Previous studies have established that alterations in gene expression influence the development of Alzheimer’s disease (AD). These changes can be affected by methylation and miRNA regulation. Due to the important role of gene expression and regulation in this disease, much current research has focused on determining the exact changes in gene expression involved in AD and the mechanisms that cause those changes. Greater understanding of the disease would result in better methods of treatment and diagnosis. To determine which genes are turned on or off in AD, genome-wide expression changes were analyzed by RNA-sequencing of mRNA from hippocampus and blood of control and AD mice. Expression of miRNA known to change methylation status in AD was also assessed by qPCR to determine how miRNA and methylation work together to affect this disease. Sequencing data found 230 genes in hippocampus, 58 genes in blood, and 8 overlapping genes showing significant differential expression (p value ≤ 0.05); while qPCR data showed significantly increased expression of Mir 17 in AD. The novel gene expression changes and methods of gene regulation shown by this research clarify the processes behind several aspects of AD. In addition, the changing genes identified in blood could serve as potential biomarkers for AD diagnosis.