Fig. 2: RNA sequencing shows microglia control immune responses to SCI.

a–c Volcano plots showing SCI-dependent genes (a), microglia-dependent genes in SCI (b), and microglia-dependent genes at baseline (c). Selected genes that changed the most are labeled. The main effect of SCI was increased gene expression, and the main effect of microglia depletion was decreased gene expression. a–c Data generated from analysis performed In DeSeq2 (Wold test) and Gene Network Analyst. d Pie chart showing more genes were decreased by microglia depletion in the SCI condition than the sham condition. e, f Analysis of SCI-dependent genes shows microglia depletion only had a modest effect on SCI-decreased genes (e), but prevented an increase in most of the top (51.2%) SCI-increased genes (f). g–i The 512 genes increased by SCI that failed to increase when microglia were depleted were entered into pathway analysis for biological processes (g), molecular functions (h) and cellular components (i). j Heatmap showing specific genes involved in the biological processes ‘Phagocytosis’ and/or ‘Cytokine production’ (scale = Z scores of FPKM values). k Venn diagram showing overlap between genes in the top 5 biological process. l Network analysis showing co-expression (purple) and predicted functional interactions (orange) between genes that overlapped in ≥3 of the top 5 biological processes (n = 31). m, n Interactions between the Ccl2 edge node (m) and Tlr2 center node (n) with other genes in the network. N = 3-4 mice per group. Source data are provided as a Source Data file. See also Supplemental Tables 1–3.