Selection of reference genes for gene expression studies in rats

Selection of the most stable reference gene is critical for a reliable interpretation of gene expression data using RT-PCR. In order so, 17 commonly used genes were analyzed in Wistar rat duodenum, jejunum, ileum and liver following a fat gavage and at two time periods. These reference genes were also tested in liver from Zucker (fa/fa) on a long-term dietary trial. Four strategies were used to select the most suitable reference gene for each tissue: ranking according to biological coefficient of variation and further validation by statistical comparison among groups, geNorm, NormFinder and BestKeeper programs. No agreement was observed among these approaches for a particular gene, nor a common gene for all tissues. Furthermore we demonstrated that normalising using an inadequate reference conveyed into false negative and positive results. The selection of genes provided by BestKeeper resulted in more reliable results than the other statistical packages. According to this program, Tbp, Ubc, Hprt and Rn18s were the best reference genes for duodenum, jejunum, ileum and liver, respectively following a fat gavage in Wistar rats and Rn18s for liver in another rat strain on a long-term dietary intervention. Therefore, BestKeeper is highly recommendable to select the most stable gene to be used as internal standard and the selection of a specific reference expression gene requires a validation for each tissue and experimental design.     

Selection of reference genes for gene expression studies in astrocytomas

This study was aimed to test a panel of six housekeeping genes (GAPDH, HPRT1, POLR2A, RPLP0, ACTB, and H3F) so as to identify and validate the most suitable reference genes for expression studies in astrocytomas. GAPDH was the most stable and HPRT1 was the least stable reference gene. The effect of reference gene selection on quantitative real-time polymerase chain reaction data interpretation was demonstrated, normalizing the expression data of a selected gene of interest. Thus, GAPDH may be recommended for data normalization in gene expression studies in astrocytomas. Nevertheless, a preliminary validation of reference gene stability is required prior to every study.     

Selection of reliable reference genes for qPCR studies on chondroprotective action

Background  

Chondroprotective agents (CPA) such as glucosamine, curcumin and diacerein represent potential remedies for the management of osteoarthritis and several studies have been performed on their effects in-vitro and in-vivo. For the investigation of chondroprotective action on chondrocyte gene expression, quantitative real-time RT-PCR is the method of choice. However, validation of applied normalization strategies represents a crucial and sometimes neglected step in the analysis process. Therefore, the present study aimed to determine the expression stability of common reference genes (ACTB, Beta actin; GAPDH, Glyceraldehyde-3-phosphate; B2M, Beta-2-microglobulin; HPRT1, Hypoxanthine phosphoribosyl-transferase I; SDHA, Succinate dehydrogenase complex, subunit A; YWHAZ, Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide) under the influence of glucosamine, curcumin and diacerein in the IL-1β-stimulated C-28/I2 chondrocyte model, using the geNorm software tool.     

Selection of reliable reference genes for gene expression studies in peach using real-time PCR

Background  

RT-qPCR is a preferred method for rapid and reliable quantification of gene expression studies. Appropriate application of RT-qPCR in such studies requires the use of reference gene(s) as an internal control to normalize mRNA levels between different samples for an exact comparison of gene expression level. However, recent studies have shown that no single reference gene is universal for all experiments. Thus, the identification of high quality reference gene(s) is of paramount importance for the interpretation of data generated by RT-qPCR. Only a few studies on reference genes have been done in plants and none in peach (Prunus persica L. Batsch). Therefore, the present study was conducted to identify suitable reference gene(s) for normalization of gene expression in peach.     

Selection of reference genes for gene expression studies in human neutrophils by real-time PCR

Background  

Reference genes, which are often referred to housekeeping genes, are frequently used to normalize mRNA levels between different samples. However the expression level of these genes may vary among tissues or cells, and may change under certain circumstances. Thus the selection of reference gene(s) is critical for gene expression studies. For this purpose, 10 commonly used housekeeping genes were investigated in isolated human neutrophils.     

Selection of reference genes for gene expression studies in ultraviolet B-irradiated human skin fibroblasts using quantitative real-time PCR

Background  

Reference genes are frequently used to normalise mRNA levels between different samples. The expression level of these genes, however, may vary between tissues or cells and may change under certain circumstances. Cytoskeleton genes have served as multifunctional tools for experimental studies as reference genes. Our previous studies have demonstrated that the expression of vimentin, one cytoskeletal protein, was increased in ultraviolet B (UVB)-irradiated fibroblasts. Thus, we examined the expression of other cytoskeleton protein genes, ACTB (actin, beta), TUBA1A (tubulin, alpha 1a), and TUBB1 (tubulin, beta 1), in human dermal fibroblasts irradiated by UVB to determine which of these candidates were the most appropriate reference genes.     

副溶血性弧菌毒力基因表达时内参基因的选择

[目的]筛选出合适的内参基因用于分析不同环境条件下副溶血性弧菌毒力基因的表达情况.[方法]本研究以虾样品中、海水样品中、过滤海水样品中以及TSB培养条件下的副溶血性弧菌为材料,利用qRT-PCR技术评价了GAPDH、pvuA、pvsA和rpoS4种常用管家基因在不同条件下的表达稳定性.[结果]4种管家基因均能特异扩增,表达稳定性排列顺序为pvuA(2.906)＞pvsA(3.197)＞GAPDH(3.746)＞rpoS(6.512),进一步通过geNorm软件分析,最终选择两个表达最为稳定的内参基因即pvuA和pvsA,以二者的几何平均值作为参照可更为准确地校正目的基因的表达.[结论]pvuA和pvsA可作为环境样品中副溶血性弧菌毒力基因表达变化研究的内参基因.     

