ArticleScientific reports2018
Systematic evaluation of RNA quality, microarray data reliability and pathway analysis in fresh, fresh frozen and formalin-fixed paraffin-embedded tissue samples.
Article in Scientific reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
65 citing papers in PubMed.
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- Immune-stromal dysregulation and senescence in chronic spontaneous urticaria.The journal of allergy and clinical immunology. Global · 2026Article
- Preserved and Accessible: Quantifying PFAS in Formalin-Fixed and Paraffin-Embedded Tissues for Retrospective Exposure and Dose Assessment.Environmental science & technology · 2026Article
- Exploring the human brain: spatial transcriptomics challenges and approaches in post-mortem analysis.Brain : a journal of neurology · 2026Review
- Spaceflight alters molecular networks linked to diverse human diseases in a single cellular model.Science advances · 2026Article
- Mismatch Repair System Gene Expression in FFPE Samples from Breast Cancer Patients.Medical sciences (Basel, Switzerland) · 2025Article
- Transcriptomic profiles of endocrine-resistant breast cancer.BMC cancer · 2025Article
- Next-generation RNA sequencing of spatially mapped material from human body donors for testing the impact of fetal environments on the liver transcriptome.Scientific reports · 2025Article
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- Expression of SOX10, and micro-RNA 221 and Micro-RNA 222 in Oral Squamous Cell Carcinoma and Correlation with Clinicopathological Characteristics.Head and neck pathology · 2025Article
- An accurate DNA and RNA based targeted sequencing assay for clinical detection of gene fusions in solid tumors.Scientific reports · 2025Article
- Spatial oncology: Translating contextual biology to the clinic.Cancer cell · 2024Review
- Spatial landscapes of cancers: insights and opportunities.Nature reviews. Clinical oncology · 2024Review
- An optimized workflow for transcriptomic analysis from archival paraformaldehyde-fixed retinal tissues collected by laser capture microdissection.Experimental eye research · 2024Article
- A consensus molecular subtypes classification strategy for clinical colorectal cancer tissues.Life science alliance · 2024Article
- Development of a novel non-invasive biomarker panel for hepatic fibrosis in MASLD.Nature communications · 2024Article
- Extracting high-quality RNA from formaldehyde-fixed naturally aged neuromusculoskeletal tissues.BioTechniques · 2024Article
- Pregnancy-specific beta-1-glycoprotein 6 is a potential novel diagnostic biomarker of placenta accreta spectrum.Medical molecular morphology · 2024Article
- Article
- [Chinese Expert Consensus on the Clinical Practice of Non-small Cell Lung Cancer Fusion Gene Detection Based on RNA-based NGS].Zhongguo fei ai za zhi = Chinese journal of lung cancer · 2023Article
5 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors.
Funding
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissues are valuable resources commonly used in pathology. However, formalin fixation modifies nucleic acids challenging the isolation of high-quality RNA for genetic profiling. Here, we assessed feasibility and reliability of microarray studies analysing transcriptome data from fresh, fresh-frozen (FF) and FFPE tissues. We show that reproducible microarray data can be generated from only 2 ng FFPE-derived RNA. For RNA quality assessment, fragment size distribution (DV200) and qPCR proved most suitable. During RNA isolation, extending tissue lysis time to 10 hours reduced high-molecular-weight species, while additional incubation at 70 °C markedly increased RNA yields. Since FF- and FFPE-derived microarrays constitute different data entities, we used indirect measures to investigate gene signal variation and relative gene expression. Whole-genome analyses revealed high concordance rates, while reviewing on single-genes basis showed higher data variation in FFPE than FF arrays. Using an experimental model, gene set enrichment analysis (GSEA) of FFPE-derived microarrays and fresh tissue-derived RNA-Seq datasets yielded similarly affected pathways confirming the applicability of FFPE tissue in global gene expression analysis. Our study provides a workflow comprising RNA isolation, quality assessment and microarray profiling using minimal RNA input, thus enabling hypothesis-generating pathway analyses from limited amounts of precious, pathologically significant FFPE tissues.
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