Fig. 5

Single-cell data identifies contrasted genetic signatures of neuronal maturation amongst PSNs subpopulations. a t-SNE plots representing the two groups of PSNs at E11.5 described in Fig. 4. b, c Gene set enrichment analysis of Runx3^High and Runx3^Low neurons visualized by network. Each node represents a GO term, edges are drawn when there are shared genes between two GO terms. Interestingly, the neurotransmission category is highly represented in the Runx3^High population while apoptosis and DNA-binding are more represented in the Runx3^Low population. c Gene ontology analysis of the Runx3^High (top panel) and Runx3^Low (bottom panel). The graph shows most significant terms reflecting neuronal features. d Examples of differentially expressed genes found in Runx3^High or Runx3^Low subpopulations of PSNs. e Expression of select genes that encode proteins relevant to neuronal physiology (asterisks depict genes important for the generation of action potentials). Note that this category of genes is uniquely over-represented in Runx3^High PSNs. f Expression of genes important for the generation a mature action potentials (Scn3b/7a/9a) and for mechanotransduction in PSNs (see text for details). Boxplots visualize the summary of the dataset (minimum, lower quartile, median, upper quartile and maximum). g Summary of the differential expression profile of the two subpopulations of PSNs, with a majority of genes (17,352 genes) showing similar patterns; genes enriched in Runx3^High PSNs encode proteins associated with synaptic communication. h UMAP plot of PSNs single cells RNA-seq data from E11.5 and E12.5 (before and after cell death period, respectively), revealing two clusters at E11.5 (blue and red, corresponding to the clusters in a) and only one cluster at E12.5 (green). i Expression pattern using UMAP plots with specific Runx3^High and Runx3^Low marker genes shows that marker genes of E11.5 Runx3^High remain expressed at E12.5. j Unspliced–spliced phase portraits (left, cells colored according to a) and u residuals (right) are shown for each gene in i. k Velocity estimates projected onto the two-dimensional UMAP plot of the dataset shown in h, and with a similar color code. Velocity vectors indicate positive velocity (strong directional flow) from one cell state to another and overall can be interpreted as a maturation directionality from Cluster 1 to Cluster 3. Source data are available as a Source Data file