Selection of reference genes for studies of porcine endometrial gene expression on gestational day 12

Comparing gene expression patterns in the endometrium on gestational day 12 (GD12) between Erhualian (ER) and Landrace × Large White (LL) pigs is helpful to understand the biological mechanisms of fecundity. Selecting genes that have stable expression levels as the internal standards in a comparative study is essential for identifying real gene-specific variation by quantitative RT-PCR (qRT-PCR). Five genes expressed in sow endometria on GD12 were evaluated for their suitability as internal control for relative quantification by qRT-PCR. These genes were beta-actin (ACTB), beta-2-microglobulin (B2M), phosphoglycerate kinase 1 (PGK1), RNA polymerase II polypeptide G (RPG), and ribosomal protein S20 (RPS20), which represent different functional classes. Our results indicated that ACTB, B2M, and PGK1 were not suitable as internal standards for normalization because of their huge variability between the two breeds. RPS20 and RPG were most stable, and the former is recommended to serve as the internal standard when the use of multiple housekeeping genes is unpractical.     

孟氏隐唇瓢虫qRT-PCR分析中内参基因的筛选

选择合适的内参基因是qRT-PCR研究的关键。本文以孟氏隐唇瓢虫Cryptolaemus montrouzieri Mulsant为研究材料,利用qRT-PCR技术,对孟氏隐唇瓢虫4个候选内参基因Actin、RPS23、GAPDH和β-tubulin的mRNA的表达量进行了分析,并用Ge Norm、Norm Finder和Best Keeper软件分析它们在孟氏隐唇瓢虫不同发育阶段及成虫不同组织中的表达稳定性。结果表明,以成虫不同组织为材料时,综合三种软件分析结果显示4个候选基因表达稳定性平均等级值排名为RPS23(rank=1)β-tubulin(rank=2.3)GAPDH(rank=3)Actin(rank=3.7),以不同发育时期虫体为材料时,综合分析结果显示4个候选内参基因表达稳定性平均等级值排名为RPS23(rank=1.7)Actin(rank=2)GAPDH(rank=2.7)β-tubulin(rank=3.7)。综合分析在瓢虫不同发育阶段及成虫不同组织两种处理下,三种软件的评价效果,4个候选基因表达稳定性等级值的总平均排名为RPS23(rank=1.3)Actin(rank=2.8)=GAPDH(rank=2.8)β-tubulin(rank=3)。RPS23在瓢虫不同发育阶段及成虫不同组织中均显示出较高的表达稳定性及与其它基因之间极大的相关性,可以确定为孟氏隐唇虫不同发育阶段及成虫不同组织基因表达分析中一个稳定表达的基因,可作为单个内参基因或者其它内参基因的协同基因,本实验为开展孟氏隐唇瓢虫功能基因表达分析奠定了方法学基础。     

Candidate reference genes for gene expression studies in water lily

The selection of an appropriate reference gene(s) is a prerequisite for the proper interpretation of quantitative Real-Time polymerase chain reaction data. We report the evaluation of eight candidate reference genes across various tissues and treatments in the water lily by the two software packages geNorm and NormFinder. Across all samples, clathrin adaptor complexes medium subunit (AP47) and actin 11 (ACT11) emerged as the most suitable reference genes. Across different tissues, ACT11 and elongation factor 1-alpha (EF1α) exhibited a stable expression pattern. ACT11 and AP47 also stably expressed in roots subjected to various treatments, but in the leaves of the same plants the most stably expressed genes were ubiquitin-conjugating enzyme 16 (UBC16) and ACT11.     

Selection of housekeeping genes for gene expression studies in human reticulocytes using real-time PCR

Background  

Control genes, which are often referred to as housekeeping genes, are frequently used to normalise mRNA levels between different samples. However, the expression level of these genes may vary among tissues or cells and may change under certain circumstances. Thus, the selection of housekeeping genes is critical for gene expression studies. To address this issue, 7 candidate housekeeping genes including several commonly used ones were investigated in isolated human reticulocytes. For this, a simple ΔCt approach was employed by comparing relative expression of 'pairs of genes' within each sample. On this basis, stability of the candidate housekeeping genes was ranked according to repeatability of the gene expression differences among 31 samples.     

Selection of internal reference genes for SYBR green qRT-PCR studies of rhesus monkey (<Emphasis Type="Italic">Macaca mulatta</Emphasis>) tissues

Background  

The rhesus monkey (Macaca mulatta) is a valuable and widely used model animal for biomedical research. However, quantitative analyses of rhesus gene expression profiles under diverse experimental conditions are limited by a shortage of suitable internal controls for the normalization of mRNA levels. In this study, we used a systematic approach for the selection of potential reference genes in the rhesus monkey and compared their suitability to that of the corresponding genes in humans.