Fig. 3

Transcriptomic profiling of hippocampal mRNA in 3-month-old WT and 5×FAD mice shows that the expression profiles mainly overlap with only minimal differences. A RNA-sequencing was performed on three independent samples from each group. A total of 16,123 mRNAs (raw count > 1) were detected in at least two WT samples, and 16,108 mRNAs were detected in the 5×FAD group. Non-overlapping regions indicate mRNAs detected only in isolated samples. B Correlation analysis demonstrated strong intra-group and inter-group consistency, visualized through an ellipse plot where Spearman’s correlation coefficients are shown in black. Flatter ellipses indicate stronger correlations. C Based on the PCA of the top 50% most variable mRNAs, normalized by Transcripts Per Million (TPM), there was no clear separation between the WT (blue dots) and 5×FAD (red dots) samples along PC1, suggesting overlapping transcriptomic profiles between the two groups. D A Venn diagram illustrating the overlap of mRNAs detected in both WT and 5×FAD mice, revealing 16,108 shared mRNAs, with 15 unique to WT. E Scatter plot comparing average TPM values for mRNAs between WT (x-axis) and 5×FAD (y-axis) groups, showing high overall correlation (R = 0.9942), indicating largely conserved expression levels. F Volcano plot of mRNA expression differences, indicating that 16,433 mRNAs showed no significant change. G Pie chart depicting the percentage of differentially expressed mRNAs versus non-significant mRNAs in 5×FAD compared to WT, from a total of 16,510 mRNAs. H Sector graph showing the number of differentially expressed mRNAs versus non-significant mRNAs related to upregulated and downregulated proteins. Only 3 up-regulated and 6 down-regulated proteins corresponded to differentially expressed mRNAs. I Venn diagram illustrating the intersection of differentially expressed mRNAs between this study and an AD-model online database, revealing 66 overlapping mRNAs. J Scatter plot of the 66 overlapping differentially expressed mRNAs between this study (x-axis) and the AD-model online database (y-axis), showing a high correlation in fold change (R = 0.9126)