Fig. 1

Cortical microglia isolated from 2-month-old WT and APP-KI mice showed aberrant diurnal clock gene rhythms. a Summary of the CAGE sequencing from microglia pooled from 2-month-old WT and APP-KI mice: APP-KI resulted in the significant upregulation of 20% TSS (FDR < 0.05, Log₂Fc ≥ 1.5) and downregulation of 19% (FDR < 0.05, Log₂Fc ≤ − 1) at ZT2 as well as the upregulation of 14% TSS and downregulation of 31% at ZT14. b The circadian clock gene expression in microglia pooled from 2-month-old WT and APP-KI mice at ZT2 and ZT14. A total of ten clock genes were clustered into five color-coded modules with blue-red representation in each group. Values are represented as the Log₂ fold case/WT ZT2 from three different experiments carried out with microglia pooled from 12 2-month-old WT and 12 2-month-old APP-KI mice. c, e, g, and i Temporal changes in the mRNA levels of clock genes in cortical microglia of 2-month-old WT and APP-KI mice. The mRNA levels of BMAL1 (c), PER1 (e), PER2 (g), and REV-ERBα (i) were quantified using real-time PCR. Samples of each time point were pooled from three to four mice. Data are represented as the mean ± SEM of three independent experiments. The asterisks indicate a statistically significant difference from the WT group (*P < 0.05, **P < 0.01, and ***P < 0.001, two-way ANOVA test, interaction between time and genotypes). d, f, h, and j The average values of BMAL1 (d), PER1 (f), PER2 (h), and REV-ERBα (j) over the course of the day were calculated. Results were further analyzed using JTK_Cycle. The daggers indicate a statistically significant difference from the WT group (^{† † †}P < 0.001, two-way ANOVA test, interaction between genotypes)