Fig. 2.

The premigratory neural crest displays high transcriptomic heterogeneity. (A) Leiden clustering revealed 16 distinct states (clusters) before and during EMT (developmental stages 12 to 22) (SI Appendix, Supplementary Text) (B) Dotplot depicting the expression of the top NC-specific genes within the different clusters. (C) Top three enriched genes for each cluster (Top and Bottom lines respectively), with their expression in the other clusters and hierarchical clustering between clusters. (D) Expression of key cluster-specific genes, including rpe65 (cluster 10), cyp26c1 (clusters 4/6/15), itga4, dlx2 (cluster 11), egr2, mafb (cluster 12), tnc (cluster 13), early olig4, hnf1b (cluster 3) and muscle-like NC specific myl1 (cluster 16). Gjb1 is expressed by all clusters but is highest in cluster 2. Genes expressed broadly in NC cells define a “canonical NC” signature: early tfap2b, tfap2c, sox9, snai2, and c9. Multipotency-related genes are present mostly until mid-neurula stage (pou5f1-1). (E) PAGA estimates cluster connectivity where line thickness increases with stronger connections.