Selection of appropriate reference genes for gene expression studies by quantitative real-time polymerase chain reaction in cucumber

Wan, Hongjian; Zhao, Zhenguo; Qian, Chuntao; YiHu, Sui; Malik, Ahmed Abbas; Chen, Jinfeng

doi:10.1016/j.ab.2009.12.008

Cited by 391 publications

(343 citation statements)

References 17 publications

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“…However, the analysis results of BestKeeper are different to those observed with GeNorm and NormFinder. Previous studies hypothesize that this may be due to differences in the statistical model that BestKeeper uses; therefore, it is less effective for ranking reference gene stability compared with GeNorm and NormFinder (20)(21)(22). Based on comparisons of results among the three programs, the present study recommends the following most stable reference genes, which have been confirmed through analysis by ≥2 programs: Total samples group, RPL29; CCA tissue group, TBP; CCA cell line and CCA tissue group, ACTB; CCA cell line group, 18SrRNA; CCA tissue and adjacent non-neoplastic tissue group, ALAS1; and adjacent non-neoplastic tissue group, HPRT1.…”

Section: Discussionmentioning

confidence: 99%

“…Therefore, during the detection of target gene expression, a gene with a stable expression is required as a reference. Recent studies have revealed defects in all commonly used reference genes, which often vary greatly in expression quantity in various types of cells and tissues, stages of cell amplification and organ development and in vitro culture and experimental conditions (9,10,(20)(21)(22). To the best of our knowledge, there have been no systematic comparisons performed concerning the stability of commonly-used reference genes in CCA tissues and cell lines.…”

Section: Discussionmentioning

confidence: 99%

“…However, as stated by Wan et al (20), 0.15 is not an absolute cutoff value, but rather an ideal value, which is dependent on the expression of the …”

mentioning

confidence: 99%

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Evaluation and validation of suitable reference genes for reverse transcription-quantitative polymerase chain reaction studies in cholangiocarcinoma patients and cell lines

Yang

et al. 2016

Oncology Letters

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Abstract.Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) has become a frequently used method in gene expression studies. The relative quantification method is an important and common method for the evaluation of RT-qPCR data. One of the key requirements of this method is to identify an applicable internal reference gene. However, to the best of our knowledge, no suitable reference genes have been identified for the genetic analysis of cholangiocarcinoma (CCA) in humans and cell lines. In the present study, screening was conducted using 12 common reference genes, which were selected in order to provide an experimental basis for the study of the gene expression in CCA patients and cell lines. Tumor samples and adjacent non-neoplastic tissues from 20 patients with CCA were obtained for the present study. The stability and applicability of the 12 reference gene candidates were validated using GeNorm, NormFinder and BestKeeper software. Based on a comparison of the results, the following reference genes are recommended for various tissue groups: Total sample group, ribosomal protein L29; CCA tissue group, TATA-box binding protein; CCA cell line and tissue group, actin-β; CCA cell line group, 18S ribosomal RNA; CCA tissue and adjacent non-neoplastic tissue group, 5'-aminolevulinate synthase 1; and adjacent non-neoplastic tissue group, hypoxanthine phosphoribosyltransferase 1. The results of the search also clearly reveal that a systematic study regarding the selection of suitable reference genes for studying the target gene profiling in CCA tissues and cell lines has not been previously published. The present study may provide useful information for future studies that examine the gene expression of CCA for choosing suitable reference genes.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Evaluation and validation of suitable reference genes for reverse transcription-quantitative polymerase chain reaction studies in cholangiocarcinoma patients and cell lines

Yang

et al. 2016

Oncology Letters

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“…For the study of cell lines, Tca-8113 and CAL-27, which are the most commonly used tongue carcinoma cell lines for in vitro studies, were used. For the study of tissues, due to limitations for tongue carcinoma surgery, biopsy specimens were not selected by grades and stages as, according to previous research, the expression of reference genes is not directly associated with the grade or stage of a malignant tumor (12,21). The specimens were confirmed by the Pathology Department of China-Japan Union Hospital, Jilin University (Changchun, China) as malignant and the tongue cancer samples used were the most common pathological types of squamous cell carcinomas.…”

Section: Discussionmentioning

confidence: 99%

Validation of reference genes for the normalization of RT-qPCR expression studies in human tongue carcinoma cell lines and tissue

