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https://www.readbyqxmd.com/read/29209038/a-simple-method-to-assess-group-difference-in-rt-qpcr-reference-gene-selection-using-genorm-the-case-of-the-placental-sex
#1
Joey St-Pierre, Jean-Charles Grégoire, Cathy Vaillancourt
Normalization with proper reference genes is a crucial step in obtaining accurate mRNA expression levels in RT-qPCR experiments. GeNorm and NormFinder are two commonly used software packages that help in selecting the best reference genes, based on their expression stability. However, GeNorm does not take into account a group variable, such as sample sex, in its calculation. We demonstrate a simple calculation step to assess the variability of such parameters by multiplying the GeNorm M value with the difference of Cq values between groups...
December 5, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29208024/selection-of-a-suitable-reference-gene-for-quantitative-gene-expression-in-mouse-lymph-nodes-after-vaccination
#2
Yung-Yi C Mosley, Harm HogenEsch
BACKGROUND: The quantification of gene expression is an important tool in the evaluation of the immune response to vaccines. Reliable reference genes for gene expression studies in mouse draining lymph nodes after vaccination have not been reported. RESULTS: The utility of seven potential reference genes was investigated using commercially available Taq-man primer/probe mixes. Results were evaluated with RefFinder, a web-based program including multiple algorithm methods such as geNorm, NormFinder, BestKeeper and the comparative delta-Ct...
December 6, 2017: BMC Research Notes
https://www.readbyqxmd.com/read/29201562/evaluation-of-potential-reference-genes-for-real-time-qpcr-analysis-in-a-biparental-beetle-lethrus-apterus-coleoptera-geotrupidae
#3
Nikoletta A Nagy, Zoltán Németh, Edit Juhász, Szilárd Póliska, Rita Rácz, András Kosztolányi, Zoltán Barta
Hormones play an important role in the regulation of physiological, developmental and behavioural processes. Many of these mechanisms in insects, however, are still not well understood. One way to investigate hormonal regulation is to analyse gene expression patterns of hormones and their receptors by real-time quantitative polymerase chain reaction (RT-qPCR). This method, however, requires stably expressed reference genes for normalisation. In the present study, we evaluated 11 candidate housekeeping genes as reference genes in samples of Lethrus apterus, an earth-boring beetle with biparental care, collected from a natural population...
2017: PeerJ
https://www.readbyqxmd.com/read/29197992/identification-of-reference-genes-for-analysis-of-microrna-expression-patterns-in-equine-chorioallantoic-membrane-and-serum
#4
Pouya Dini, Shavahn C Loux, Kirsten E Scoggin, Alejandro Esteller-Vico, Edward L Squires, Mats H T Troedsson, Peter Daels, Barry A Ball
MicroRNAs (miRNAs) have important posttranscriptional regulatory abilities, and there is considerable interest in evaluating their expression patterns in different pathophysiological states. The most common method of quantifying miRNA expression is quantitative reverse transcription PCR; however, the identification of tissue-specific and species-specific reference miRNA is a prerequisite for miRNA expression analysis. Currently, no reference genes have been described for evaluating miRNA expression in equine serum and chorioallantoic membrane (CAM) during pregnancy...
December 2, 2017: Molecular Biotechnology
https://www.readbyqxmd.com/read/29190301/identification-and-validation-of-reference-genes-for-gene-expression-analysis-in-aphidius-gifuensis-hymenoptera-aphidiidae
#5
Xue-Ke Gao, Shuai Zhang, Jun-Yu Luo, Chun-Yi Wang, Li-Min Lü, Li-Juan Zhang, Xiang-Zhen Zhu, Li Wang, Jin-Jie Cui
Reference genes have been utilized in estimating gene expression levels using quantitative reverse transcriptase-quantitative polymerase chain reaction (qRT-PCR) analysis. Aphidius gifuensis Ashmaed is one of the most widely used biological control agents for aphids. The biological properties of this species have been studied in detail, and current investigations are focused on elucidating the regulatory mechanisms in its host However, the appropriate reference genes for target gene expression studies have not been identified...
