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https://www.readbyqxmd.com/read/27922100/evaluation-of-candidate-reference-genes-for-rt-qpcr-studies-in-three-metabolism-related-tissues-of-mice-after-caloric-restriction
#1
Huan Gong, Liang Sun, Beidong Chen, Yiwen Han, Jing Pang, Wei Wu, Ruomei Qi, Tie-Mei Zhang
Reverse transcription quantitative-polymerase chain reaction (RT-qPCR) is a routine method for gene expression analysis, and reliable results depend on proper normalization by stable reference genes. Caloric restriction (CR) is a robust lifestyle intervention to slow aging and delay onset of age-associated diseases via inducing global changes in gene expression. Reliable normalization of RT-qPCR data becomes crucial in CR studies. In this study, the expression stability of 12 candidate reference genes were evaluated in inguinal white adipose tissue (iWAT), skeletal muscle (Sk...
December 6, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27889881/identification-of-reference-genes-and-mirnas-for-qrt-pcr-in-human-esophageal-squamous-cell-carcinoma
#2
Li Chen, Yulin Jin, Lin Wang, Fenghao Sun, Xiaodong Yang, Mengkun Shi, Cheng Zhan, Yu Shi, Qun Wang
It is important to select an appropriate reference gene and miRNA when using quantitative real-time polymerase chain reaction (qRT-PCR) to analyze gene and miRNA expression. However, many commonly used reference genes and miRNAs are not stably expressed and therefore not suitable for normalization or quantification of qRT-PCR data. This study aims to identify appropriate reference genes and miRNAs for use in human esophageal squamous carcinoma qRT-PCR analysis. Using data provided by The Cancer Genome Atlas, we identified DDX5, LAPTM4A, P4HB, RHOA, miR-28-5p, miR-34a-5p, and miR-186-5p as candidate reference genes and miRNAs...
January 2017: Medical Oncology
https://www.readbyqxmd.com/read/27878453/evaluation-of-stability-and-validation-of-reference-genes-for-rt-qpcr-expression-studies-in-rice-plants-under-water-deficit
#3
Priscila Ariane Auler, Letícia Carvalho Benitez, Marcelo Nogueira do Amaral, Isabel Lopes Vighi, Gabriela Dos Santos Rodrigues, Luciano Carlos da Maia, Eugenia Jacira Bolacel Braga
Many studies use strategies that allow for the identification of a large number of genes expressed in response to different stress conditions to which the plant is subjected throughout its cycle. In order to obtain accurate and reliable results in gene expression studies, it is necessary to use reference genes, which must have uniform expression in the majority of cells in the organism studied. RNA isolation of leaves and expression analysis in real-time quantitative polymerase chain reaction (RT-qPCR) were carried out...
November 23, 2016: Journal of Applied Genetics
https://www.readbyqxmd.com/read/27878262/identification-of-suitable-reference-genes-for-bdv-infected-primary-rat-hippocampal-neurons
#4
Qiang Mao, Lujun Zhang, Yujie Guo, Lu Sun, Siwen Liu, Peng He, Rongzhong Huang, Lin Sun, Shigang Chen, Hong Zhang, Peng Xie
Borna disease virus (BDV) is a neurotropic RNA virus that infects the limbic system of mammals and results in behavioral disorders. The hippocampus is a core region in the limbic system, which contributes to memory and learning and is important in the regulation of emotion. However, no validated microRNA housekeeping genes have yet been identified in BDV‑infected rat primary hippocampal neurons. Proper normalization is key in accurate miRNA expression analysis. The present study used reverse transcription‑quantitative polymerase chain reaction (RT‑qPCR) to evaluate the expression stability of 10 commonly used reference genes [miR‑92a, 5S, U6, miR‑103, miR‑101a, miR-let-7a, miR‑16, E2 small nucleolar RNA (snoRNA), U87 and miR‑191] in BDV‑infected rat hippocampal neurons and non‑infected controls across 12 days post‑infection...
