Fig. 1: scRNAseq and pseudotime analysis of the developing somatosensory system.

a UMAP embedding representation of the single-cell RNA sequencing dataset, annotated by embryonic day. b RNA Velocity vectors projected onto the UMAP embedding, indicating differentiation directionality. c Differentiation trajectories inferred in a semi-supervised way on Diffusion space using ElPiGraph, revealing 12 main clusters represented within two main trajectories (branches A and B), 10 branches and 3 bifurcations (1, 2 and 3) on branch A. List of genes is provided in the Source data file. d, e Most significant biological aspects extracted using pagoda2 indicate cell state changes from cycling (Sox10⁺ and Sox2⁺) to post-mitotic cells (d) and from non-neuronal to neuronal cells (e) (Isl1⁺ and Tubb3⁺). f PC score from gene set related to GO term “positive regulation of cell migration” (GO:0030335) subtracted by the PC score for “negative regulation of cell migration” (GO:0030336) indicates a transition from migratory neural crest progenitors to settling neuronal populations. g UMAP plots of selected genes distributed along the trajectories and among cells states represented in (c–e). h Transcriptomic dynamic during neurogenesis and neuronal specification show that the different states account for the differentiation of sensory sub-classes that can be distinguished based on their specific expression of neurotrophic factors receptor and transcription factors (Ntrk1, Ntrk2, Ntrk3, Ret, Runx1 and Runx3). i E12.5 DRG sections immunostained for markers highlighted in (h) representing major sensory subpopulation at the trajectories endpoints and quantification (n = 3−5). Scale bar, 20 µm. Data are presented as mean values ± SEM. j Hierarchical bifurcation model of NCCs-derived sensory neurons differentiation within Branch A based on our scRNAseq data analysis (color code and cluster identity according to panel h). Mixed color squares reflect the potential fate choice that the lineage retains at the corresponding developmental point.