Fig. 6

Identification of the microglia clusters, cellular communication analysis, cell cycle analysis, and pseudo-time analysis. a Dimensionality reduction analysis of microglia from SCI samples (1 day, 3 days, and 7 days after SCI) and uninjured samples. b Unsupervised clustering identified 6 microglia subclusters (Microglia1-6). c Bar plot showed the cell number and percentage of the 6 microglia subclusters in all SCI and uninjured samples. d The Cleveland's dot plot showed the expression levels of 4 classical marker genes of microglia; the stacked bar plot displayed the proportion of 6 microglia clusters in different samples (7 SCI samples and 3 uninjured samples). e Heatmaps of the most variable markers of 6 microglia subclusters. f The cell cross-talk network showed the intersected cellular communication among 6 microglia clusters. g Cell cycle analysis of the 6 microglia subclusters. h The heat map showed the biological features and expression levels of 31 signaling pathways in 6 microglia clusters by gene set variation analysis (GSVA). i The cell trajectory state plot illustrated the developmental trajectory of microglia with pseudo-time, 5 cell states shown in different colors, and all cell subpopulations illustrated in the trajectory. j Violin diagrams showing the expression level of DEFIRGs and potential upstream TFs in 6 microglia subclusters. k Violin diagrams showing the expression level of M1 polarization markers in 6 microglia subclusters