November 22, 2016: Molecular Medicine Reports
https://www.readbyqxmd.com/read/27877186/selection-of-reference-genes-for-rt-qpcr-analysis-in-coccinella-septempunctata-to-assess-un-intended-effects-of-rnai-transgenic-plants
#5
Chunxiao Yang, Evan L Preisser, Hongjun Zhang, Yong Liu, Liangying Dai, Huipeng Pan, Xuguo Zhou
The development of genetically engineered plants that employ RNA interference (RNAi) to suppress invertebrate pests opens up new avenues for insect control. While this biotechnology shows tremendous promise, the potential for both non-target and off-target impacts, which likely manifest via altered mRNA expression in the exposed organisms, remains a major concern. One powerful tool for the analysis of these un-intended effects is reverse transcriptase-quantitative polymerase chain reaction, a technique for quantifying gene expression using a suite of reference genes for normalization...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27869224/selection-of-reliable-reference-genes-for-normalization-of-quantitative-rt-pcr-from-different-developmental-stages-and-tissues-in-amphioxus
#6
Qi-Lin Zhang, Qian-Hua Zhu, Xin Liao, Xiu-Qiang Wang, Tao Chen, Han-Ting Xu, Juan Wang, Ming-Long Yuan, Jun-Yuan Chen
Amphioxus is a closest living proxy to the ancestor of cephalochordates with vertebrates, and key animal for novel understanding in the evolutionary origin of vertebrate body plan, genome, tissues and immune system. Reliable analyses using quantitative real-time PCR (qRT-PCR) for answering these scientific questions is heavily dependent on reliable reference genes (RGs). In this study, we evaluated stability of thirteen candidate RGs in qRT-PCR for different developmental stages and tissues of amphioxus by four independent (geNorm, NormFinder, BestKeeper and deltaCt) and one comparative algorithms (RefFinder)...
November 21, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27835695/reference-genes-for-addressing-gene-expression-of-bladder-cancer-cell-models-under-hypoxia-a-step-towards-transcriptomic-studies
#7
Luís Lima, Cristiana Gaiteiro, Andreia Peixoto, Janine Soares, Manuel Neves, Lúcio Lara Santos, José Alexandre Ferreira
Highly aggressive, rapidly growing tumors contain significant areas of hypoxia or anoxia as a consequence of inadequate and/or irregular blood supply. During oxygen deprivation, tumor cells withstand a panoply of adaptive responses, including a shift towards anaerobic metabolism and the reprogramming of the transcriptome. One of the major mediators of the transcriptional hypoxic response is the hypoxia-inducible factor 1 (HIF-1), whose stabilization under hypoxia acts as an oncogenic stimulus contributing to chemotherapy resistance, invasion and metastasis...
2016: PloS One
https://www.readbyqxmd.com/read/27825774/identification-and-evaluation-of-reference-genes-for-expression-studies-by-rt-qpcr-during-embryonic-development-of-the-emerging-model-organism-macrobrachium-olfersii
#8
Michael L Jaramillo, Dib Ammar, Ruth L Quispe, Frank Guzman, Rogerio Margis, Evelise M Nazari, Yara M R Müller
RT-qPCR is a sensitive and highly efficient technique that is widely used in gene expression analysis and to provide insight into the molecular mechanisms underlying embryonic development. The freshwater prawn, Macrobrachium olfersii is an emerging model organism, but, the stable reference genes of this species need to be identified and validated for RT-qPCR analysis. Thus, the aim of this study was to evaluate the expression stability of six genes (β-act, GAPDH, EF-1α, RpL8, RpS6, AK) in embryos and in adult tissues (cerebral ganglia, muscle and hepatopancreas) of M...
November 5, 2016: Gene
https://www.readbyqxmd.com/read/27824922/identification-of-reference-genes-for-quantitative-real-time-pcr-in-date-palm-phoenix-dactylifera-l-subjected-to-drought-and-salinity
#9
Himanshu V Patankar, Dekoum V M Assaha, Rashid Al-Yahyai, Ramanjulu Sunkar, Mahmoud W Yaish
Date palm is an important crop plant in the arid and semi-arid regions supporting human population in the Middle East and North Africa. These areas have been largely affected by drought and salinity due to insufficient rainfall and improper irrigation practices. Date palm is a relatively salt- and drought-tolerant plant and more recently efforts have been directed to identifying genes and pathways that confer stress tolerance in this species. Quantitative real-time PCR (qPCR) is a promising technique for the analysis of stress-induced differential gene expression, which involves the use of stable reference genes for normalizing gene expression...
2016: PloS One
https://www.readbyqxmd.com/read/27819206/reference-gene-selection-and-evaluation-for-expression-analysis-using-qrt-pcr-in-galeruca-daurica-joannis
#10
Y Tan, X-R Zhou, B-P Pang
Quantitative real-time PCR (qRT-PCR) has been used extensively to analyze gene expression and decipher gene function. To obtain the optimal and stable normalization factors for qRT-PCR, selection and validation of reference genes should be conducted in diverse conditions. In insects, more and more studies confirmed the necessity and importance of reference gene selection. In this study, eight traditionally used reference genes in Galeruca daurica (Joannis) were assessed, using qRT-PCR, for suitability as normalization genes under different experimental conditions using four statistical programs: geNorm, Normfinder, BestKeeper and the comparative ΔC t method...
