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https://www.readbyqxmd.com/read/28198810/reference-genes-for-quantitative-real-time-pcr-analysis-in-symbiont-entomomyces-delphacidicola-of-nilaparvata-lugens-st%C3%A3-l
#1
Pin-Jun Wan, Yao-Hua Tang, San-Yue Yuan, Jia-Chun He, Wei-Xia Wang, Feng-Xiang Lai, Qiang Fu
Nilaparvata lugens (Stål) (Hemiptera: Delphacidae) is a major rice pest that harbors an endosymbiont ascomycete fungus, Entomomyces delphacidicola str. NLU (also known as yeast-like symbiont, YLS). Driving by demand of novel population management tactics (e.g. RNAi), the importance of YLS has been studied and revealed, which greatly boosts the interest of molecular level studies related to YLS. The current study focuses on reference genes for RT-qPCR studies related to YLS. Eight previously unreported YLS genes were cloned, and their expressions were evaluated for N...
February 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28184026/identification-of-tmem208-and-pqlc2-as-reference-genes-for-normalizing-mrna-expression-in-colorectal-cancer-treated-with-aspirin
#2
Yuanyuan Zhu, Chao Yang, Mingjiao Weng, Yan Zhang, Chunhui Yang, Yinji Jin, Weiwei Yang, Yan He, Yiqi Wu, Yuhua Zhang, Guangyu Wang, Riju James RajkumarEzakiel Redpath, Lei Zhang, Xiaoming Jin, Ying Liu, Yuchun Sun, Ning Ning, Yu Qiao, Fengmin Zhang, Zhiwei Li, Tianzhen Wang, Yanqiao Zhang, Xiaobo Li
Numerous evidences indicate that aspirin usage causes a significant reduction in colorectal cancer. However, the molecular mechanisms about aspirin preventing colon cancer are largely unknown. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) is a most frequently used method to identify the target molecules regulated by certain compound. However, this method needs stable internal reference genes to analyze the expression change of the targets. In this study, the transcriptional stabilities of several traditional reference genes were evaluated in colon cancer cells treated with aspirin, and also, the suitable internal reference genes were screened by using a microarray and were further identified by using the geNorm and NormFinder softwares, and then were validated in more cell lines and xenografts...
February 8, 2017: Oncotarget
https://www.readbyqxmd.com/read/28182746/selection-and-evaluation-of-new-reference-genes-for-rt-qpcr-analysis-in-epinephelus-akaara-based-on-transcriptome-data
#3
Huan Wang, Xiang Zhang, Qiaohong Liu, Xiaochun Liu, Shaoxiong Ding
Groupers are an economically important fish species in world fishery markets. Because many studies using RT-qPCR have addressed gene expression in groupers, appropriate reference genes are required to obtain reliable and accurate results. In this study, the most suitable reference genes were identified from eleven candidate genes of one of the most valuable species, Epinephelus akaara, in a range of different experimental conditions. Using the software packages geNorm, NormFinder, BestKeeper and refFinder, three traditionally used reference genes, β-actin (β-ACT), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), and beta-2-microglobulin (B2M), were identified as not suitable for E...
2017: PloS One
https://www.readbyqxmd.com/read/28182697/identification-of-reference-genes-for-qpcr-analysis-during-hasc-long-culture-maintenance
#4
Silvia Palombella, Cristina Pirrone, Mario Cherubino, Luigi Valdatta, Giovanni Bernardini, Rosalba Gornati
Up to now quantitative PCR based assay is the most common method for characterizing or confirming gene expression patterns and comparing mRNA levels in different sample populations. Since this technique is relative easy and low cost compared to other methods of characterization, e.g. flow cytometry, we used it to typify human adipose-derived stem cells (hASCs). hASCs possess several characteristics that make them attractive for scientific research and clinical applications. Accurate normalization of gene expression relies on good selection of reference genes and the best way to choose them appropriately is to follow the common rule of the "Best 3", at least three reference genes, three different validation software and three sample replicates...
2017: PloS One
https://www.readbyqxmd.com/read/28160493/analysis-of-transcriptional-responses-of-normalizing-genes-on-crassostrea-brasiliana-under-different-experimental-conditions
#5
Gabrielle do Amaral E Silva Müller, Daína de Lima, Flávia Lucena Zacchi, Rômi Sharon Piazza, Karim Hahn Lüchmann, Jacó Joaquim Mattos, Daniel Schlenk, Afonso Celso Dias Bainy
Bivalves show remarkable plasticity to environmental changes and have been proposed as sentinel organisms in biomonitoring. Studies related to transcriptional analysis using quantitative real-time PCR (qRT-PCR) in these organisms have notably increased, imposing a need to identify and validate adequate reference genes for an accurate and reliable analysis. In the present study, nine reference genes were selected from transcriptome data of Crassostrea brasiliana in order to identify their suitability as qRT-PCR normalizer genes...
