ArticlePloS one2014
Expressed repeat elements improve RT-qPCR normalization across a wide range of zebrafish gene expression studies.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
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- Bone cell differentiation and mineralization in wild-type and osteogenesis imperfecta zebrafish are compromised by per- and poly-fluoroalkyl substances (PFAS).Scientific reports · 2025Article
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- Zebrafish Tric-b is required for skeletal development and bone cells differentiation.Frontiers in endocrinology · 2023Article
- AP-3 complex subunit delta gene, ap3d1, regulates melanogenesis and melanophore survival via autophagy in zebrafish (Danio rerio).Pigment cell & melanoma research · 2022Article
- Structure, evolution and expression of zebrafish cartilage oligomeric matrix protein (COMP, TSP5). CRISPR-Cas mutants show a dominant phenotype in myosepta.Frontiers in endocrinology · 2022Article
- Hypoplasia of dopaminergic neurons by hypoxia-induced neurotoxicity is associated with disrupted swimming development of larval zebrafish.Frontiers in cellular neuroscience · 2022Article
- Bi-allelic premature truncating variants in LTBP1 cause cutis laxa syndrome.American journal of human genetics · 2021Article
- Zebrafish mbnl mutants model physical and molecular phenotypes of myotonic dystrophy.Disease models & mechanisms · 2021Article
- Identification and Characterization of Zebrafish Tlr4 Coreceptor Md-2.Journal of immunology (Baltimore, Md. : 1950) · 2021Article
- Comprehensive evaluation of candidate reference genes for quantitative real-time PCR-based analysis in Caucasian clover.Scientific reports · 2021Article
- Selection of suitable reference genes for gene expression studies in myxosporean (Myxozoa, Cnidaria) parasites.Scientific reports · 2019Article
- Purification of high-quality RNA from a small number of fluorescence activated cell sorted zebrafish cells for RNA sequencing purposes.BMC genomics · 2019Article
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- Modeling Tuberculosis in Mycobacterium marinum Infected Adult Zebrafish.Journal of visualized experiments : JoVE · 2018Article
- Expressed repetitive elements are broadly applicable reference targets for normalization of reverse transcription-qPCR data in mice.Scientific reports · 2018Article
- Identification of transcripts potentially involved in neural tube closure using RNA sequencing.Genesis (New York, N.Y. : 2000) · 2018Article
- Priming of innate antimycobacterial immunity by heat-killedDisease models & mechanisms · 2018Article
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11 authors.
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Abstract
The selection and validation of stably expressed reference genes is a critical issue for proper RT-qPCR data normalization. In zebrafish expression studies, many commonly used reference genes are not generally applicable given their variability in expression levels under a variety of experimental conditions. Inappropriate use of these reference genes may lead to false interpretation of expression data and unreliable conclusions. In this study, we evaluated a novel normalization method in zebrafish using expressed repetitive elements (ERE) as reference targets, instead of specific protein coding mRNA targets. We assessed and compared the expression stability of a number of EREs to that of commonly used zebrafish reference genes in a diverse set of experimental conditions including a developmental time series, a set of different organs from adult fish and different treatments of zebrafish embryos including morpholino injections and administration of chemicals. Using geNorm and rank aggregation analysis we demonstrated that EREs have a higher overall expression stability compared to the commonly used reference genes. Moreover, we propose a limited set of ERE reference targets (hatn10, dna15ta1 and loopern4), that show stable expression throughout the wide range of experiments in this study, as strong candidates for inclusion as reference targets for qPCR normalization in future zebrafish expression studies. Our applied strategy to find and evaluate candidate expressed repeat elements for RT-qPCR data normalization has high potential to be used also for other species.
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