2017: PloS One
https://www.readbyqxmd.com/read/29183612/suitable-reference-genes-for-accurate-gene-expression-analysis-in-papaver-rhoeas-under-2-4-d-herbicide-stress
#6
L Scarabel, A Milani, S Panozzo, A Rasori
Resistance to 2,4-D (2,4-diclorophenoxyacetic acid) herbicide is increasing in various dicotyledonous weed species, including Papaver rhoeas, a weed infesting Southern European wheat crops. Non-target-site resistance to this herbicide is governed by a range of genes involved in herbicide stress response. To enable reliable measurement of gene expression levels in herbicide-resistant and susceptible plants it is necessary to normalize qPCR data using internal control genes with stable expression. In an attempt to find the best reference genes, the stability of seven candidate reference genes was assessed in plants resistant and susceptible to 2,4-D, subjected or not to herbicide stress...
November 2017: Pesticide Biochemistry and Physiology
https://www.readbyqxmd.com/read/29173213/evaluation-of-reference-genes-for-reverse-transcription-quantitative-pcr-assays-in-organs-of-zebrafish-exposed-to-glyphosate-based-herbicide-roundup
#7
M L Jaramillo, A G Pereira, C E Davico, L Nezzi, D Ammar, Y M R Müller, E M Nazari
Roundup is a glyphosate-based herbicide (GBH) widely used in agriculture and may cause toxic effects in non-target organisms. Model organisms, as zebrafish, and analysis of gene expression by reverse transcription-quantitative PCR (RT-qPCR) could be used to better understand the Roundup toxicity. A prerequisite for RT-qPCR is the availability of appropriate reference genes; however, they have not been described for Roundup-exposed fish. The aim of this study was to evaluate the expression stability of six reference genes (rpl8, β-act, gapdh, b2m, ef1α, hprt1) and one expressed repetitive element (hatn10) in organs of males (brain, gill, testis) and females (ovary) of zebrafish exposed to Roundup WG at three concentrations (0...
November 27, 2017: Animal: An International Journal of Animal Bioscience
https://www.readbyqxmd.com/read/29166265/selection-of-reference-genes-for-quantitative-real-time-rt-pcr-on-gene-expression-in-golden-pompano-trachinotus-ovatus
#8
X J Chen, X Q Zhang, S Huang, Z J Cao, Q W Qin, W T Hu, Y Sun, Y C Zhou
Golden pompano (Trachinotus ovatus) is an important economically fish species. In this study, with an aim to identify reliable reference genes for quantitative real-time PCR (qRT-PCR) in golden pompano, we evaluated the expression stability of eight housekeeping genes in the presence and absence of poly I:C stimulation in eight tissues. The PCR data was analyzed by geNorm and NormFinder algorithms. The results showed that the expression of all the examined genes exhibited tissue-dependent variations. When under normal physiological condition, geNorm and NormFinder identified B2M and 18S as suitable genes...
September 26, 2017: Polish Journal of Veterinary Sciences
https://www.readbyqxmd.com/read/29152197/selection-of-reference-genes-for-qrt-pcr-and-expression-analysis-of-high-altitude-related-genes-in-grassland-caterpillars-lepidoptera-erebidae-gynaephora-along-an-altitude-gradient
#9
Li Zhang, Qi-Lin Zhang, Xiao-Tong Wang, Xing-Zhuo Yang, Xiao-Peng Li, Ming-Long Yuan
Changes in gene expression patterns can reflect the adaptation of organisms to divergent environments. Quantitative real-time PCR (qRT-PCR) is an important tool for ecological adaptation studies at the gene expression level. The quality of the results of qRT-PCR analysis largely depends on the availability of reliable reference genes (RGs). To date, reliable RGs have not been determined for adaptive evolution studies in insects using a standard approach. Here, we evaluated the reliability of 17 candidate RGs for five Gynaephora populations inhabiting various altitudes of the Tibetan Plateau (TP) using four independent (geNorm, NormFinder, BestKeeper, and the deltaCt method) and one comprehensive (RefFinder) algorithms...
