Major depressive disorder (MDD) is a highly prevalent psychiatric disorder that has been ranked as the 4th leading cause of disability worldwide. Past clinical and laboratory evidence has confirmed that abnormalities of the hypothalamic-pituitary-adrenal (HPA)-axis are involved in MDD development. In this study, we took advantage of corticosterone treatment of PC12 cells as a model to identify genes regulated by HPA-axis hormones. Next-generation RNA-Seq technology was utilized to explore genome-wide differentially expressed gene profiles between control and corticosterone treated PC12 cells. 1,274 genes with at least two-fold expression level change were identified. Gene ontology analysis showed that the top enriched biological processes included response to glucocorticoid signaling, apoptosis, cell division/DNA replication, and neuron projection/axon guidance, highly consistent with phenotypes of PC12 cells treated with corticosterone. Taken together, RNA-seq data is reliable and comprehensive, thus providing a valuable resource for understanding underlying mechanisms of glucocorticoid-induced neuron malfunction.