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Updated: May 16, 2026

Isolation of Region-specific Microglia from One Adult Mouse Brain Hemisphere for Deep Single-cell RNA Sequencing

Isolation of Region-specific Microglia from One Adult Mouse Brain Hemisphere for Deep Single-cell RNA Sequencing

Published on: December 3, 2019

Adapted Smart-seq3xpress Facilitates Selective Microglial Transcriptomic Profiling From Frozen Brain Tissue.

Dominika Dostalova^1,2, Pavel Abaffy^1,3, Eva Rohlova³

¹Laboratory of Glial Biology and Omics Technologies, Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czech Republic.

Cellular and Molecular Neurobiology

|May 14, 2026

Summary

This summary is machine-generated.

Researchers developed a novel method for single-nucleus RNA sequencing of microglia from fresh-frozen brain tissue. This technique enables high-resolution transcriptomic analysis of microglia in archival samples, advancing neuroinflammation research.

Keywords:

Enrichment Frozen tissue Microglia PU.1 Single-nucleus RNA - sequencing Stroke

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Harnessing the Power of MicroRNA Cargoes in Small Extracellular Vesicles Released from Fresh-Frozen Human Brain Sections

Harnessing the Power of MicroRNA Cargoes in Small Extracellular Vesicles Released from Fresh-Frozen Human Brain Sections

Published on: November 8, 2024

Area of Science:

Neuroscience
Immunology
Genomics

Background:

Microglia play a critical role in brain health and disease, particularly neuroinflammation.
Single-cell RNA sequencing (scRNA-seq) is powerful for studying microglia but limited to fresh tissue.
Analyzing microglia in cryopreserved or archival samples is challenging due to lack of specific protocols.

Purpose of the Study:

To develop a method for microglial nuclei profiling from fresh-frozen brain tissue using Smart-seq3xpress.
To enable high-resolution transcriptomic analysis of microglia in archival samples.
To overcome limitations of standard single-nucleus RNA sequencing for microglial studies.

Main Methods:

PU.1-based enrichment of microglial nuclei from fresh-frozen tissue after brief formaldehyde fixation.
Thermolabile Proteinase K treatment to reverse cross-links for Smart-seq3xpress compatibility.
Benchmarking in a mouse model of ischemic stroke.

Main Results:

The developed method yielded higher gene and UMI counts and a greater proportion of coding reads compared to standard protocols.
Transcriptomic profiles accurately reflected whole-cell RNA sequencing data.
The method successfully detected microglial activation markers and subpopulations.

Conclusions:

This approach enables high-resolution transcriptomic analysis of microglia from fresh-frozen and archival brain samples.
It expands the utility of biobanked material for neuroinflammatory disease research.
Facilitates basic and translational studies by providing cellular insights from preserved tissues.