interest: AvPe/MnPO cell types are fairly well differentiated at E14, similar to E16, whereas MPN anterior cell types are less differentiated at E14 than at E16. (e) Distributions of identity score, defined as the average prediction score given to the assigned cell type, for E14 and E16 cell types. E16 identity scores correspond to the values on the diagonals in Fig. 1d and Extended Data Fig. 3b. (f) Identity scores (as defined in legend for (d)) at E14 and E16, separated by POA sub-region. Certain sub-regions, such as excitatory MPN anterior neurons (e-M), appear less differentiated than others at E14 but not E16. Boxplots show median, interquartile range, and 1.5 * interquartile range calculated across cell types, with cells from n = 4 E14 and n = 2 E16 biological replicates. (g) Expression of progenitor cell markers in a subset of E14 cell types. MPN cell types express higher levels than LPO + PS cell types. (h) UMAP of E14 progenitor cells, colored according to unsupervised clustering results. (i) Expression of progenitor marker Hes5 and migrating neuron marker Dcx. (j) Mapping of E14 progenitor clusters onto E16 brain region labels using canonical correlation analysis. Prediction score is averaged across cells within a cluster. (k) Expression of region-specific marker genes defined at E16 and P65 (as in Extended Data Fig. 3l) among E14 progenitor cell clusters.