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Related Experiment Video

Updated: May 6, 2026

Laser Capture Microdissection of Paraformaldehyde-Fixed Mouse Liver Tissue for RNA Analysis
09:21

Laser Capture Microdissection of Paraformaldehyde-Fixed Mouse Liver Tissue for RNA Analysis

Published on: April 17, 2026

152

Laser Capture Microdissection of Paraformaldehyde-Fixed Mouse Liver Tissue for RNA Analysis.

Wei-Lan Zeng1, Ming-Ming Zhang2, Wei-Jie Zeng3

  • 1Biomedical Research Center, Southern Medical University; School of Traditional Chinese Medicine, Southern Medical University; weilanlan21810500@smu.edu.cn.

Journal of Visualized Experiments : Jove
|May 4, 2026
PubMed
Summary

This study presents a laser capture microdissection (LCM) protocol for extracting high-quality RNA from fixed mouse liver tissue. The method enables targeted gene expression analysis in specific histological regions.

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Area of Science:

  • Molecular Biology
  • Histology
  • Genomics

Background:

  • Laser capture microdissection (LCM) allows isolation of specific cells from tissue sections.
  • Analyzing gene expression in fixed tissues requires efficient RNA extraction protocols.
  • Paraformaldehyde (PFA) fixation is common but can impact RNA integrity.

Purpose of the Study:

  • To present a detailed protocol for RNA extraction from PFA-fixed, OCT-embedded mouse liver using LCM.
  • To assess the purity and integrity of RNA obtained for downstream transcriptomic analysis.
  • To enable spatially resolved gene expression studies in fixed liver tissues.

Main Methods:

  • Tissue fixation with PFA, sucrose dehydration, OCT embedding, and cryosectioning.
  • Hematoxylin staining for histological visualization.
  • LCM for collecting microscale samples (approx. 1,000 cells) from targeted areas.

Main Results:

  • High-purity RNA obtained (A260/A280: 1.9-2.1).
  • RNA Integrity Number (RIN) of 6.7 ± 0.9, indicating expected PFA-induced fragmentation.
  • Quantitative PCR and RNA sequencing confirmed RNA suitability for sensitive analyses (e.g., high Q20/Q30 scores).

Conclusions:

  • The developed LCM protocol successfully yields RNA of defined purity and integrity from specific histological regions of PFA-fixed liver.
  • This method supports spatially resolved, targeted gene expression analysis in fixed tissues.
  • The protocol is valuable for researchers studying gene expression in defined cellular compartments of archival or fixed samples.