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https://www.readbyqxmd.com/read/28440415/udp-and-ntf2-are-the-most-consistently-expressed-genes-in-panax-ginseng-roots-at-different-growth-stages
#1
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...
April 21, 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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
https://www.readbyqxmd.com/read/28381210/identification-of-suitable-reference-genes-for-real-time-quantitative-pcr-analysis-of-hydrogen-peroxide-treated-human-umbilical-vein-endothelial-cells
#8
Tianyi Li, Hongying Diao, Lei Zhao, Yue Xing, Jichang Zhang, Ning Liu, Youyou Yan, Xin Tian, Wei Sun, Bin Liu
BACKGROUND: Oxidative stress can induce cell injury in vascular endothelial cells, which is the initial event in the development of atherosclerosis. Although quantitative real-time polymerase chain reaction (qRT-PCR) has been widely used in gene expression studies in oxidative stress injuries, using carefully validated reference genes has not received sufficient attention in related studies. The objective of this study, therefore, was to select a set of stably expressed reference genes for use in qRT-PCR normalization in oxidative stress injuries in human umbilical vein endothelial cells (HUVECs) induced by hydrogen peroxide (H2O2)...
April 5, 2017: BMC Molecular Biology
https://www.readbyqxmd.com/read/28368031/housekeeping-in-tephritid-insects-the-best-gene-choice-for-expression-analyses-in-the-medfly-and-the-olive-fly
#9
Efthimia Sagri, Panagiota Koskinioti, Maria-Eleni Gregoriou, Konstantina T Tsoumani, Yiannis C Bassiakos, Kostas D Mathiopoulos
Real-time quantitative-PCR has been a priceless tool for gene expression analyses. The reaction, however, needs proper normalization with the use of housekeeping genes (HKGs), whose expression remains stable throughout the experimental conditions. Often, the combination of several genes is required for accurate normalization. Most importantly, there are no universal HKGs which can be used since their expression varies among different organisms, tissues or experimental conditions. In the present study, nine common HKGs (RPL19, tbp, ubx, GAPDH, α-TUB, β-TUB, 14-3-3zeta, RPE and actin3) are evaluated in thirteen different body parts, developmental stages and reproductive and olfactory tissues of two insects of agricultural importance, the medfly and the olive fly...
April 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28362875/identification-and-validation-of-reference-genes-for-quantitative-real-time-pcr-studies-in-long-yellow-daylily-hemerocallis-citrina-borani
#10
Feifan Hou, Sen Li, Jinyao Wang, Xiuping Kang, Yiqun Weng, Guoming Xing
Gene expression analysis using reverse transcription quantitative real-time PCR (RT-qPCR) requires the use of reference gene(s) in the target species. The long yellow daylily, Hemerocallis citrina Baroni. is rich in beneficial secondary metabolites and is considered as a functional vegetable. It is widely cultivated and consumed in East Asian countries. However, reference genes for use in RT-qPCR in H. citrina are not available. In the present study, six potential reference genes, actin (ACT), AP-4 complex subunit (AP4), tubulin (TUB), ubiquitin (UBQ), 18S and 60S ribosomal RNA, were selected and their expression stability in different developmental stages, organs and accessions was evaluated using four statistical software packages (geNorm, NormFinder, BestKeeper, and RefFinder)...
2017: PloS One
https://www.readbyqxmd.com/read/28355475/identification-and-evaluation-of-suitable-reference-genes-for-normalization-of-microrna-expression-in-helicoverpa-armigera-lepidoptera-noctuidae-using-quantitative-real-time-pcr
#11
Yuhui Yang, Zhen Li, Jinjun Cao, Yanrong Li, Hui Li, Qingpo Yang, Qingwen Zhang, Xiaoxia Liu
More and more studies have focused on microRNAs (miRNAs) expression in the pest Helicoverpa armigera (Lepidoptera: Noctuidae) recently. Quantitative real-time PCR (qRT-PCR) is being widely used in miRNA expression studies. Suitable reference genes are necessary for the correct analysis of results. In this study, 10 candidate genes of H. armigera were selected and analyzed for their expression stability under different biotic and abiotic conditions with 3 statistical methods, including geNorm, NormFinder, and Bestkeeper...
