Extended Data Fig. 4: Transcriptomic analysis of microglia in the spinal cord following microglial Tgfbr2 deletion.

a A Venn diagram displays the number of differentially expressed genes (DEGs) in sorted microglia between Cx3cr1^CreER:Tgfbr2^fl/fl (KO) mice at 18 (D18) or 28 (D28) days post-tamoxifen administration, compared to Tgfbr2^fl/fl (WT) mice. DEGs were identified using DESeq2 normalization (Log₂ fold change≥2, q-value < 0.01). There were 668 DEGs at D18 compared to WT and 585 DEGs at D28 compared to WT. The 416 overlapping genes were defined as the core DEGs. b Top 50 hub genes from the 416 core DEGs and their interacting network were revealed using Cytohubba with the MCC algorithm. Genes in red bubbles represent upregulated genes following microglial Tgfbr2 depletion (compared to the WT group), while genes in blue bubbles represent downregulated genes. c Representative gene groups that were suppressed and induced following microglial Tgfbr2 deletion, compared to WT microglia. d, e The Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology Biological Process (GO_BP) enrichment analyses of the 416 core DEGs were performed using the Dr. Tom analysis platform (BGI), which employs the phyper function in R for two-sided hypergeometric testing. P values were adjusted for multiple comparisons using the Benjamini–Hochberg method to obtain q values, and pathways with q < 0.05 were considered significantly enriched. In the bubble plots, bubble size indicates the number of DEGs, while color represents the q value (red = low, blue = high). The ‘rich ratio’ denotes the proportion of DEGs annotated to each term relative to the total number of genes annotated to that term.