Fig. 4

Transcriptional changes following long-term peripheral myeloid cell engraftment. a Venn diagrams displaying the number of differentially expressed genes (DEGs, numbers provided) generated in transcriptional comparisons between mice (control, WT CON; irradiated, GFP-BM CON; monocyte-engrafted, GFP-BM REPOP) in the hippocampus (HC, gray), cortex (CTX, red), and thalamus + striatum (THAL, tan). b–d Volcano plots displaying the fold change of genes (log2 scale) and their p values (−log10 scale) between WT CON vs GFP-BM REPOP in the cortex (b), hippocampus (c), and thalamus + striatum (d). Plots are further separated by the effect of irradiation and presence of monocytes alone. e Heatmap of the monocyte signature (selected DEGs conserved in all three brain regions in monocyte-engrafted mice). f Signed bicor network shows the effects of brain region (BrainRegion), irradiation, and treatment, which are separated into distinct colored modules. g–i Monocyte signature: Module eigengene trajectory of darkgreen (g), heatmap of gene expression value in darkgreen (h), and a STRING interaction map of darkgreen (i). Red nodes indicate genes enriched in the gene ontology (GO) term defense response. (j–k) Irradiation: Module eigengene trajectory of salmon (j) and heatmap of gene expression value in salmon (K). l–n Effects of monocytes specific to the hippocampus: Module eigengene trajectory of red (l), heatmap of gene expression value in red (m), and a STRING interaction map of red (n). Red nodes indicate genes enriched in the GO term cilium organization. o Cell-type enrichment heatmap displays genes associated with specific cell types within a given color module. Values provided indicate the number of genes within the network associated with that a specific cell type. *** = 6+ genes. ** = 3+ genes.