January 1, 2017: Journal of Insect Science
https://www.readbyqxmd.com/read/28328930/validation-of-qpcr-reference-genes-in-lymphocytes-from-patients-with-amyotrophic-lateral-sclerosis
#12
Ewa Usarek, Anna Barańczyk-Kuźma, Beata Kaźmierczak, Beata Gajewska, Magdalena Kuźma-Kozakiewicz
Quantitative polymerase chain reaction (qPCR) is the most specific and reliable method for determination of mRNA gene expression. Crucial point for its accurate normalization is the choice of appropriate internal control genes (ICGs). In the present work we determined and compare the expression of eight commonly used ICGs in lymphocytes from 26 patients with amyotrophic lateral sclerosis (ALS) and 30 control subjects. Peripheral blood mononuclear cells (PBMCs) before and after immortalization by EBV transfection (lymphoblast cell lines-LCLs) were used for qPCR analysis...
2017: PloS One
https://www.readbyqxmd.com/read/28326094/selection-and-validation-of-reference-genes-for-accurate-rt-qpcr-data-normalization-in-coffea-spp-under-a-climate-changes-context-of-interacting-elevated-co2-and-temperature
#13
Madlles Q Martins, Ana S Fortunato, Weverton P Rodrigues, Fábio L Partelli, Eliemar Campostrini, Fernando C Lidon, Fábio M DaMatta, José C Ramalho, Ana I Ribeiro-Barros
World coffee production has faced increasing challenges associated with ongoing climatic changes. Several studies, which have been almost exclusively based on temperature increase, have predicted extensive reductions (higher than half by 2,050) of actual coffee cropped areas. However, recent studies showed that elevated [CO2] can strongly mitigate the negative impacts of heat stress at the physiological and biochemical levels in coffee leaves. In addition, it has also been shown that coffee genotypes can successfully cope with temperatures above what has been traditionally accepted...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28323834/selection-and-validation-of-reference-genes-for-qrt-pcr-analysis-during-biological-invasions-the-thermal-adaptability-of-bemisia-tabaci-med
#14
Tian-Mei Dai, Zhi-Chuang Lü, Wan-Xue Liu, Fang-Hao Wan
The Bemisia tabaci Mediterranean (MED) cryptic species has been rapidly invading to most parts of the world owing to its strong ecological adaptability, which is considered as a model insect for stress tolerance studies under rapidly changing environments. Selection of a suitable reference gene for quantitative stress-responsive gene expression analysis based on qRT-PCR is critical for elaborating the molecular mechanisms of thermotolerance. To obtain accurate and reliable normalization data in MED, eight candidate reference genes (β-act, GAPDH, β-tub, EF1-α, GST, 18S, RPL13A and α-tub) were examined under various thermal stresses for varied time periods by using geNorm, NormFinder and BestKeeper algorithms, respectively...
2017: PloS One
https://www.readbyqxmd.com/read/28300076/evaluation-of-reference-genes-at-different-developmental-stages-for-quantitative-real-time-pcr-in-aedes-aegypti
#15
Najat Dzaki, Karima N Ramli, Azali Azlan, Intan H Ishak, Ghows Azzam
The mosquito Aedes aegypti (Ae. aegypti) is the most notorious vector of illness-causing viruses such as Dengue, Chikugunya, and Zika. Although numerous genetic expression studies utilizing quantitative real-time PCR (qPCR) have been conducted with regards to Ae. aegypti, a panel of genes to be used suitably as references for the purpose of expression-level normalization within this epidemiologically important insect is presently lacking. Here, the usability of seven widely-utilized reference genes i.e. actin (ACT), eukaryotic elongation factor 1 alpha (eEF1α), alpha tubulin (α-tubulin), ribosomal proteins L8, L32 and S17 (RPL8, RPL32 and RPS17), and glyceraldeyde 3-phosphate dehydrogenase (GAPDH) were investigated...
