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. 2023 Jul 27;12:e84679. doi: 10.7554/eLife.84679

Figure 6. Pseudotemporal trajectory analyses identify distinct progression routes and enriched genes among macrophage and neutrophil subpopulations.

Figure 6.

(A) Pseudotemporal trajectory analyses of macrophages and neutrophils in zebrafish heart. Macrophages and neutrophils were subset using Seurat and input in Monocle3. The root of the pseudotime trajectory of macrophages was set based on resident macrophage cluster Mac 3 highly express progenitor genes spi1 and coro1. Cells are colored by dark blue to bright yellow according to the earliest state to the latest state in pseudotime. Arrows indicate the direction of the cell-state transition through the pseudotime. Purple highlights the regenerative-associated direction, whereas green highlights the macrophage-delayed-associated direction. Directions of cell-state transition are indicated by Roman numerals. (B) Pseudotime of macrophages and neutrophils under each time point and condition is shown in the split UMAP plots. (C) GO and KEGG analysis of macrophage DEGs along pseudotime. DEGs, differentially expressed genes; GO, Gene Ontology; BP, biological process; KEGG, Kyoto Encyclopedia of Genes and Genomes; UMAP, Uniform Manifold Approximation and Projection.

Figure 6—source data 1. R script of pseudotemporal trajectory analysis.