Cost-effective next-generation sequencing has made unbiased gene expression investigations possible. Gene expression studies at the level of single neurons may be especially important for understanding nervous system structure and function because of neuron-specific functionality and plasticity. While cellular dissociation is a prerequisite technical manipulation for such single-cell studies, the extent to which the process of dissociating cells affects neural gene expression has not been determined. Here, we examine the effect of cellular dissociation on gene expression in the mouse hippocampus. We also determine to which extent such changes might confound studies on the behavioral and physiological functions of hippocampus. This dataset contains the data, software, and results the accompany a manuscript that is in the process of submission to the journal Hippocampus.