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Enhanced RNA Preservation in Mouse Brain Tissue: A Strategy Combining Cardiac Perfusion with Hypersaline Immersion
Qinyu Ge1, Erteng Jia2, Tian Wen3
1State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
ACS Omega
|October 27, 2025
Summary
A new preservation strategy protects RNA integrity during spatial transcriptomics sampling. This method ensures high-quality RNA for accurate gene expression analysis in mouse brain studies.
Area of Science:
- Molecular Biology
- Neuroscience
- Genomics
Background:
- Spatial transcriptomics enables gene expression mapping within tissues.
- Capillary microneedle sampling for spatial transcriptomics risks RNA degradation.
- Preanalytical variability impacts low-density spatial transcriptomics accuracy.
Purpose of the Study:
- To develop and assess a preservation strategy for RNA integrity during capillary-based spatial transcriptomics.
- To minimize preanalytical variability in mouse brain spatial omics.
- To improve RNA quality for enhanced gene detection.
Main Methods:
- Mouse cardiac perfusion with phosphate-buffered saline (PBS).
- Brain tissue immersion in a hypersaline solution before sectioning.
- Microregion sampling conducted under low-temperature conditions.
Main Results:
- Preservation strategy maintained RNA integrity number (RINe) >7.5 for 6h at 25°C and >8.5 for 24h at 4°C.
- Reduced 3' transcript bias compared to controls.
- Enhanced detection of cell-type marker genes (p < 0.05).
Conclusions:
- The developed strategy effectively preserves RNA integrity for spatial transcriptomics.
- This method provides a standardized framework to reduce preanalytical variability.
- Improved RNA quality supports more accurate spatial omics analyses in mouse brain studies.
