This file contains Table S1–Table S8.

Table S1. Age-dependent gene expression changes in rTg4510 female hippocampus. List of the 165 probe sets that show altered age-dependent expression in rTg4510 animals, but not in controls, sorted by fold change between 6.1 month old rTg4510 animals and tTA controls. The presence of each gene in the microglial and synaptic transmission modules identified by Weighted Gene Coexpression Network Analysis (WGCNA) in AD patients [14] is indicated. Table S2. Inflammatory response pathways altered with age in rTg4510 female hippocampus. Inflammatory response pathways were the most significantly affected disease and biological functions represented by genes with age-dependent expression changes in the hippocampi of rTg4510 females. The activation z-score, calculated in IPA, predicts the direction of change for the function, with an absolute z-score≥2 considered significant. The number and identity of the molecules in the query set are indicated. Table S3. Pathways altered with age in rTg4510 female hippocampus. Inflammatory pathways were the most significantly affected canonical pathways represented by the genes with age-dependent expression changes in the hippocampi of rTg4510 females. Microglial gene expression modules identified in AD [14], were also highly represented in this dataset. The p-values indicate the probability that the gene set represented the canonical pathway by chance, as determined by the Fisher’s Exact Test, while the ratio is the quotient of the number of genes from the query gene set in the canonical pathway to the total number of genes in the pathway. Table S4. Gene expression changes in the CA1 hippocampal subregion of 6.1 month old rTg4510 females. List of the 1,734 probe sets that show altered expression in the CA1 region of rTg4510 animals compared to controls at 6.1 months, sorted by fold change between rTg4510 animals and tTA controls. If the probe set was also differentially expressed in other regions analyzed in this study, the fold change between rTg4510 and tTA are shown for that brain region. Table S5. Gene expression changes in the CA3 hippocampal subregion of 6.1 month old rTg4510 females. List of the 169 probe sets that show altered expression in the CA3 region of rTg4510 animals compared to controls at 6.1 months, sorted by fold change between rTg4510 animals and tTA controls. If the probe set was also differentially expressed in other regions analyzed in this study, the fold change between rTg4510 and tTA are shown for that brain region. Table S6. Gene expression changes in the DG hippocampal subregion of 6.1 month old rTg4510 females. List of the 118 probe sets that show altered expression in the dentate gyrus of rTg4510 animals compared to controls at 6.1 months, sorted by fold change between rTg4510 animals and tTA controls. If the probe set was also differentially expressed in other regions analyzed in this study, the fold change between rTg4510 and tTA are shown for that brain region. Table S7. AD-related expression moduels altered in the CA1 region of 6.1 month old rTg4510 femles. Microglial and synaptic transmission gene expression modules identified in AD [14]significantly altered in the CA1 region of rTg4510 mice. The p-values indicate the probability that the gene set represented the canonical pathway by chance, as determined by the Fisher’s Exact Test, while the ratio is the quotient of the number of genes from the query gene set in the canonical pathway to the total number of genes in the pathway. The genes in the query set from the rTg4510 data are indicated. Table S8. Pathways downregulated in the CA1 hippocampal region of 6.1 month old rTg4510 females. Canonical pathways and AD-related synaptic transmission gene expression modules [14] overrepresented by genes that are downregulated in the CA1 subfield of 6.1 month old rTg4510 females compared to tTA controls. The p-values indicate the probability that the gene set represented the canonical pathway by chance, as determined by the Fisher’s Exact Test, while the ratio is the quotient of the number of genes from the query gene set in the canonical pathway to the total number of genes in the pathway. (XLSX)