February 4, 2017: Environmental Toxicology and Chemistry
https://www.readbyqxmd.com/read/28133578/selection-and-evaluation-of-reference-genes-for-analysis-of-mouse-mus-musculus-sex-dimorphic-brain-development
#6
Tanya T Cheung, Mitchell K Weston, Megan J Wilson
The development of the brain is sex-dimorphic, and as a result so are many neurological disorders. One approach for studying sex-dimorphic brain development is to measure gene expression in biological samples using RT-qPCR. However, the accuracy and consistency of this technique relies on the reference gene(s) selected. We analyzed the expression of ten reference genes in male and female samples over three stages of brain development, using popular algorithms NormFinder, GeNorm and Bestkeeper. The top ranked reference genes at each time point were further used to quantify gene expression of three sex-dimorphic genes (Wnt10b, Xist and CYP7B1)...
2017: PeerJ
https://www.readbyqxmd.com/read/28120870/selection-of-suitable-reference-genes-for-quantitative-real-time-pcr-gene-expression-analysis-in-salix-matsudana-under-different-abiotic-stresses
#7
Yunxing Zhang, Xiaojiao Han, Shuangshuang Chen, Liu Zheng, Xuelian He, Mingying Liu, Guirong Qiao, Yang Wang, Renying Zhuo
Salix matsudana is a deciduous, rapidly growing willow species commonly cultivated in China, which can tolerate drought, salt, and heavy metal stress conditions. Selection of suitable reference genes for quantitative real-time PCR is important for normalizing the expression of the key genes associated with various stresses. To validate suitable reference genes, we selected 11 candidate reference genes (five traditional housekeeping genes and six novel genes) and analyzed their expression stability in various samples, including different tissues and under different abiotic stress treatments...
January 25, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28117343/selection-of-reference-genes-is-critical-for-mirna-expression-analysis-in-human-cardiac-tissue-a-focus-on-atrial-fibrillation
#8
Michela Masè, Margherita Grasso, Laura Avogaro, Elvira D'Amato, Francesco Tessarolo, Angelo Graffigna, Michela Alessandra Denti, Flavia Ravelli
MicroRNAs (miRNAs) are emerging as key regulators of complex biological processes in several cardiovascular diseases, including atrial fibrillation (AF). Reverse transcription-quantitative polymerase chain reaction is a powerful technique to quantitatively assess miRNA expression profile, but reliable results depend on proper data normalization by suitable reference genes. Despite the increasing number of studies assessing miRNAs in cardiac disease, no consensus on the best reference genes has been reached...
January 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28115499/selection-and-evaluation-of-reference-genes-for-expression-analysis-using-qrt-pcr-in-chilo-suppressalis-lepidoptera-pyralidae
#9
Jing Xu, Ming-Xing Lu, Ya-Dong Cui, Yu-Zhou Du
Quantitative real-time polymerase chain reaction (qRT-PCR) is a valuable tool for estimating gene expression; however, the validity is largely dependent on the selection of stable reference genes. The suitability of various reference genes for qRT-PCR analysis was evaluated in, Chilo suppressalis (Walker). The ΔCt method, geNorm, NormFinder, and BestKeeper were used to evaluate the suitability of nine candidate reference genes for normalizing gene expression in larval tissues and organs and during high and low temperature stress...
January 22, 2017: Journal of Economic Entomology
https://www.readbyqxmd.com/read/28090788/selection-of-suitable-reference-genes-for-quantitative-real-time-pcr-in-trabecular-meshwork-cells-under-oxidative-stress
#10
Jing Zhao, HongYan Zhou, Lixia Sun, Ben Yang, Lin Zhang, Hongfeng Shi, Yajuan Zheng
Oxidative stress-induced dysfunction in trabecular meshwork (TM) cells is considered a major alteration that can lead to glaucoma. H2O2 is the most widely used agent for inducing oxidation in TM cells in vitro. Quantitative real-time PCR (qPCR) is an important method for studying alterations in gene expression, and suitable (i.e., invariant) reference genes must be defined to normalize expression levels. In this study, eight common reference genes, i.e., PRS18, ACTB, B2M, GAPDH, PPIA, HPRT1, YWHAZ, and TBP, were evaluated for use in studies of H2O2-induced dysfunction in TM cells...