November 7, 2016: Bulletin of Entomological Research
https://www.readbyqxmd.com/read/27814359/whole-transcriptome-selection-and-evaluation-of-internal-reference-genes-for-expression-analysis-in-protocorm-development-of-dendrobium-officinale-kimura-et-migo
#11
Hongqiang An, Qiankun Zhu, Wei Pei, Jing Fan, Yi Liang, Yihui Cui, Nan Lv, Wanjun Wang
Dendrobium officinale Kimu et Migo has increased many researchers' interest for its high medical and horticultural values and the molecular mechanism of its protocorm development remains unclear. In this study, 19 genes from 26 most stably expressed genes in whole transcriptome of protocorms and 5 housekeeping genes were used as candidate reference genes and screened with 4 application softwares (geNorm, NormFinder, BestKeeper and RefFinder). The results showed that a few reference genes could effectively normalize expression level of specific genes in protocorm development and the optimal top 2 reference genes were ASS and APH1L...
2016: PloS One
https://www.readbyqxmd.com/read/27803707/selection-of-reliable-reference-genes-for-gene-expression-studies-on-rhododendron-molle-g-don
#12
Zheng Xiao, Xiaobo Sun, Xiaoqing Liu, Chang Li, Lisi He, Shangping Chen, Jiale Su
The quantitative real-time polymerase chain reaction (qRT-PCR) approach has become a widely used method to analyze expression patterns of target genes. The selection of an optimal reference gene is a prerequisite for the accurate normalization of gene expression in qRT-PCR. The present study constitutes the first systematic evaluation of potential reference genes in Rhododendron molle G. Don. Eleven candidate reference genes in different tissues and flowers at different developmental stages of R. molle were assessed using the following three software packages: GeNorm, NormFinder, and BestKeeper...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27802291/actb-cdkn1b-gapdh-grb2-rhoa-and-sdcbp-were-identified-as-reference-genes-in-neuroendocrine-lung-cancer-via-the-ncounter-technology
#13
Robert Fred Henry Walter, Robert Werner, Claudia Vollbrecht, Thomas Hager, Elena Flom, Daniel Christian Christoph, Jan Schmeller, Kurt Werner Schmid, Jeremias Wohlschlaeger, Fabian Dominik Mairinger
BACKGROUND: Neuroendocrine lung cancer (NELC) represents 25% of all lung cancer cases and large patient collectives exist as formalin-fixed, paraffin-embedded (FFPE) tissue only. FFPE is controversially discussed as source for molecular biological analyses and reference genes for NELC are poorly establishes. MATERIAL AND METHODS: Forty-three representative FFPE-specimens were used for mRNA expression analysis using the digital nCounter technology (NanoString). Based on recent literature, a total of 91 mRNA targets were investigated as potential tumor markers or reference genes...
2016: PloS One
https://www.readbyqxmd.com/read/27788825/identification-of-suitable-reference-genes-for-mrna-studies-in-bone-marrow-in-a-mouse-model-of-hematopoietic-stem-cell-transplantation
#14
H Li, C Chen, H Yao, X Li, N Yang, J Qiao, K Xu, L Zeng
BACKGROUND: Bone marrow micro-environment changes during hematopoietic stem cell transplantation (HSCT) with subsequent alteration of genes expression. Quantitative polymerase chain reaction (q-PCR) is a reliable and reproducible technique for the analysis of gene expression. To obtain more accurate results, it is essential to find a reference during HSCT. However, which gene is suitable during HSCT remains unclear. This study aimed to identify suitable reference genes for mRNA studies in bone marrow after HSCT...
October 2016: Transplantation Proceedings
https://www.readbyqxmd.com/read/27765062/the-60s-ribosomal-protein-l13-is-the-most-preferable-reference-gene-to-investigate-gene-expression-in-selected-organs-from-turkeys-and-chickens-in-context-of-different-infection-models
#15
Taniya Mitra, Ivana Bilic, Michael Hess, Dieter Liebhart
Evaluation of reference genes for expression studies in chickens and turkeys is very much limited and unavailable for various infectious models. In this study, eight candidate reference genes HMBS, HPRT1, TBP, VIM, TFRC, RPLP0, RPL13 and RPS7 were evaluated by five different algorithms (GeNorm, NormFinder, BestKeeper©, delta CT, RefFinder) to assess their stability. In order to analyze a broad variation of tissues, spleen, liver, caecum and caecal tonsil of different aged specific pathogen free (SPF) layer chickens and commercial turkeys, uninfected or infected with the extracellular pathogen Histomonas meleagridis, were included...
