Primer for immunohistochemistry on cryosectioned rat brain tissue: Example staining for microglia and neurons

Megan N. Evilsizor, Helen F. Ray-Jones, Jonathan Lifshitz, Jenna Ziebell

Research output: Contribution to journalArticlepeer-review

16 Scopus citations


Immunohistochemistry is a widely used technique for detecting the presence, location, and relative abundance of antigens in situ. This introductory level protocol describes the reagents, equipment, and techniques required to complete immunohistochemical staining of rodent brain tissue, using markers for microglia and neuronal elements as an example. Specifically, this paper is a step-by-step protocol for fluorescent visualization of microglia and neurons via immunohistochemistry for Iba1 and Pan-neuronal, respectively. Fluorescence double-labeling is particularly useful for the localization of multiple proteins within the same sample, providing the opportunity to accurately observe interactions between cell types, receptors, ligands, and/or the extracellular matrix in relation to one another as well as protein co-localization within a single cell. Unlike other visualization techniques, fluorescence immunohistochemistry staining intensity may decrease in the weeks to months following staining, unless appropriate precautions are taken. Despite this limitation, in many applications fluorescence double-labeling is preferred over alternatives such as 3,3'-diaminobenzidine tetrahydrochloride (DAB) or alkaline phosphatase (AP), as fluorescence is more time efficient and allows for more precise differentiation between two or more markers. The discussion includes troubleshooting tips and advice to promote success.

Original languageEnglish (US)
Article numbere52293
JournalJournal of Visualized Experiments
Issue number99
StatePublished - May 12 2015
Externally publishedYes


  • Antibody
  • Double-Labeling
  • Fluorescence
  • Iba1
  • Immunohistochemistry
  • Issue 99
  • Microglia
  • Neuron
  • Neuroscience
  • Pan-Neuronal
  • Rat

ASJC Scopus subject areas

  • Neuroscience(all)
  • Chemical Engineering(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)


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