January 15, 2017: Free Radical Research
https://www.readbyqxmd.com/read/28067273/validation-of-reference-genes-for-cryopreservation-studies-with-the-gorgonian-coral-endosymbiont-symbiodinium
#11
Gabriella Chong, Fu-Wen Kuo, Sujune Tsai, Chiahsin Lin
Quantification by real-time RT-PCR requires a stable internal reference known as a housekeeping gene (HKG) for normalising the mRNA levels of target genes. The present study identified and validated stably expressed HKGs in post-thaw Symbiodinium clade G. Six potential HKGs, namely, pcna, gapdh, 18S rRNA, hsp90, rbcl, and ps1, were analysed using three different algorithms, namely, GeNorm, NormFinder, and BestKeeper. The GeNorm algorithm ranked the candidate genes as follows in the order of decreasing stability: pcna and gapdh > ps1 > 18S rRNA > hsp90 > rbcl...
January 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28056110/selection-of-reference-genes-for-qrt-pcr-analysis-of-gene-expression-in-stipa-grandis-during-environmental-stresses
#12
Dongli Wan, Yongqing Wan, Qi Yang, Bo Zou, Weibo Ren, Yong Ding, Zhen Wang, Ruigang Wang, Kai Wang, Xiangyang Hou
Stipa grandis P. Smirn. is a dominant plant species in the typical steppe of the Xilingole Plateau of Inner Mongolia. Selection of suitable reference genes for the quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) is important for gene expression analysis and research into the molecular mechanisms underlying the stress responses of S. grandis. In the present study, 15 candidate reference genes (EF1 beta, ACT, GAPDH, SamDC, CUL4, CAP, SNF2, SKIP1, SKIP5, SKIP11, UBC2, UBC15, UBC17, UCH, and HERC2) were evaluated for their stability as potential reference genes for qRT-PCR under different stresses...
2017: PloS One
https://www.readbyqxmd.com/read/28050855/selection-of-reference-genes-from-shiraia-bambusicola-for-rt-qpcr-analysis-under-different-culturing-conditions
#13
Chen Zhang, Tong Li, Cheng-Lin Hou, Xiao-Ye Shen
Stable reference genes are necessary to analyse quantitative real-time reverse transcription PCR (qRT-PCR) data and determine the reliability of the final results. For further studies of the valuable fungus Shiraia bambusicola, the identification of suitable reference genes has become increasingly urgent. In this study, three conventional reference genes and nine novel candidates were evaluated under different light conditions (all-dark, all-light and 12-h light/dark) and in different media (rice medium, PD medium, and Czapek-Dox medium)...
December 2017: AMB Express
https://www.readbyqxmd.com/read/28046130/evaluation-of-reference-genes-for-normalization-of-gene-expression-using-quantitative-rt-pcr-under-aluminum-cadmium-and-heat-stresses-in-soybean
#14
Mengmeng Gao, Yaping Liu, Xiao Ma, Qin Shuai, Junyi Gai, Yan Li
Quantitative reverse transcription polymerase chain reaction (qRT-PCR) is widely used to analyze the relative gene expression level, however, the accuracy of qRT-PCR is greatly affected by the stability of reference genes, which is tissue- and environment- dependent. Therefore, choosing the most stable reference gene in a specific tissue and environment is critical to interpret gene expression patterns. Aluminum (Al), cadmium (Cd), and heat stresses are three important abiotic factors limiting soybean (Glycine max) production in southern China...
2017: PloS One
https://www.readbyqxmd.com/read/28040059/validation-of-housekeeping-genes-for-the-normalization-of-rt-qpcr-expression-studies-in-oral-squamous-cell-carcinoma-cell-line-treated-by-5-kinds-of-chemotherapy-drugs
#15
W Song, W H Zhang, H Zhang, Y Li, Y Zhang, W Yin, Q Yang
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 of this method is to identify an applicable internal control gene because the usage of different internal control genes may lead to distinct conclusions. Herein, we report the validation of 12 common housekeeping genes for RT-qPCR for gene expression analysis in the Oral squamous cell carcinoma (OSCC) cell line (KB and Tca-8113) treated by 5 kinds of Chemotherapy Drugs...