November 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/29134774/identifying-suitable-reference-genes-for-developing-and-injured-mouse-cns-tissues
#10
Dongchao Xu, Ajuan Liu, Xuan Wang, Ming Zhang, Zunyi Zhang, Tan Zhou, Mengsheng Qiu
Accurate quantification of gene expression is fundamental for understanding the molecular, genetic and functional bases of tissue development and diseases. Quantitative real-time PCR (qPCR) is now the most widely used method of quantifying gene expression due to its simplicity, specificity, sensitivity and wide quantification range. The use of appropriate reference genes to ensure accurate normalization is crucial for the correct quantification of gene expression from the early development, maturation, aging to injury processes in the central nervous system (CNS)...
November 14, 2017: Developmental Neurobiology
https://www.readbyqxmd.com/read/29116140/valid-gene-expression-normalization-by-rt-qpcr-in-studies-on-hpdl-fibroblasts-with-focus-on-orthodontic-tooth-movement-and-periodontitis
#11
Christian Kirschneck, Sarah Batschkus, Peter Proff, Josef Köstler, Gerrit Spanier, Agnes Schröder
Meaningful, reliable and valid mRNA expression analyses by real-time quantitative PCR (RT-qPCR) can only be achieved, if suitable reference genes are chosen for normalization and if appropriate RT-qPCR quality standards are met. Human periodontal ligament (hPDL) fibroblasts play a major mediating role in orthodontic tooth movement and periodontitis. Despite corresponding in-vitro gene expression studies being a focus of interest for many years, no information is available for hPDL fibroblasts on suitable reference genes, which are generally used in RT-qPCR experiments to normalize variability between samples...
November 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29113238/selection-of-reference-genes-for-gene-expression-studies-in-human-bladder-cancer-using-sybr-green-quantitative-polymerase-chain-reaction
#12
Chuanxia Zhang, Yong Qiang Wang, Guangyi Jin, Song Wu, Jun Cui, Rong-Fu Wang
Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) is a rapid, reliable and widely used method of studying gene expression profiles that requires appropriate normalization for accurate and reliable results. Reference genes are usually used to normalize mRNA levels; however, the expression levels of these reference genes may vary between cell types, developmental stages, species and experimental conditions. Therefore, a normalization strategy is an important precondition for reliable conclusions, with endogenous controls requiring determination for every experimental system...
November 2017: Oncology Letters
https://www.readbyqxmd.com/read/29095075/suitable-reference-gene-selection-for-gene-expression-studies-in-knee-osteoarthritis-synovium-using-quantitative-pcr-analysis
#13
Hiroshi Watanabe, Hirotaka Ishii, Kenji Takahashi, Shinro Takai, Hitoshi Ozawa
Osteoarthritis (OA) is the leading cause of musculoskeletal disability in the elderly. Insights into the biological features of OA are obtained by characterization of the molecular features by gene expression profiling using reverse transcription-quantitative PCR (RT-qPCR). However, it has recently become evident that the use of suitable reference genes is required for appropriate normalization of this technique. Here total RNA was isolated from the synovium of 18 men and 20 women who underwent total knee arthroplasty for knee OA (KOA)...
November 2, 2017: Connective Tissue Research
https://www.readbyqxmd.com/read/29091948/selection-and-validation-of-appropriate-reference-genes-for-quantitative-real-time-pcr-analysis-in-salvia-hispanica
#14
Rahul Gopalam, Sunny D Rupwate, Ajay W Tumaney
Quantitative real-time polymerase chain reaction (qRT-PCR) has become the most popular choice for gene expression studies. For accurate expression analysis, it is pertinent to select a stable reference gene to normalize the data. It is now known that the expression of internal reference genes varies considerably during developmental stages and under different experimental conditions. For Salvia hispanica, an economically important oilseed crop, there are no reports of stable reference genes till date. In this study, we chose 13 candidate reference genes viz...