October 20, 2016: Veterinary Research
https://www.readbyqxmd.com/read/27761137/selection-of-reliable-reference-genes-for-gene-expression-analysis-under-abiotic-stresses-in-the-desert-biomass-willow-salix-psammophila
#16
Jianbo Li, Huixia Jia, Xiaojiao Han, Jin Zhang, Pei Sun, Mengzhu Lu, Jianjun Hu
Salix psammophila is a desert shrub willow that has extraordinary adaptation to abiotic stresses and plays an important role in maintaining local ecosystems. Moreover, S. psammophila is regarded as a promising biomass feedstock because of its high biomass yields and short rotation coppice cycle. However, few suitable reference genes (RGs) for quantitative real-time polymerase chain reaction (qRT-PCR) constrain the study on normalization of gene expression in S. psammophila until now. Here, we investigated the expression stabilities of 14 candidate RGs across tissue types and under four abiotic stress treatments, including heat, cold, salt, and drought treatments...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27759076/identification-of-reference-genes-for-circulating-microrna-analysis-in-colorectal-cancer
#17
Yanqin Niu, Yike Wu, Jinyong Huang, Qing Li, Kang Kang, Junle Qu, Furong Li, Deming Gou
Quantitative real-time PCR (qPCR) is the most frequently used method for measuring expression levels of microRNAs (miRNAs), which is based on normalization to endogenous references. Although circulating miRNAs have been regarded as potential non-invasive biomarker of disease, no study has been performed so far on reference miRNAs for normalization in colorectal cancer. In this study we tried to identify optimal reference miRNAs for qPCR analysis across colorectal cancer patients and healthy individuals. 485 blood-derived miRNAs were profiled in serum sample pools of both colorectal cancer and healthy control...
October 19, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27754318/selection-of-suitable-reference-genes-for-analysis-of-salivary-transcriptome-in-non-syndromic-autistic-male-children
#18
Yasin Panahi, Fahimeh Salasar Moghaddam, Zahra Ghasemi, Mandana Hadi Jafari, Reza Shervin Badv, Mohamad Reza Eskandari, Mehrdad Pedram
Childhood autism is a severe form of complex genetically heterogeneous and behaviorally defined set of neurodevelopmental diseases, collectively termed as autism spectrum disorders (ASD). Reverse transcriptase quantitative real-time PCR (RT-qPCR) is a highly sensitive technique for transcriptome analysis, and it has been frequently used in ASD gene expression studies. However, normalization to stably expressed reference gene(s) is necessary to validate any alteration reported at the mRNA level for target genes...
October 12, 2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/27754102/os-21-07-expression-of-catecholaminergic-system-genes-in-adrenal-medulla-or-sympathetic-ganglia-of-spontaneously-hypertensive-rat
#19
Anna Vavřínová, Michal Behuliak, Josef Zicha
OBJECTIVE: Catecholaminergic system plays an important role in blood pressure regulation and hypertension development. The available information concerning mRNA expression of catecholaminergic system genes in spontaneously hypertensive rats (SHR) are often contradictory. This might be due to various reference genes used as internal controls. We therefore searched for suitable reference genes for gene expression profiling in adrenal medulla and sympathetic ganglia of SHR and Wistar-Kyoto (WKY) rats, which would enable reliable comparison of mRNA expression of genes of catecholaminergic system between these strains...
September 2016: Journal of Hypertension
https://www.readbyqxmd.com/read/27752147/identification-of-reliable-reference-genes-for-qrt-pcr-studies-of-the-developing-mouse-mammary-gland
#20
Anoeska Agatha Alida van de Moosdijk, Renée van Amerongen
Cell growth and differentiation are often driven by subtle changes in gene expression. Many challenges still exist in detecting these changes, particularly in the context of a complex, developing tissue. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) allows relatively high-throughput evaluation of multiple genes and developmental time points. Proper quantification of gene expression levels by qRT-PCR requires normalization to one or more reference genes. Traditionally, these genes have been selected based on their presumed "housekeeping" function, with the implicit assumption that they are stably expressed over the entire experimental set...
October 18, 2016: Scientific Reports
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