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Updated: Dec 12, 2025

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Isolation of Region-specific Microglia from One Adult Mouse Brain Hemisphere for Deep Single-cell RNA Sequencing
Published on: December 3, 2019
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Isolation of Microglia from Mouse or Human Tissue
Evan A Bordt1,2, Carina L Block3, Tiziana Petrozziello4
1Department of Pediatrics, Lurie Center for Autism, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
STAR Protocols
|August 13, 2020
Summary
This study optimized a method to isolate microglia, the brain's immune cells, using magnetic bead columns. This technique preserves microglial function for studying neuroinflammatory diseases and developing new therapies.
Area of Science:
- Neuroscience
- Immunology
- Cell Biology
Background:
- Microglia are the primary innate immune cells in the central nervous system.
- Current isolation methods can alter microglial function, impacting research outcomes.
- Understanding microglial behavior is crucial for neuroinflammatory disease research.
Purpose of the Study:
- To present an optimized protocol for isolating microglia from brain tissue.
- To ensure isolated microglia retain their functional integrity for downstream applications.
- To facilitate research into neuroinflammatory diseases and therapeutic development.
Main Methods:
- Utilized magnetic bead column separation for isolating CD11b+ cells (microglia).
- Applied the protocol to both mouse and human brain tissue.
- Focused on optimizing dissociation and isolation steps to preserve cell function.
Main Results:
- Successfully isolated functional microglia from diverse brain samples.
- The optimized protocol minimizes alterations to microglial cell state.
- Demonstrated the utility of isolated microglia for disease modeling.
Conclusions:
- The developed protocol provides a reliable method for obtaining viable microglia.
- This technique supports advanced research in neuroinflammation and therapeutic discovery.
- Preserving microglial function is key for accurate disease modeling and treatment development.

