Fig. 6: Monocyte-derived macrophages (MDMs) adopt diverse, time-dependent transcriptional phenotype in response to SCI.

a MDMs were computationally isolated for analysis between experimental conditions. b, c MDMs subdivided into 10 subsets based on dominant gene expression. d, e UMAP plots showing MDM subsets split by diet group and time post-SCI. Numbers in pie charts show major subsets as a percent of total MDMs in each group. f–k Violin plots showing gene-level changes within individual MDMs. Wilcox rank-sum tests, **p < 0.01, ***p < 0.0001, ****p < 0.0001. l–o Volcano plots showing increased genes (orange) and decreased genes (blue) in following SCI and microglia depletion. Selected genes are labeled. Wilcox rank-sum tests. p, q Pie charts of data in m and o showing that microglia depletion mostly caused an increase in MDM genes. Gene ontology shows these increased genes carbohydrate metabolism, calcium signaling and cell adhesion. r, s The effect of microglia depletion on MDM genes that were increased (r) or decreased (s) by SCI (see Sup. Fig. 10 for gene names in s). t, u Pathway analysis of all MDM genes affected by SCI and 7 or 28 dpi and also increased by microglia depletion, showing that microglia normally suppress several biological processes (t) and molecular functions (u) in intraspinal MDMs after injury. Data for each condition were pooled from n = 3–4 mice. Source data are provided as a Source Data file. See also Sup. Figs. 9 and 10.