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https://www.readbyqxmd.com/read/28527971/identification-and-comprehensive-evaluation-of-reference-genes-for-rt-qpcr-analysis-of-host-gene-expression-in-brassica-juncea-aphid-interaction-using-microarray-data
#1
Chet Ram, Murali Krishna Koramutla, Ramcharan Bhattacharya
Brassica juncea is a chief oil yielding crop in many parts of the world including India. With advancement of molecular techniques, RT-qPCR based study of gene-expression has become an integral part of experimentations in crop breeding. In RT-qPCR, use of appropriate reference gene(s) is pivotal. The virtue of the reference genes, being constant in expression throughout the experimental treatments, needs to be validated case by case. Appropriate reference gene(s) for normalization of gene-expression data in B...
May 11, 2017: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/28523004/selection-of-suitable-reference-genes-for-quantitative-real-time-pcr-in-sapium-sebiferum
#2
Xue Chen, Yingji Mao, Shengwei Huang, Jun Ni, Weili Lu, Jinyan Hou, Yuting Wang, Weiwei Zhao, Minghao Li, Qiaojian Wang, Lifang Wu
Chinese tallow (Sapium sebiferum L.) is a promising landscape and bioenergy plant. Measuring gene expression by quantitative real-time polymerase chain reaction (qRT-PCR) can provide valuable information on gene function. Stably expressed reference genes for normalization are a prerequisite for ensuring the accuracy of the target gene expression level among different samples. However, the reference genes in Chinese tallow have not been systematically validated. In this study, 12 candidate reference genes (18S, GAPDH, UBQ, RPS15, SAND, TIP41, 60S, ACT7, PDF2, APT, TBP, and TUB) were investigated with qRT-PCR in 18 samples, including those from different tissues, from plants treated with sucrose and cold stresses...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28521492/validation-of-reference-genes-for-the-normalization-of-rt-qpcr-expression-studies-in-human-tongue-carcinoma-cell-lines-and-tissue
#3
Xiaofeng Wang, Xin Liu, Cong Liu, Ming Ren, Sujie Gao, Guanjie Zhao, Tianfu Zhang, Qiwei 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 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...
May 2017: Oncology Letters
https://www.readbyqxmd.com/read/28515733/stable-internal-reference-genes-for-normalizing-real-time-quantitative-pcr-in-baphicacanthus-cusia-under-hormonal-stimuli-and-uv-irradiation-and-in-different-plant-organs
#4
Yuxiang Huang, Hexin Tan, Jian Yu, Yue Chen, Zhiying Guo, Guoquan Wang, Qinglei Zhang, Junfeng Chen, Lei Zhang, Yong Diao
Baphicacanthus cusia (Nees) Bremek, the plant source for many kinds of drugs in traditional Chinese medicine, is widely distributed in South China, especially in Fujian. Recent studies about B. cusia mainly focus on its chemical composition and pharmacological effects, but further analysis of the plant's gene functions and expression is required to better understand the synthesis of its effective compounds. Real-time quantitative polymerase chain reaction (RT-qPCR) is a powerful method for gene expression analysis...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28515453/validation-of-reference-genes-for-the-normalization-of-the-rt-qpcr-gene-expression-of-virulence-genes-of-erwinia-amylovora-in-apple-shoots
#5
Monika Kałużna, Anita Kuras, Joanna Puławska
To study the expression of pathogenicity-related genes in Erwinia amylovora, seven candidate reference genes (ffh, glyA, gyrA, proC, pykA, recA, rpoB) were selected and validated with the following five different mathematic algorithms: geNorm, NormFinder, BestKeeper, the delta CT method and the RefFinder web-based tool. An overall comprehensive ranking output from each of the selected software programs revealed that proC and recA, followed by ffh and pykA, were the most stably expressed genes and can be recommended for the normalization of RT-qPCR data...