March 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28299307/identification-of-appropriate-housekeeping-genes-for-gene-expression-analysis-in-long-term-hypoxia-treated-kidney-cells
#16
Shiva Moein, Shaghayegh Haghjooy Javanmard, Maryam Abedi, Mohammad Hosein Izadpanahi, Yousof Gheisari
BACKGROUND: Selection of stably expressing housekeeping genes (HKGs) is a crucial step in gene expression analysis. However, there are no universal HKGs for all experiments, and they should be determined by each biologic condition. The aim of this study was to detect appropriate HKGs for kidney cells cultured in long-term hypoxia. MATERIALS AND METHODS: Based on a screening step using a microarray data available from gene expression omnibus database, a set of candidate HKGs were chosen to be assessed in human kidney cells cultured in hypoxic or normoxic conditions for about 2 weeks in a time course manner...
2017: Advanced Biomedical Research
https://www.readbyqxmd.com/read/28294410/reference-gene-selection-for-reverse-transcription-quantitative-polymerase-chain-reaction-in-chicken-hypothalamus-under-different-feeding-status
#17
Á Simon, A Jávor, P Bai, J Oláh, L Czeglédi
This study was designed to investigate the stability of 10 candidate reference genes, namely ACTB, B2M, GAPDH, HMBS, LBR, POLR2B, RN18S, RPS17, TBP, and YWHAZ for the normalization of gene expression data obtained by quantitative real-time polymerase chain reaction (qPCR) in studies related to feed intake of chicken. Samples were isolated from hypothalamus under three different nutritional status (ad libitum, fasted for 24 hr, fasted for 24 hr then refed for 2 hr). Five different algorithms were applied for the analysis of reference gene stability: BestKeeper, geNorm, NormFinder, the comparative ΔCt method, and a novel approach using multivariate linear mixed-effects modelling for stable reference gene selection...
March 15, 2017: Journal of Animal Physiology and Animal Nutrition
https://www.readbyqxmd.com/read/28262749/identification-of-stable-housekeeping-genes-in-response-to-ionizing-radiation-in-cancer-research
#18
Gopal Iyer, Albert R Wang, Sean R Brennan, Shay Bourgeois, Eric Armstrong, Pari Shah, Paul M Harari
Housekeeping genes (HKGs) are essential for basic maintenance of a variety of cellular processes. They ideally maintain uniform expression independent of experimental conditions. However, the effects of ionizing radiation (IR) on HKG expression is unclear. Statistical algorithms, geNorm and Normfinder were used for estimating the stability of HKGs as raw quantification cycle (Cq) values were not a reliable factor for normalization. Head and neck, non-small lung and pancreas cells were exposed to 2, 4 and 6 Gy IR doses and expression of fourteen HKGs was measured at 5 min to 48 h post-irradiation within a given tissue...
March 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28261247/selection-of-candidate-reference-genes-for-gene-expression-analysis-in-kentucky-bluegrass-poa-pratensis-l-under-abiotic-stress
#19
Kuiju Niu, Yi Shi, Huiling Ma
Kentucky bluegrass (Poa pratensis L.) belong to Gramineae and is widely used in lawns, golf courses, landscapes, and sport fields as a prominent cool-season grass. Gene expression patterns during different stages of plant development can provide clues toward the understanding of its biological functions. The selection and validation of reference genes are the first steps in any real-time quantitative PCR gene expression study. Therefore, suitable reference genes are necessary for obtaining reliable results in real-time quantitative PCR analyses of Kentucky bluegrass...
2017: Frontiers in Plant Science
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
#20
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
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