Hippocampal transcriptomic responses to enzyme-mediated cellular dissociation

Rayna M. Harris, Hsin Yi Kao, Juan Marcos Alarcon, Hans A. Hofmann, André A. Fenton

Research output: Contribution to journalArticlepeer-review


Single-neuron gene expression studies may be especially important for understanding nervous system structure and function because of the neuron-specific functionality and plasticity that defines functional neural circuits. Cellular dissociation is a prerequisite technical manipulation for single-cell and single cell-population studies, but the extent to which the cellular dissociation process affects neural gene expression has not been determined. This information is necessary for interpreting the results of experimental manipulations that affect neural function such as learning and memory. The goal of this research was to determine the impact of cellular dissociation on brain transcriptomes. We compared gene expression of microdissected samples from the dentate gyrus (DG), CA3, and CA1 subfields of the mouse hippocampus either prepared by a standard tissue homogenization protocol or subjected to enzymatic digestion used to dissociate cells within tissues. We report that compared to homogenization, enzymatic dissociation alters about 350 genes or 2% of the hippocampal transcriptome. While only a few genes canonically implicated in long-term potentiation and fear memory change expression levels in response to the dissociation procedure, these data indicate that sample preparation can affect gene expression profiles, which might confound interpretation of results depending on the research question. This study is important for the investigation of any complex tissues as research effort moves from subfield level analysis to single cell analysis of gene expression.

Original languageEnglish (US)
Pages (from-to)876-882
Number of pages7
Issue number9
StatePublished - 2019


  • genomics
  • hippocampus
  • reproducible research
  • transcriptomics

ASJC Scopus subject areas

  • Cognitive Neuroscience


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