ArticleBMC genomics2022
Genes expressed at low levels raise false discovery rates in RNA samples contaminated with genomic DNA.
Article in BMC genomics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 22 citations in OpenAlex.
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- Residual eDNA in eRNA Extracts Skews eRNA-Based Biodiversity Assessment: Call for Optimised DNase Treatment.Molecular ecology resources · 2026Article
- In-depth comparison of methods to isolate RNA from common human cell lines.BMC genomics · 2026Article
- Optimized methods for obtaining sequencing-quality RNA from blubber of free-ranging cetaceans collected under field conditions.Conservation physiology · 2026Article
- Unraveling the intra-species genomic diversity of sweetpotato-infecting CRESS-DNA and RNA viruses in Burkina Faso using Oxford Nanopore sequencing.Frontiers in microbiology · 2026Article
- Transcriptomes of thirteen healthy feline tissue types.BMC genomics · 2025Article
- Development of an End-to-End Total RNA Sequencing Quality Control Framework for Blood-Based Biomarker Discovery.The Journal of molecular diagnostics : JMD · 2025Article
- Efficient profiling of total RNA in single cells with STORM-seq.bioRxiv : the preprint server for biology · 2025Article
- Serum RNA Profile Reflects Fluid Status and Atrophic Retinal Changes in Neovascular Age-Related Macular Degeneration.International journal of molecular sciences · 2025Article
- Phylogenomic Inference Suggests Differential Deep Time Phylogenetic Signals from Nuclear and Organellar Genomes in Gymnosperms.Plants (Basel, Switzerland) · 2025Article
- Genome-wide identification and expression pattern analysis of the chloride channel gene family in potato (Frontiers in plant science · 2025Article
- Assessing and mitigating batch effects in large-scale omics studies.Genome biology · 2024Review
- CleanUpRNAseq: An R/Bioconductor Package for Detecting and Correcting DNA Contamination in RNA-Seq Data.Biotech (Basel (Switzerland)) · 2024Article
- A single workflow for multi-species blood transcriptomics.BMC genomics · 2024Article
- Reverse transcription-quantitative PCR (RT-qPCR) without the need for prior removal of DNA.Scientific reports · 2023Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundRNA preparations contaminated with genomic DNA (gDNA) are frequently disregarded by RNA-seq studies. Such contamination may generate false results; however, their effect on the outcomes of RNA-seq analyses is unknown. To address this gap in our knowledge, here we added different concentrations of gDNA to total RNA preparations and subjected them to RNA-seq analysis.
resultsWe found that the contaminating gDNA altered the quantification of transcripts at relatively high concentrations. Differentially expressed genes (DEGs) resulting from gDNA contamination may therefore contribute to higher rates of false enrichment of pathways compared with analogous samples lacking numerous DEGs. A strategy was developed to correct gene expression levels in gDNA-contaminated RNA samples, which assessed the magnitude of contamination to improve the reliability of the results.
conclusionsOur study indicates that caution must be exercised when interpreting results associated with low-abundance transcripts. The data provided here will likely serve as a valuable resource to evaluate the influence of gDNA contamination on RNA-seq analysis, particularly related to the detection of putative novel gene elements.
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