Fig. 1

Transcriptomic profiling of innate spinal cord repair in adult zebrafish. A Experimental pipeline to generate a single-cell atlas of zebrafish cells after SCI. SC tissue collection, nuclear isolation and single nuclear RNA-seq (snRNA-seq) were performed on wild-type fish at 1, 3 and 6 wpi. Uninjured SC nuclei were used as 0 wpi controls. 10x genomics sequencing with v3.1 chemistry was performed. Two biological replicates were used at each time point, and SC tissues from 50 animals were pooled into a single biological replicate. B Merged UMAP representation of the complete dataset. Two biological replicates, 4 time points and 58,973 cells were clustered into major spinal cell populations including Neurons A and B, glia/ependymo-radial glial cells (glia/ERGs), oligodendrocyte precursor cells (OPCs), oligodendrocytes (Oligos) A and B, Leukocytes A and B, and Erythrocytes. C Marker gene expression in the major cell types identified after SCI. Dot plot shows canonical markers are enriched in their respective cell types. Dot colors and diameters represent average gene expression and percent cells with at least one UMI detected per gene, respectively. Feature plots depicting the distributions of canonical markers corresponding to the major cell populations are shown. D Distribution of major cell types during SC regeneration. For each time point, cell proportions were normalized to the total number of cells present at that time point. E Heatmap showing top 10 differentially expressed (DE) genes in the major cell populations identified by snRNA-seq. Yellow and black represent highly enriched and low-expression genes, respectively. Source data are provided as a Source Data file.