Fig. 6
DCN is basally enriched for cytokine proteins and homogenates induce an inflammatory response in a cultured microglia cell line. A, B Differences in cytokine protein expression between regions in WT mice measured by multiplex array (N = 5). A DCN vs. EC. B Cerebellum (CBM) vs. cortex (CTX). C Heatmap of expression z-scores from multiplex cytokine array for each protein across regions and genotypes for WT and App KI mice. Two-way ANOVAs were performed to test for main effects of region and genotype and interaction effects, followed by Tukey HSD post hoc tests (p < 0.05). D Schematic of experiment stimulating cultured BV2 microglia with homogenates of EC or DCN, LPS (positive control) or DPBS (negative control), followed by RNA extraction after 4 h. E Venn diagram of the number of differentially expressed genes (DEGs) in each stimulation condition compared to control (LFC >  ± 1, FDR < 0.1). F Log2-fold changes in gene expression in EC and DCN conditions compared to control, with DEGs in each condition indicated by colour. Top DCN-specific DEGs are labelled. G Heatmap showing differential expression in DCN vs. EC (p < 0.01, 115 genes) across all samples