Liu

Ren

et al. 2017

Oncology Letters

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Abstract. Reverse transcription quantitative polymerase chain reaction (RT-qPCR) has become a frequently used strategy in gene expression studies. The relative quantification method is an important and commonly used method for the evaluation of RT-qPCR data. The key aim of this method is to identify an applicable internal reference gene. However, there are currently no data concerning the expression of reference genes for gene analysis in human tongue carcinoma cell lines and tissues. In the present study, screening was performed using 12 common reference genes, which were selected in order to provide an experimental basis for the investigation of gene expression in human tongue carcinoma. Tca-8113 and CAL-27 cell lines and a total of 8 tongue carcinoma tissue samples were investigated. The gene expression stability and the applicability of the 12 reference gene candidates were determined using the geNorm, NormFinder and BestKeeper software programs. The results from the three software programs were demonstrated to be variable following comparison. The recommended combinations were 5'-aminolevulinate synthase 1 + glucuronidase β + ribosomal protein L29 (RPL29) for the cell line + tissue group, β-2-microglobulin + RPL29 for the cell line group and peptidylprolyl isomerase A + hydroxymethylbilane synthase + RPL29 for the tissue group. These recommended internal reference genes may improve the accuracy of relative quantitation analysis of target gene expression performed by the RT-qPCR method in further gene expression research on human tongue carcinoma.

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“…Gene expression-based studies are now regarded as a promising vehicle towards acquiring a deeper and more precise understanding of different mechanisms governing different complex regulatory networks of the genetic, signalling and metabolic pathways (24)(25)(26). Compared to other cultivated solanaceous plant species including pepper, tomato and potato, less information is available regarding gene expression analysis alongside SGA accumulation in eggplant.…”

Section: Introductionmentioning

confidence: 99%

Evaluation of Solasonine Content and Expression Patterns of SGT1 Gene in Different Tissues of Two Iranian Eggplant (Solanum melongena L.) Genotypes

Bagheri

Bushehri

Hassandokht

et al. 2017

Food Technol. Biotechnol.

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The family of Solanaceae (also known as nightshade family) is considered as a large plant family including essential crops such as potato, tomato, sweet pepper and lastly eggplant (1). In both tropical and temperate regions of the world, eggplant (Solanum melongena L., 2n=2x=24) has been cultivated for years, and regarded currently as an economically important vegetable plant (2). Phylogenetically, contrary to the other important Solanaceae fam- SummaryEggplant (Solanum melongena L.) is one of the most consumed vegetables in the world. The eggplant glycoalkaloids (GAs) are toxic secondary metabolites that may have detrimental effects on human health, particularly if the magnitudes of GAs are higher than the recommended food safety level (200 mg per kg of fresh mass). In this study, the content of solasonine compound and the expression patterns of solasodine galactosyltransferase (SGT1) gene were assessed in different tissues (mature leaves, flower buds, young, mature, and physiologically ripe fruits) of two Iranian eggplant genotypes (D1 and J10) under field conditions. The maximum mass fraction of solasonine in D1 was detected in flower buds (135.63 μg/g), followed by leaf (113.29 μg/g), physiologically ripe fruit (74.74 μg/g), young fruit (61.33 μg/g), and mature fruit (21.55 μg/g). Comparing both genotypes, the genotype of bitter fruits (J10) contained higher mass fraction of solasonine, as one of the main factors for producing bitter flavour of the plant. Regarding the expression profiles of SGT1, in both genotypes, the activity of the gene was increased nearly parallel with the concentration of solasonine. In the J10 geno type, transcript level of the gene was significantly higher than the genotype of sweet fruits (D1). Although both D1 and J10 genotypes are possibly recommendable for human food consumption, D1 is more suitable for daily diet.

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Selection of appropriate reference genes for gene expression studies by quantitative real-time polymerase chain reaction in cucumber

Cited by 391 publications

References 17 publications

Evaluation and validation of suitable reference genes for reverse transcription-quantitative polymerase chain reaction studies in cholangiocarcinoma patients and cell lines

Evaluation and validation of suitable reference genes for reverse transcription-quantitative polymerase chain reaction studies in cholangiocarcinoma patients and cell lines

Validation of reference genes for the normalization of RT-qPCR expression studies in human tongue carcinoma cell lines and tissue

Evaluation of Solasonine Content and Expression Patterns of SGT1 Gene in Different Tissues of Two Iranian Eggplant (Solanum melongena L.) Genotypes

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