Fig. 3

scRNA-seq of zebrafish neutrophils reveals a continuous maturation process.

a Schema showing the workflow for cell isolation, multiplexing and scRNA-seq, as well as the bioinformatics analyses applied. NO = no expression; INT = intermediate expression; HI = high expression. WKM = whole kidney marrow. b Uniform Manifold Approximation and Projection (UMAP) of single-cell RNA-seq data (n = 18,150 cells) showing cells from FACS-sorted neutrophil populations (lysC⁺/ mmp9 = NO, INT, HI) and unsorted whole-kidney marrow cells. The cluster labeled with an asterisk (*) represents a group of cells dominated by cell cycle effects (cp. Supplementary Fig. 3k–m). c, d Reference-based labeling of cell types by projecting cells to two zebrafish hematopoietic reference atlases in the same UMAP as in panel b^24,38. As expected, a strong overlap with genetically labeled Tg(mpx:GFP) neutrophils is observed (highlighted in color). e Harmony⁸² plot of the inferred neutrophil maturation trajectory in zebrafish (n = 15,876 cells). A continuous trajectory indicating a maturation continuum is observed. f Line plots of the distribution of sorted (NO, INT, HI) and unsorted neutrophil populations along the inferred trajectory. g Smoothed expression of lyz and mmp9 in neutrophils along the inferred trajectory.