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Additional file 1: Supplementary Figure S1. a-c. Assessment of soluble Aβ42 and Aβ40 levels as well as Aβ42 and Aβ40 ratio of hippocampal samples from mice with A+ transgene (APPswe/PS1dE9) revealed no significant diet effect. Data are presented as mean + SEM, n = 5–6, Two-way ANOVA. d Representative immunofluorescence images of β-amyloid plaques stained with X-34 (blue) surrounded by 22C11-positive dystrophic neurites (red), and Iba1-positive microglia (green) from A+Tw and A+T+ mice from both STD and TWD groups. Scale bar 10 μm. e Counting of 22C11-positive neurites revealed no diet nor genotype effect. f Quantification of 22C11-positive area (pixels) around β-amyloid plaques revealed a statistically significant genotype x diet interaction (p 2.5 or 2.5 or 0.5) with Trem2”, “Genes correlated (r>0.3) with Trem2”, “Upregulated in AD-associated microglia (Keren-Shaul)”, and “Regulation of canonical Wnt signaling pathway”. Right heatmap: respective log2 fold change (log2(FC)) values from TWD vs. STD comparison. Highlighted are top significantly up- and down-regulated genes for TWD vs. STD comparison regarding each term (FDR