Alzheimer's disease (AD) is a significant neurodegenerative disorder of the elderly. In order to develop potential therapeutic strategies for the management of this order, it is very critical to obtain a better understanding of the global gene changes underlying the progression of AD pathogenesis. In this study, we used RNA-seq technology to analyze global differential gene expression in the model neuroblastoma cell line NG108-15, transfected with α4β2 nAChRs, and treated or untreated with full-length beta amyloid (Aβ1-42), to gain insights into the underlying mechanisms of beta amyloid-induced neurotoxicity. Cells were treated with media or 100nM of Aβ1-42 for 3 days, followed by extraction and purification of their RNA. Multiplexed RNA-seq libraries were prepared from the cellular RNA and paired-end 100-bp sequencing was conducted using an Illumina HiSeq 2500 sequencer. Fold changes in the expression of transcripts (and hence, genes) between untreated and Aβ-treated samples were determined. Ingenuity pathway analysis (IPA) was employed to determine the cellular pathways. Treatment with Aβ1-42 in α4β2 nAChR-transfected cells differentially modulated the expression of 15 prominent genes as compared to that of untreated cells. Most notably, chrna4 and rcan3 (Regulator of Calcineurin) were upregulated 3-fold and 2-fold, respectively. The differential gene expression data identified by RNA-seq was validated by real time PCR, western blot and immunocytochemistry. Additionally, we used Cas9/CRISPR gene-editing system to knock out Rcan3. The sorted cells were further treated or not with Aβ1-42 for 3 days and the impact of loss of Rcan3 was examined in terms of oxidative stress, mitochondrial membrane potential and cell viability. The absence of Rcan3 was expected to reduce the extent of oxidative stress, as measured by counting reactive oxygen species (ROS)-positive cells and mitochondrial membrane potential, as determined by tetramethyl rhodamine ethyl ester (TMRE) staining, on exposure to beta amyloid. This is the first study to conduct an entire transcriptome profile of model nerve cells expressing a defined high-affinity target receptor, namely nAChR, for beta amyloid. Characterizing the genes associated with calcium signaling, specifically Rcan3 after beta amyloid treatment will have significant impact on developing neuroprotective agents to reduce or prevent neuronal death in AD patients.