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Updated: Dec 27, 2025
Optimized Quantitative Assessment of Enhancer RNA Stability in Mouse Embryonic Stem Cells
Published on: November 21, 2025
Impact of different stabilization methods on RT-qPCR results using human lung tissue samples
Margalida Esteva-Socias1,2,3, Fernando Gómez-Romano1,2,3, José Antonio Carrillo-Ávila3,4
1Centro de Investigación Biomédica en Red in Respiratory Diseases (CIBERES), Plataforma Biobanco Pulmonar CIBERES, Hospital Universitari Son Espases, Palma, Spain.
Choosing the right tissue stabilization method is crucial for preserving RNA quality and integrity in biomedical research. RNAlater and snap freezing with Optimal Cutting Tissue compound yield superior RNA compared to standard snap freezing or formalin-fixed paraffin-embedding.
Area of Science:
- Biomedical Research
- Molecular Biology
- Biobanking
Background:
- Biobanks aim to enhance biomedical research reproducibility by optimizing human tissue preservation.
- Limited data exists on how various tissue stabilization methods impact biomolecule quality and functionality.
- Standardization of pre-analytical workflows is essential for improving research reproducibility.
Purpose of the Study:
- To evaluate the impact of four distinct stabilization methods on RNA quality and integrity in human lung tissue.
- To assess the influence of stabilization techniques on the functionality of derived RNA for gene expression analysis.
- To provide evidence-based recommendations for optimal tissue stabilization in biobanking and research.
Main Methods:
- Paired lung tissue samples were subjected to four stabilization methods: RNAlater (RNL), snap freezing (SF), snap freezing with Optimal Cutting Tissue compound (SF-OCT), and formalin-fixed paraffin-embedded (FFPE).
- RNA integrity was assessed using PCR-endpoint assays targeting different gene fragment lengths and the RNA Integrity Number (RIN).
- Gene expression analysis of HPRT1, SNRPD3, and Jun was performed using RT-qPCR to evaluate tissue functionality.
Main Results:
- RNA extracted from samples preserved with RNAlater (RNL) or SF-OCT showed better integrity compared to SF and FFPE methods.
- Statistically significant differences in gene expression (HPRT1, SNRPD3, Jun) were observed between FFPE-preserved RNA and RNA from other methods.
- High correlation was found between Cq values and RIN for the three analyzed housekeeping genes.
Conclusions:
- RNAlater and SF-OCT are superior methods for preserving RNA quality and integrity in lung tissue compared to SF and FFPE.
- The FFPE method significantly impacts gene expression analysis, necessitating careful consideration in experimental design.
- Standardizing pre-analytical tissue stabilization is critical for enhancing the reproducibility of biomedical research findings.