May 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28514730/circulating-micrornas-as-novel-biomarkers-of-alk-positive-nonsmall-cell-lung-cancer-and-predictors-of-response-to-crizotinib-therapy
#6
Liang-Liang Li, Li-Li Qu, Han-Jiang Fu, Xiao-Fei Zheng, Chuan-Hao Tang, Xiao-Yan Li, Jian Chen, Wei-Xia Wang, Shao-Xing Yang, Lin Wang, Guan-Hua Zhao, Pan-Pan Lv, Min Zhang, Yang-Yang Lei, Hai-Feng Qin, Hong Wang, Hong-Jun Gao, Xiao-Qing Liu
Circulating microRNAs are potential diagnostic and predictive biomarkers, but have not been investigated for patients with anaplastic lymphoma kinase (ALK)-positive lung cancer. In this exploratory study, we sought to identify potential plasma biomarkers for ALK-positive non-small cell lung cancer (NSCLC). A microRNA microarray was used to select ALK-related microRNAs in ALK-positive NSCLC (n = 3), ALK-negative NSCLC (n = 3), and healthy subjects (n = 3). Plasma levels of 21 microRNAs were differentially expressed for ALK-positive and ALK-negative NSCLC, including 14 down-regulated and 7 up-regulated microRNAs...
April 30, 2017: Oncotarget
https://www.readbyqxmd.com/read/28509880/analysis-of-different-approaches-for-the-selection-of-reference-genes-in-rt-qpcr-experiments-a-case-study-in-skeletal-muscle-of-growing-mice
#7
Verónica G Piazza, Andrzej Bartke, Johanna G Miquet, Ana I Sotelo
The reliability of reverse transcription-quantitative PCR (RT-qPCR) results in gene expression studies depends on the approaches used to account for non-biological variations. In order to find a proper normalization strategy for the study of genes related to growth hormone signaling in skeletal muscle of growing mice, nine unrelated genes were evaluated as internal controls. According to the most used algorithms-geNorm, the Comparative ΔCq method, NormFinder and BestKeeper-GSK3B, YWHAZ, RPL13A and RN18S were found as the most stable...
May 16, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28496155/selection-of-reference-genes-for-microrna-analysis-associated-to-early-stress-response-to-handling-and-confinement-in-salmo-salar
#8
Eduardo Zavala, Daniela Reyes, Robert Deerenberg, Rodrigo Vidal
MicroRNAs are key non-coding RNA molecules that play a relevant role in the regulation of gene expression through translational repression and/or transcript cleavage during normal development and physiological adaptation processes like stress. Quantitative reverse transcription polymerase chain reaction (RT-qPCR) has become the approach normally used to determine the levels of microRNAs. However, this approach needs the use of endogenous reference. An improper selection of endogenous references can result in confusing interpretation of data...
May 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28487721/validation-of-reference-genes-for-quantitative-real-time-pcr-during-bicolor-tepal-development-in-asiatic-hybrid-lilies-lilium-spp
#9
Leifeng Xu, Hua Xu, Yuwei Cao, Panpan Yang, Yayan Feng, Yuchao Tang, Suxia Yuan, Jun Ming
Quantitative real-time PCR (qRT-PCR) is a reliable and high-throughput technique for gene expression studies, but its accuracy depends on the expression stability of reference genes. To date, several reliable reference gene identifications have been reported in Lilium spp., but none has been obtained for lily tepals at different developmental stages. In this study, ten candidate reference genes were selected and evaluated for their expression stability in Lilium 'Tiny Padhye' during the process of bicolor tepal development...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28466785/identification-of-plasma-micrornas-as-new-potential-biomarkers-with-high-diagnostic-power-in-human-cutaneous-melanoma
#10
Stefano Fogli, Beatrice Polini, Sara Carpi, Barbara Pardini, Alessio Naccarati, Nevio Dubbini, Maria Lanza, Maria Cristina Breschi, Antonella Romanini, Paola Nieri
Melanoma is a devastating disease with few therapeutic options in the advanced stage and with the urgent need of reliable biomarkers for early detection. In this context, circulating microRNAs are raising great interest as diagnostic biomarkers. We analyzed the expression profiles of 21 selected microRNAs in plasma samples from melanoma patients and healthy donors to identify potential diagnostic biomarkers. Data analysis was performed using global mean normalization and NormFinder algorithm. Linear regression followed by receiver operating characteristic analyses was carried out to evaluate whether selected plasma miRNAs were able to discriminate between cases and controls...
