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Brunner, Amy M.; Yakovlev, Igor; Strauss, Steven H.

doi:10.1186/1471-2229-4-14

Cited by 486 publications

(245 citation statements)

References 16 publications

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“…Tuba1, encoding cytoskeletal protein, has long been attributed to having major roles in setting up the scaffolding needed to elaborate new neurites and to enable transport of organelles within the neurites. Tuba1 was identified as being stably expressed across various developmental stages of soybean (Jian et al 2008) and different tissues of poplar (Brunner et al 2004). Tuba1 was recognized as the most stable gene in the four tissues (including spleen, heart, muscle, and gill) in Japanese flounder, Paralichthys olivaceus (Temminck et Schlegel, 1846) (see Zheng and Sun 2011).…”

Section: Discussionmentioning

confidence: 99%

Characterization of Reference Genes in Rare Minnow, <I>Gobiocypris Rarus</I> (Actinopterygii: Cypriniformes: Cyprinidae), in Early Postembryonic Development and in Response to Edcs Treatment

Qin

Wang

Liu

et al. 2013

Acta Icth et Piscat

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Section: Discussionmentioning

confidence: 99%

Characterization of Reference Genes in Rare Minnow, <I>Gobiocypris Rarus</I> (Actinopterygii: Cypriniformes: Cyprinidae), in Early Postembryonic Development and in Response to Edcs Treatment

Qin

Wang

Liu

et al. 2013

Acta Icth et Piscat

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“…This gene was present in a single copy in the soybean genome, but it is not necessarily constitutive. If its expression shows variations, relative quantification would be difficult (Brunner et al, 2004;Czechowski et al, 2005). However, it could still be used as a reference to provide the number of copies of the genome.…”

Section: Resultsmentioning

confidence: 99%

“…Jain et al (2006) showed that the best genes in various tissue samples from rice (Oryza sativa) were those encoding ubiquitin 5 and elongation factor-1 alpha. Genes that encode the proteins GAPDH (Wall & Edwards, 2002), β-actin (Kreuzer et al, 1999), tubulin (Brunner et al, 2004) or RNAr18S have been used for other species (Bhatia et al, 2002).…”

Section: Introductionmentioning

confidence: 99%

Identification of reference genes for expression analysis by real-time quantitative PCR in drought-stressed soybean

Stolf-Moreira

Lemos

Abdelnoor

et al. 2011

Pesq. agropec. bras.

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-The objective of this work was to validate, by quantitative PCR in real time (RT-qPCR), genes to be used as reference in studies of gene expression in soybean in drought-stressed trials. Four genes commonly used in soybean were evaluated: Gmβ-actin, GmGAPDH, GmLectin and GmRNAr18S. Total RNA was extracted from six samples: three from roots in a hydroponic system with different drought intensities (0, 25, 50, 75 and 100 minutes of water stress), and three from leaves of plants grown in sand with different soil moistures (15, 5 and 2.5% gravimetric humidity). The raw cycle threshold (Ct) data were analyzed, and the efficiency of each primer was calculated for an overall analysis of the Ct range among the different samples. The GeNorm application was used to evaluate the best reference gene, according to its stability. The GmGAPDH was the least stable gene, with the highest mean values of expression stability (M), and the most stable genes, with the lowest M values, were the Gmβ-actin and GmRNAr18S, when both root and leaves samples were tested. These genes can be used in RT-qPCR as reference gene for expression analysis.Index terms: Glycine max, expression stability, RT-qPCR, water deficit. Identificação de genes de referência para análise de expressão por PCR quantitativo em tempo real, em soja submetida à secaResumo -O objetivo deste trabalho foi validar, pela técnica de PCR quantitativo em tempo real (RT-qPCR) genes para serem utilizados como referência em estudos de expressão gênica em soja, em ensaios de estresse hídrico. Foram avaliados quatro genes comumente utilizados em soja: Gmβ-actin, GmGAPDH, GmLectin e GmRNAr18S. O RNA total foi extraído de seis amostras: três amostras de raízes em sistema de hidroponia com diferentes intensidades de déficit hídrico (0, 25, 50, 75 e 100 minutos de estresse hídrico), e três amostras de folhas de plantas cultivadas em areia com diferentes umidades do solo (15, 5 e 2,5% de umidade gravimétrica). Os dados brutos do intervalo "cycle threshold" (Ct) foram analisados, e a eficiência de cada iniciador foi calculada para uma analise da Ct entre as diferentes amostras. A aplicação do programa GeNorm foi utilizada para a avaliação dos melhores genes de referência, de acordo com a estabilidade. O GmGAPDH foi o gene menos estável, com o maior valor médio de estabilidade de expressão (M), e os genes mais estáveis, com menor valor de M, foram o Gmβ-actin e GmRNAr18S, tanto nas amostras de raízes como nas de folhas. Estes genes podem ser usados em RT-qPCR como gens de referência para análises de expressão gênica.Termos para indexação: Glycine max, estabilidade de expressão, RT-qPCR, déficit hídrico.

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“…The suitability of individual ‘reference genes’ as internal RT-PCR controls for a specific experimental design can be tested with various approaches, including methods of overall variance [3], ANOVA models [4], Bayesian models [5] and equivalence testing [6, 7]. More recently, genome-wide expression technologies have been recognized as an effective tool for the identification and evaluation of endogenous RT-PCR controls [8, 9].…”

Section: Introductionmentioning

confidence: 99%

Validation of Endogenous Internal Real-Time PCR Controls in Renal Tissues

Cui

Zhou²,

Qiu³

et al. 2009

Am J Nephrol

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Background: Endogenous internal controls (‘reference’ or ‘housekeeping’ genes) are widely used in real-time PCR (RT-PCR) analyses. Their use relies on the premise of consistently stable expression across studied experimental conditions. Unfortunately, none of these controls fulfills this premise across a wide range of experimental conditions; consequently, none of them can be recommended for universal use. Methods: To determine which endogenous RT-PCR controls are suitable for analyses of renal tissues altered by kidney disease, we studied the expression of 16 commonly used ‘reference genes’ in 7 mildly and 7 severely affected whole kidney tissues from a well-characterized cystic kidney disease model. Expression levels of these 16 genes, determined by TaqMan® RT-PCR analyses and Affymetrix GeneChip® arrays, were normalized and tested for overall variance and equivalence of the means. Results: Both statistical approaches and both TaqMan- and GeneChip-based methods converged on 3 out of the 4 top-ranked genes (Ppia, Gapdh and Pgk1) that had the most constant expression levels across the studied phenotypes. Conclusion: A combination of the top-ranked genes will provide a suitable endogenous internal control for similar studies of kidney tissues across a wide range of disease severity.

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Cited by 486 publications

References 16 publications

Characterization of Reference Genes in Rare Minnow, <I>Gobiocypris Rarus</I> (Actinopterygii: Cypriniformes: Cyprinidae), in Early Postembryonic Development and in Response to Edcs Treatment

Characterization of Reference Genes in Rare Minnow, <I>Gobiocypris Rarus</I> (Actinopterygii: Cypriniformes: Cyprinidae), in Early Postembryonic Development and in Response to Edcs Treatment

Identification of reference genes for expression analysis by real-time quantitative PCR in drought-stressed soybean

Validation of Endogenous Internal Real-Time PCR Controls in Renal Tissues

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