Figure 6. Integrated atlas of posterior sox10:GFP⁺ cell types spanning the embryonic to larval transition.

(A) Global UMAP embedding demonstrating the clustering of cell types across 48–50 hpf and 68–70 hpf. Cell labels were transferred from the original curation (Figure 1—source data 2) to the new atlas after its creation, allowing for assessment of cell type organization. (B) Previously identified mesenchyme clusters form a large discernible cluster marked by prrx1b, twist1a, foxc1a, and snai1a, which was separated into both chondrogenic and general mesenchyme, as denoted by its differential expression of barx1 and dlx2a. Importantly, nearly every 48–50 hpf cell type nests with a cluster at 68–70 hpf. (C) Pigment cells clusters reflect differentiation paths described in Figure 4A. Melanophores at 48–50 hpf group near to the 68–70 hpf melanophore cluster, bipotent pigment progenitors bridges both the iridophores and melanophores. Xanthophores cluster separately, reflecting their distinct lineage of origin at this developmental window. (D) Detailed analysis of the larger neural/neuronal cluster shows clear progression of cell fates from progenitor to differentiating glia or neuron. The expression of enteric neuronal markers is distinct from other subtypes at this dataset.

Figure 6—figure supplement 1. Annotated sox10:GFP⁺ atlas labeled by cell types.

(A) UMAP labeling the 27 new clusters formed after merging the 48–50 and 68–70 hpf sox10:GFP⁺ datasets. (B) Following label transfer integration, major cell type classifications (Figure 1) group together into distinct clusters across the UMAP. (C) High-resolution visualization of both clustering of original cluster labels, as well as their position within the UMAP. Cell categories segregate in the dendrogram largely as expected from the UMAP visualization. (D) Additional markers, including foxd3, dla, phox2a, hoxb5b, etv1, and pbx3b, are shown by UMAP for validation of the neural/neuronal clusters.

Figure 6—figure supplement 2. Differential expression among pigment, mesenchyme and neural/neuronal subsets of the sox10:GFP⁺ atlas (A) UMAP visualization of cells labeled by source identity (either 48–50 hpf or 68–70 hpf) following integration.

All 48–50 hpf cells (pink) approximately map to a major cluster found at 68–70 hpf (aqua). (B–D) Subset of the pigment clusters (B), the mesenchyme clusters (C), and the neural/neuronal clusters (D) highlighting several differentially expressed genes between the cells derived from each timepoint.