Fig. 3: Expression of gene modules defining fate choice and commitment along the differentiation trajectories.

a Overview of the analyzed bifurcations on UMAP embedding. b Analysis of the bifurcation representing fate choice between proprioceptor and mechanoreceptor lineages (branches 8 and 9 of Fig. 1c). c UMAP plots showing expression of markers for mechanoreceptor and proprioceptor lineages and validated in vivo (see Supplementary Fig. 3). d, e Scatter plots show average expression of mechanoreceptor and proprioceptor modules in each cell along the mechanoreceptor and proprioceptor lineages. Early competing modules (d) show gradual co-activation, followed by selective upregulation of one fate-specific module and downregulation of the alternative fate-specific module. Late modules (e) show almost mutually exclusive expression within the proprioceptors and mechanoreceptors after bifurcation reflecting commitment to either fates. Color codes as in (a). Top ten highest differentially expressed genes are shown, as well as transcription factors (TF). f Analysis of the bifurcation representing mechanoreceptor fate choice between Ntrk2 and Ret/Ntrk2 lineages (branches 10 and 11 of Fig. 1c). g, h In vivo validation of the branches, with expression of Anxa2 for Ntrk2 fate and Grik1 for Ret/Ntrk2 fate (n = 3 animals). Scale bars, 10 µm. i, j Scatter plots show average expression of Ntrk2 and Ret/Ntrk2 modules in each cell among the two mechanoreceptor sub-lineages. Early competing modules (i) show gradual co-activation, followed by selective upregulation of one fate-specific module and downregulation of the alternative fate-specific module. Late modules (j) show almost mutually exclusive expression within the two mechanoreceptors lineage after bifurcation. Color codes as in (a). Top ten highest differentially expressed genes are shown, as well as transcription factors (TF).