Journal: bioRxiv

Article Title: The nail mesenchyme creates a regeneration-specific ligand environment that orchestrates mammalian regeneration versus fibrotic wound healing

doi: 10.64898/2026.04.18.719303

Figure Lengend Snippet: (A) UMAPs of regenerating digit tip transcriptomes generated using Xenium-based single cell spatial transcriptomics with a custom 480 gene probeset (Table 2) optimized based on our scRNA-seq datasets to distinguish different digit tip cell types, including transcriptionally-distinct mesenchymal cell populations. The UMAPs show the merged 5 and 7 DPA datasets (top panel), the 10 DPA dataset (middle panel) and the 14 DPA dataset (bottom panel). In all cases, the UMAPs are annotated and color-coded to show cell types as identified by marker gene analysis (see Fig. S2). (B) Spatial plots of the datasets in (A), showing all detected cell types on representative regenerating digit tip midline sections. Individual cell types are color-coded as per the legend. (C) High-resolution Xenium Explorer images of the same representative sections as in (B), showing expression of Pdgfra mRNA to highlight mesenchymal cells (blue dots) and Spp1 mRNA to highlight the proximal bone (orange). Hatched white lines outline the regenerated tissue. Scale bars = 100 µm. (D-G) Spatial plots of the same representative sections as in (B), showing (D) transcriptionally-distinct mesenchymal cell populations, (E) vasculature-associated endothelial and mural cells (pericytes and VSM cells), (F) macrophages and neutrophils, or (G) epithelial cell populations. For both vasculature and immune cells, they did not cleanly segregate transcriptionally at earlier timepoints due to lower cell numbers, and thus are shown together. All Seurat-based spatial plots (B, D, E-G) are sized relative to the unprocessed Xenium Explorer images of the same sections (as in C).

Article Snippet: Hybridization was performed using a custom 480-gene mesenchymal panel (10x Genomics, 9XXV3X) or a custom 473-gene mesenchymal panel (10x Genomics, UT7ADC) prepared in TE buffer for 18–22 hours at 50°C.

Techniques: Generated, Single Cell, Spatial Transcriptomics, Marker, Expressing