Fig. 5
Comprehensive analysis of Single-cell sequencing (scRNA-seq) and spatial transcriptome analysis. a Dimensionality reduction analysis of SCI samples (1 day, 3 days, and 7 days after SCI) and uninjured samples. b Unsupervised clustering identified 39 clusters based on 66,428 single cells. c Unsupervised clustering and dimension reduction analysis annotated 15 main cell types (astrocyte, dendritic cell, myeloid-derived cells, endothelial cell, ependymal cell, fibroblast, lymphocyte, macrophage, microglia, monocyte, neuron, neutrophil, oligodendrocyte, oligodendrocyte progenitor cell, and pericyte) based on known cell markers. d Bar plot showed the cell number and percentage of the 15 cell types in all SCI and uninjured samples. e Venn diagram showing the intersection of microglial markers, DEFIRGs, DETIRGs, DEFIRG-related TFs, and DETIRG-related TFs. f Cellular feature plots of DEFIRGs in microglia. g Cellular feature plots of overlapping DETIRGs in microglia. h Cellular feature plots of overlapping TFs in microglia. i Normalization and clustering of the cell types with similar gene expression. j Hematoxylin and eosin (H&E)-stained sections and spatial gene expression in traumatic brain injury mice models