May 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28459824/influence-of-heat-stress-sex-and-genetic-groups-on-reference-genes-stability-in-muscle-tissue-of-chicken
#11
Haniel Cedraz de Oliveira, Antonio Amandio Pinto Garcia, Juliana Gracielle Gonzaga Gromboni, Ronaldo Vasconcelos Farias Filho, Carlos Souza do Nascimento, Amauri Arias Wenceslau
Quantitative RT-PCR is an important technique for assessing gene expression. However, a proper normalization of reference genes prior to expression analyses of target genes is necessary. The best normalizer is that gene which remains stable in all samples from different treatments. The aim of this study was to identify stable reference genes for normalization of target genes in muscle tissue from three genetically divergent chickens groups (Peloco, Cobb 500® and Caneluda) under environmental (heat stress and comfort) and sex influence...
2017: PloS One
https://www.readbyqxmd.com/read/28454689/identification-of-appropriate-reference-genes-for-qpcr-analyses-of-placental-expression-of-slc7a3-and-induction-of-slc5a1-in-porcine-endometrium
#12
Chelsie B Steinhauser, Theodore T Wing, Haijun Gao, Xilong Li, Robert C Burghardt, Guoyao Wu, Fuller W Bazer, Greg A Johnson
INTRODUCTION: Endometria and placentae undergo developmental changes that affect the stability of genes used as references for normalization of qPCR data. We identified genes that are stable within the porcine endometrium and placenta throughout pregnancy, and elucidated the temporal/spatial mRNA localization of the glucose and arginine transporters, solute carrier family (SLC) 5A1 and SLC7A3, respectively. MATERIALS AND METHODS: qPCR was performed for 10 genes within porcine endometria from Days 5, 11, and 15 of the estrous cycle and 11, 15, 25, 40, 60, and 85 of pregnancy; and chorioallantois from Days 30, 35, 45, 50, 60, and 85...
April 2017: Placenta
https://www.readbyqxmd.com/read/28453515/reliable-reference-genes-for-normalization-of-gene-expression-data-in-tea-plants-camellia-sinensis-exposed-to-metal-stresses
#13
Ming-Le Wang, Qing-Hui Li, Hua-Hong Xin, Xuan Chen, Xu-Jun Zhu, Xing-Hui Li
Tea plants [Camellia sinensis (L.) O. Kuntze] are an important leaf-type crop that are widely used for the production of non-alcoholic beverages in the world. Exposure to excessive amounts of heavy metals adversely affects the quality and yield of tea leaves. To analyze the molecular responses of tea plants to heavy metals, a reliable quantification of gene expression is important and of major importance herein is the normalization of the measured expression levels for the target genes. Ideally, stably expressed reference genes should be evaluated in all experimental systems...
2017: PloS One
https://www.readbyqxmd.com/read/28440415/udp-and-ntf2-are-the-most-consistently-expressed-genes-in-panax-ginseng-roots-at-different-growth-stages
#14
Meichen Liu, Qun Wang, Hongmei Xie, Shichao Liu, Siming Wang, Hui Zhang, Yu Zhao
Reverse transcription‑quantitative polymerase chain reaction (RT‑qPCR) analysis relies on normalization against a consistently expressed reference gene. However, it has been reported that reference gene expression levels often vary markedly between samples as they are usually selected based solely on convention. The advent of RNA sequencing technology offers the opportunity to select reference genes with the least variability in steady‑state transcript levels. To identify the most consistently stable genes, which are a prerequisite for obtaining reliable gene expression data, the present study analyzed transcriptomes from six Panax ginseng transcriptome data sets, representing six growth stages, and selected 21 candidate reference genes for screening using RT‑qPCR...
June 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28429149/a-spiking-strategy-facilitates-housekeeping-selection-for-rt-qpcr-analysis-under-different-biotic-stresses-in-eggplant
#15
Valeria Barbierato, Tea Sala, Paola Rinaldi, Laura Bassolino, Lorenzo Barchi, Giuseppe Leonardo Rotino, Laura Toppino
Endogenous housekeeping genes are traditionally employed to normalize the expression of target genes in RT-qPCR studies. Assuming that a perfect housekeeping suitable for every condition does not exist, expression stability of the chosen reference gene should be evaluated at every new experiment. The housekeeping selection process reveals furthermore complicated and time-consuming when different conditions have to be compared in the same experimental dataset. As an alternative strategy, we spiked an external reference transcript (ERT) into all RNA samples of our dataset (eggplant roots subjected to different biotic stresses), and used it to normalize the expression levels of native candidate housekeeping...
