Supplementary Materials aba2084_Tables_S1_to_S7. to regenerate their entire systems, many avian and mammalian types mostly visit the wound curing stage with out a reparative regeneration procedure (and and and and and distributed very similar epithelial-hematopoietic enrichments (fig. S2D). The individual homologs of the genes (and distributed a differential appearance signature similar compared to that of and is necessary for the differentiation from the mucosal-producing goblet cells in the intestinal epithelium (in both uninjured and regenerating fin tissue (see Components and Strategies). transcripts are spread within the epithelium regardless of the sample collection stage and reflect a round morphology of the cell expressing it (fig. S3, A, C, E, and G to I). A proportion of were included for assessment. Cells were 1st grouped by major cell types and then separated into preinjury and regenerating phases. Darkness of dot color: relative expression level. Dot size: percentage of cells in the cluster that express the specified gene. (C) In situ hybridization targeting of 4-dpa fin tissues. Brown dots indicate positive RNA signals from target genes, while pale blue blocks represent hematoxylin-stained cell nuclei. Zoomed-in views are presented. Original images can be found in fig. S4. All epithelial layers are above the black dotted lines. (D) Clustering assignment of epithelial cells plotted on UMAP axes calculated with only epithelial cells. Cells are colored by their epithelial layer identity as in (A). (E) The same UMAP visualization as in (D), with cells colored by stage of collection. Arrows connect the groups of comparison, with a direction from preinjury stage to regenerating stages (1, 2, and 4 dpa). Numbers next to the green AC-4-130 triangle: number of genes up-regulated in regenerating stage. Numbers next to the red triangle: number of genes down-regulated in regenerating stage. (F) Clustered GO enrichment for genes up-regulated in regenerating basal, intermediate, and AC-4-130 superficial epithelial cells comparing to their preinjury counterparts. GTPase, guanosine triphosphatase; ER, endoplasmic reticulum; PKN, protein kinases N; snRNP, small nuclear ribonucleoprotein. Although the same three-layer classification of epithelial cells could be defined when cells from regenerating stages RB were integrated with the preinjury cells, the expression of the commonly used layer-specific marker genes changed dramatically during regeneration: Superficial epithelial marker expanded into basal and intermediate layers of the epithelium, the intermediate layer marker was also highly expressed in the AC-4-130 basal layer, and the basal epithelial marker was barely detectable in the postinjury cell populations AC-4-130 (Fig. 3B) (value of 0.0001). We focused on expression patterns of all claudin and keratin genes in zebrafish and found that labeled the superficial cluster; labeled the mucosal-like cluster; labeled the intermediate cluster; and and labeled the basal cluster (Fig. 3B). Claudin genes are expressed in a tissue-specific manner in zebrafish and are generally considered to be the proteins responsible for regulating the paracellular permeability in the vertebrate epithelium (and new candidates, including (Fig. 3C) as well as (fig. S4, A to H). Comparing with the known marker value of 0.01; Fig. 3E). We performed gene ontology (GO) enrichment analysis on genes up-regulated in the regenerating stage by layer and found both common and layer-specific programs associated with regeneration ((fig. S5, A to C) (and was first observed at the basal layer of the wound epidermis at 1 dpa but diminished as regeneration proceeded (fig. S4, I to K). On the contrary, showed expression at later stages and was enriched in.