Chronic wasting disease (CWD) is a neurodegenerative disorder in cervids and a member of the transmissible spongiform encephalopathies (TSEs), also known as prion diseases. We previously generated a persistently CWD prion infected RK13 cell line (RKC1-11) using elk PrPC expressing cells (elkRK13) that were generated with the lentiviral expression system. To investigate the differentially expressed (DE) genes involved in prion infection at the cellular level, we performed microarray analysis and identified the DE genes between CWD-infected (RKC1-11) and non-infected cells (elkRK13). Collectively, 88 genes were found to be differentially expressed (42 genes upregulated > 2-fold; 46 genes downregulated < 0.5-fold); additionally, 10 up- and 8 downregulated genes agreed with the results of the qRT-PCR. Among these genes, we chose 8 DE genes associated with cell growth, signal transduction, transport, immune response and apoptosis based on gene function analysis for further analysis. The expression of the selected genes was further validated using an animal model in normal- and CWD-infected TgElk mice showing clinical signs at 185 dpi. These identified DE genes in both the in vitro and in vivo model could help in understanding the diagnosis and pathogenesis of prion diseases.