ArticleNAR genomics and bioinformatics2024
Optimization of FFPE preparation and identification of gene attributes associated with RNA degradation.
Article in NAR genomics and bioinformatics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers, 1 of them a synthesis that pooled it.
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Who cites it
12 citing papers in PubMed, 1 synthesis or guideline pooled it, 12 citations in OpenAlex.
- Enhancing RNA Capture Efficiency in Spatial Transcriptomics: A Review of Innovative Technologies and Strategies.International journal of molecular sciences · 2025Pooled it
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- Pre-analytical Best Practices for RNA Sequencing from Small Biopsies and Cytologic Specimens.Molecular diagnosis & therapy · 2026Review
- Integrative analysis reveals the role of SUMOylation-related patterns in shaping the tumor microenvironment and predicting treatment sensitivity of colorectal cancer.Translational cancer research · 2026Article
- DeepGene-BC: Deep Learning-Based Breast Cancer Subtype Prediction via Somatic Point Mutation Profiles.Cancers · 2026Article
- Advances in Spatial Transcriptomics in Bone.Current osteoporosis reports · 2026Review
- Evaluating plasma and tissue biopsy for DNA methylation markers in early colorectal cancer detection: a systematic review.Asian biomedicine : research, reviews and news · 2025Article
- Conserved methylation signature accurately predicts heavily irradiated CNS tumour with perplexing histopathology: A case report.Biomedical reports · 2025Article
- Spatial Gene Expression of Human Coronary Arteries Revealed the Molecular Features of Diffuse Intimal Thickening in Explanted Hearts.International journal of molecular sciences · 2025Article
- Long-term fixation impact on archived human nervous tissues for sequencing-based transcriptomics.Brain communications · 2025Article
- snRNA-seq of long-preserved FFPE samples from colorectal liver metastasis lesions with diverse prognoses.Scientific data · 2024Article
Corrections and comments
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Authors and funding
8 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissues are widely available specimens for clinical studies. However, RNA degradation in FFPE tissues often restricts their utility. In this study, we determined optimal FFPE preparation conditions, including tissue ischemia at 4°C (<48 h) or 25°C for a short time (0.5 h), 48-h fixation at 25°C and sampling from FFPE scrolls instead of sections. Notably, we observed an increase in intronic reads and a significant change in gene rank based on expression level in the FFPE as opposed to fresh-frozen (FF) samples. Additionally, we found that more reads were mapped to genes associated with chemical stimulus in FFPE samples. Furthermore, we demonstrated that more degraded genes in FFPE samples were enriched in genes with short transcripts and high free energy. Besides, we found 40 housekeeping genes exhibited stable expression in FF and FFPE samples across various tissues. Moreover, our study showed that FFPE samples yielded comparable results to FF samples in dimensionality reduction and pathway analyses between case and control samples. Our study established the optimal conditions for FFPE preparation and identified gene attributes associated with degradation, which would provide useful clues for the utility of FFPE tissues in clinical practice and research.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.