November 30, 2016: Cellular and Molecular Biology
https://www.readbyqxmd.com/read/28039034/development-and-evaluation-of-a-novel-rt-qpcr-based-test-for-the-quantification-of-her2-gene-expression-in-breast-cancer
#16
Hicham El Hadi, Imane Abdellaoui-Maane, Denise Kottwitz, Manal El Amrani, Nadia Bouchoutrouch, Zineb Qmichou, Mehdi Karkouri, Hicham ElAttar, Hassan Errihani, Pedro L Fernandez, Youssef Bakri, Hassan Sefrioui, Abdeladim Moumen
Accurate measurement of Human epidermal growth factor receptor (HER2) gene expression is central for breast or stomach cancer therapy orientation and prognosis. The current standards testing methods for HER2 expression are immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH). In the current study, we explored the use of quantitative real time reverse transcription-PCR (RT-qPCR) as a potential method for the accurate relative quantification of the HER2 gene using formalin fixed paraffin embedded (FFPE) breast cancer biopsy samples...
March 20, 2017: Gene
https://www.readbyqxmd.com/read/28036291/assessing-the-clinical-value-of-micrornas-in-formalin-fixed-paraffin-embedded-liposarcoma-tissues-overexpressed-mir-155-is-an-indicator-of-poor-prognosis
#17
Nikolaos Kapodistrias, Konstantinos Mavridis, Anna Batistatou, Penelope Gogou, Vasilios Karavasilis, Ioannis Sainis, Evangelos Briasoulis, Andreas Scorilas
Liposarcoma (LPS) is a malignancy with extreme heterogeneity and thus optimization towards personalizing patient prognosis and treatment is essential. Here, we evaluated miR-155, miR-21, miR-143, miR-145 and miR-451 that are implicated in LPS, as novel FFPE tissue biomarkers.A total of 83 FFPE tissue specimens from primary LPS and lipomas (LPM) were analyzed. A proteinase K incubation-Trizol treatment coupled protocol was used for RNA isolation. After polyadenylation of total RNA and reverse transcription, expression analysis of 9 candidate reference and 5 target miRNAs was performed by qPCR...
January 24, 2017: Oncotarget
https://www.readbyqxmd.com/read/27994956/identifying-suitable-reference-genes-for-gene-expression-analysis-in-developing-skeletal-muscle-in-pigs
#18
Guanglin Niu, Yalan Yang, YuanYuan Zhang, Chaoju Hua, Zishuai Wang, Zhonglin Tang, Kui Li
The selection of suitable reference genes is crucial to accurately evaluate and normalize the relative expression level of target genes for gene function analysis. However, commonly used reference genes have variable expression levels in developing skeletal muscle. There are few reports that systematically evaluate the expression stability of reference genes across prenatal and postnatal developing skeletal muscle in mammals. Here, we used quantitative PCR to examine the expression levels of 15 candidate reference genes (ACTB, GAPDH, RNF7, RHOA, RPS18, RPL32, PPIA, H3F3, API5, B2M, AP1S1, DRAP1, TBP, WSB, and VAPB) in porcine skeletal muscle at 26 different developmental stages (15 prenatal and 11 postnatal periods)...
2016: PeerJ
https://www.readbyqxmd.com/read/27976798/identification-and-validation-of-micrornas-as-endogenous-controls-for-quantitative-polymerase-chain-reaction-in-plasma-for-stable-coronary-artery-disease
#19
Yuejuan Zhang, Wenxian Tang, Ling Peng, Jinqiang Tang, Zhaokai Yuan
BACKGROUND: Circulating microRNAs (miRNAs) have been proved to serve as biomarkers for diagnosis and assessment of prognosis of coronary artery disease (CAD). Reverse transcription quantitative polymerase chain reaction (RT-qPCR) is a widely-used technique to estimate expression levels of circulating miRNAs. Selection of optimal endogenous control (EC) remains critical to obtain reliable qPCR data of miRNAs expression. However, reference controls for normalization of circulating miRNA in CAD are still lacking...
2016: Cardiology Journal
https://www.readbyqxmd.com/read/27974876/evaluation-of-housekeeping-genes-for-quantitative-gene-expression-analysis-in-the-equine-kidney
#20
Sara Azarpeykan, Keren E Dittmer
Housekeeping genes (HKGs) are used as internal controls for normalising and calculating the relative expression of target genes in RT-qPCR experiments. There is no unique universal HKG and HKGs vary among organisms and tissues, so this study aimed to determine the most stably expressed HKGs in the equine kidney. The evaluated HKGs included 18S ribosomal RNA (18S), 28S ribosomal RNA (28S), ribosomal protein L32 (RPL32), β-2-microglobulin (B2M), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), succinate dehydrogenase complex (SDHA), zeta polypeptide (YWHAZ), and hypoxanthine phosphoribosyltransferase 1 (HPRT1)...
2016: Journal of Equine Science
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