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Related Experiment Video

Updated: Jan 14, 2026

Flow Cytometry and Single-Cell Analysis for Characterizing Microglia Activation in Early Postnatal Mouse Brain Development
09:48

Flow Cytometry and Single-Cell Analysis for Characterizing Microglia Activation in Early Postnatal Mouse Brain Development

Published on: October 3, 2025

667

Flow Cytometry and Single-Cell Analysis for Characterizing Microglia Activation in Early Postnatal Mouse Brain

Marianne Mengus1, Benjamin Boucher2, Roqaya Imane2

  • 1Azrieli Research Center of CHU Sainte-Justine; Pediatric Department, Faculty of Medicine, Université de Montréal; marianne.mengus@umontreal.ca.

Journal of Visualized Experiments : Jove
|October 20, 2025
PubMed
Summary

This study details two methods, flow cytometry and single-cell RNA sequencing, for analyzing microglia in mouse cerebellum. These protocols enable robust investigation of microglial diversity during early brain development and disease.

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Last Updated: Jan 14, 2026

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Area of Science:

  • Neuroscience
  • Immunology
  • Genomics

Background:

  • Microglia, the brain's immune cells, have diverse functions influenced by location and condition.
  • Understanding microglial heterogeneity is crucial for studying brain development and neurological diseases.

Purpose of the Study:

  • To present reproducible protocols for isolating and analyzing microglial populations in mouse cerebellar tissue.
  • To enable transcriptomic profiling of microglia for studying developmental changes and disease impacts.

Main Methods:

  • Optimized flow cytometry protocol for early postnatal mouse brain tissue, including enzymatic digestion and Percoll gradient centrifugation.
  • Single-cell RNA sequencing using 10X Genomics for transcriptomic analysis of isolated microglia.
  • Utilized CD45/CD11b gating, live/dead staining, surface marker profiling, and random forest classification for sex identification.

Main Results:

  • Established a robust method for high-quality neural cell suspension suitable for microglial analysis.
  • Enabled identification of microglial clusters and differential gene expression patterns.
  • Validated protocols for reproducible and adaptable microglial research.

Conclusions:

  • These complementary methods provide a framework for investigating microglial diversity in the cerebellum.
  • The protocols facilitate the study of microglial alterations during early brain development and following experimental perturbations.