April 21, 2017: Protoplasma
https://www.readbyqxmd.com/read/28428808/reference-genes-for-normalization-of-qpcr-assays-in-sugarcane-plants-under-water-deficit
#16
Larissa Mara de Andrade, Michael Dos Santos Brito, Rafael Fávero Peixoto Junior, Paulo Eduardo Ribeiro Marchiori, Paula Macedo Nóbile, Alexandre Palma Boer Martins, Rafael Vasconcelos Ribeiro, Silvana Creste
BACKGROUND: Sugarcane (Saccharum spp.) is the main raw material for sugar and ethanol production. Among the abiotic stress, drought is the main one that negatively impact sugarcane yield. Although gene expression analysis through quantitative PCR (qPCR) has increased our knowledge about biological processes related to drought, gene network that mediates sugarcane responses to water deficit remains elusive. In such scenario, validation of reference gene is a major requirement for successful analyzes involving qPCR...
2017: Plant Methods
https://www.readbyqxmd.com/read/28414734/micrornas-as-reference-genes-for-quantitative-pcr-in-cotton
#17
Anna Karoline Silva Fausto, Tatiane da Franca Silva, Elisson Romanel, Maite F S Vaslin
Cotton (Gossypium hirsutum) is the most important non-food plant in the world. Studies concerning the fiber quality and plant fitness of cotton at molecular level depend on high sensitive and reproducible gene-expression assays. However, only a few reports have described genes suitable for normalizing gene expression data. In this study, we report for the first time that microRNAs (miRNAs) are reliable reference genes (RGs) for cotton gene expression normalization in quantitative real-time reverse transcription (RT)-PCR...
2017: PloS One
https://www.readbyqxmd.com/read/28410879/determination-of-reference-genes-that-are-independent-of-feeding-rhythms-for-circadian-studies-of-mouse-metabolic-tissues
#18
Reiko Nakao, Hiroki Okauchi, Chiaki Hashimoto, Naoyuki Wada, Katsutaka Oishi
Real-time reverse transcription-polymerase chain reaction (RT-PCR) analysis is a popular method for the measurement of mRNA expression level and is a critical tool for basic research. The identification of suitable reference genes that are stable and not affected by experimental conditions is a critical step in the accurate normalization of RT-PCR. On the other hand, the levels of numerous transcripts exhibit circadian oscillation in various peripheral tissues and it is thought to be regulated by feeding rhythms in addition to the molecular circadian clock...
April 5, 2017: Molecular Genetics and Metabolism
https://www.readbyqxmd.com/read/28393113/evaluating-normalization-approaches-for-the-better-identification-of-aberrant-micrornas-associated-with-hepatocellular-carcinoma
#19
Jing Shen, Qiao Wang, Irina Gurvich, Helen Remotti, Regina M Santella
AIM: Dysregulated microRNAs (miRNAs) have been identified in hepatocellular carcinoma (HCC), but only a small proportion have been confirmed. An appropriate normalizer is crucial to determining the accuracy and reliability of data from miRNA studies. METHODS: Different normalization strategies were used to validate genome-wide miRNA profiles in HCC tumor and non-tumor tissues, and to determine the consistency and discrepancy of data on dysregulated miRNAs. RESULTS: Two sets of stable miRNAs (miR-30c/miR-30b and miR-30c/miR-126) were identified in HCC tissues by geNorm and NormFinder tools, respectively...
November 2016: Hepatoma Research
https://www.readbyqxmd.com/read/28390990/selection-of-reference-genes-for-gene-expression-studies-in-heart-failure-for-left-and-right-ventricles
#20
Mengmeng Li, Man Rao, Kai Chen, Jianye Zhou, Jiangping Song
Real-time quantitative reverse transcriptase-PCR (qRT-PCR) is a feasible tool for determining gene expression profiles, but the accuracy and reliability of the results depends on the stable expression of selected housekeeping genes in different samples. By far, researches on stable housekeeping genes in human heart failure samples are rare. Moreover the effect of heart failure on the expression of housekeeping genes in right and left ventricles is yet to be studied. Therefore we aim to provide stable housekeeping genes for both ventricles in heart failure and normal heart samples...
April 5, 2017: Gene
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