ArticleBMC genomics2020
Comparison of RNA isolation methods on RNA-Seq: implications for differential expression and meta-analyses.
Article in BMC genomics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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Who cites it
43 citing papers in PubMed.
- Guidelines to Study Transcriptome Remodeling by Proteins Using Deep Sequencing (RNA-Seq).Methods in molecular biology (Clifton, N.J.) · 2027Article
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- Surprising regulatory plasticity for the conserved HOG pathway in diversebioRxiv : the preprint server for biology · 2025Article
- Genome-Wide Identification, Function, and Expression Analysis of the ABC Transporter Gene Family in Forest Musk Deer (Animals : an open access journal from MDPI · 2025Article
- Transcriptomic profile of TiOArchives of toxicology · 2025Article
- Transcriptomic Signatures in IgA Nephropathy: From Renal Tissue to Precision Risk Stratification.International journal of molecular sciences · 2025Review
- Extracellular RNAs in Liquid Biopsy: Applications in MASLD and MASH Diagnosis and Monitoring.Diagnostics (Basel, Switzerland) · 2025Review
- Experimental reporting of fish transcriptomic responses in environmental toxicology and ecotoxicology.Environmental toxicology and chemistry · 2025Review
- Bioinformatics perspectives on transcriptomics: A comprehensive review of bulk and single-cell RNA sequencing analyses.Quantitative biology (Beijing, China) · 2025Review
- Genomic and transcriptomic sequencing in prostate cancer.Current opinion in oncology · 2025Review
- Unique transcriptomic responses of rat and human alveolar macrophages in an in vitro model of overload with TiOParticle and fibre toxicology · 2025Article
- Guidance on the assessment of the functionality of biomaterials for periodontal tissue regeneration: Methodologies and testing procedures.Dental materials : official publication of the Academy of Dental Materials · 2025Review
- Comparison of direct cDNA and PCR-cDNA Nanopore sequencing of RNA fromMicrobial genomics · 2024Article
- New persistent plant RNA virus carries mutations to weaken viral suppression of antiviral RNA interference.Molecular plant pathology · 2024Article
- Guidelines for mitochondrial RNA analysis.Molecular therapy. Nucleic acids · 2024Review
- Prion diseases disrupt glutamate/glutamine metabolism in skeletal muscle.PLoS pathogens · 2024Article
- Potential role of short-chain fatty acids in the pathogenesis and management of acute lymphocytic leukemia.Annals of translational medicine · 2024Review
- Natural variation in yeast reveals multiple paths for acquiring higher stress resistance.BMC biology · 2024Article
- Simple protocol for combined extraction of exocrine secretions and RNA in small arthropods.Biology methods & protocols · 2024Article
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2 authors.
Funding
Abstract
backgroundThe increasing number of transcriptomic datasets has allowed for meta-analyses, which can be valuable due to their increased statistical power. However, meta-analyses can be confounded by so-called "batch effects," where technical variation across different batches of RNA-seq experiments can clearly produce spurious signals of differential expression and reduce our power to detect true differences. While batch effects can sometimes be accounted for, albeit with caveats, a better strategy is to understand their sources to better avoid them. In this study, we examined the effects of RNA isolation method as a possible source of batch effects in RNA-seq design.
resultsBased on the different chemistries of "classic" hot phenol extraction of RNA compared to common commercial RNA isolation kits, we hypothesized that specific mRNAs may be preferentially extracted depending upon method, which could masquerade as differential expression in downstream RNA-seq analyses. We tested this hypothesis using the Saccharomyces cerevisiae heat shock response as a well-validated environmental response. Comparing technical replicates that only differed in RNA isolation method, we found over one thousand transcripts that appeared "differentially" expressed when comparing hot phenol extraction with the two kits. Strikingly, transcripts with higher abundance in the phenol-extracted samples were enriched for membrane proteins, suggesting that indeed the chemistry of hot phenol extraction better solubilizes those species of mRNA.
conclusionsWithin a self-contained experimental batch (e.g. control versus treatment), the method of RNA isolation had little effect on the ability to identify differentially expressed transcripts. However, we suggest that researchers performing meta-analyses across different experimental batches strongly consider the RNA isolation methods for each experiment.
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