2017: PloS One
https://www.readbyqxmd.com/read/29079997/validation-of-reference-genes-for-expression-studies-in-human-meningiomas-under-different-experimental-settings
#15
Diana Freitag, Arend Koch, Aaron Lawson McLean, Rolf Kalff, Jan Walter
Quantitative polymerase chain reaction (qPCR) is a sensitive technique for the quantitative analysis of gene expression levels. To compare mRNA transcripts across tumour and non-pathological tissue, appropriate reference genes are required for internal standardisation. Validation of these reference genes in meningiomas has not yet been reported. After mRNA transcription of meningioma (WHO grade I-III) and meningeal tissue from three different experimental sample types (fresh tissue, primary cell cultures and FFPE tissue), 13 candidate reference genes (ACTB, B2M, HPRT, VIM, GAPDH, YWHAZ, EIF4A2, MUC1, ATP5B, GNB2L, TUBB, CYC1, RPL13A) were chosen for quantitative expression analysis...
October 27, 2017: Molecular Neurobiology
https://www.readbyqxmd.com/read/29079779/reference-gene-selection-for-gene-expression-study-in-shell-gland-and-spleen-of-laying-hens-challenged-with-infectious-bronchitis-virus
#16
Samiullah Khan, Juliet Roberts, Shu-Biao Wu
Ten reference genes were investigated for normalisation of candidate target gene expression data in the shell gland and spleen of laying hens challenged with two strains of infectious bronchitis virus (IBV). Data were analysed with geNorm, NormFinder and BestKeeper, and a comprehensive ranking (geomean) was calculated. In the combined data set of IBV challenged shell gland samples, the comprehensive ranking showed TATA-box binding protein (TBP) and tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein zeta (YWHAZ) as the two most stable, and succinate dehydrogenase complex flavoprotein subunit A (SDHA) and albumin (ALB) as the two least stable reference genes...
October 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29075311/selection-and-validation-of-reference-genes-for-rt-qpcr-analysis-in-potato-under-abiotic-stress
#17
Xun Tang, Ning Zhang, Huaijun Si, Alejandro Calderón-Urrea
BACKGROUND: Real-time quantitative PCR (RT-qPCR) is the most commonly used method for accurately detecting gene expression patterns. As part of RT-qPCR analysis, normalization of the data requires internal control gene(s) that display uniform expression under different biological conditions. However, no invariable internal control gene exists, and therefore more than one reference gene is needed to normalize RT-qPCR results. Identification of stable reference genes in potato will improve assay accuracy for selecting stress-tolerance genes and identifying molecular mechanisms conferring stress tolerance in this species...
2017: Plant Methods
https://www.readbyqxmd.com/read/29051594/reference-genes-validation-in-phenacoccus-solenopsis-under-various-biotic-and-abiotic-stress-conditions
#18
Surjeet Kumar Arya, Gourav Jain, Santosh Kumar Upadhyay, Sarita, Harpal Singh, Sameer Dixit, Praveen Chandra Verma
Real-time PCR (RT-qPCR) expression analysis is a powerful analytical technique, but for normalization of data requires the use of stable reference genes. However, suitable reference genes are still not known in the case of Phenacoccus solenopsis under variable experimental treatments. The present study focused on the identification of stable housekeeping genes as a reference for analysis under different abiotic and biotic factors in P. solenopsis. We analyzed the relative expression of six commonly used candidate reference genes in different developmental stages, host-feeding assay, temperature treatments and field distribution conditions...
October 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29036603/identification-of-optimal-reference-genes-for-transcriptomic-analyses-in-normal-and-diseased-human-heart
#19
Cristina E Molina, Eric Jacquet, Prishila Ponien, Christian Muñoz-Guijosa, Istvan Baczkó, Lars S Maier, Patrick Donzeau-Gouge, Dobromir Dobrev, Rodolphe Fischmeister, Anne Garnier
Aims: Quantitative real-time RT-PCR (RT-qPCR) has become the method of choice for mRNA quantification, but requires an accurate normalization based on the use of reference genes showing invariant expression across various pathological conditions. Only few data exist on appropriate reference genes for the human heart. The objective of this study was to determine a set of suitable reference genes in human atrial and ventricular tissues, from right and left cavities in control and in cardiac diseases...
September 22, 2017: Cardiovascular Research
https://www.readbyqxmd.com/read/29029285/selection-of-reference-genes-for-expression-studies-in-diaphorina-citri-hemiptera-liviidae
#20
Meire Menezes Bassan, Je Ssika Angelotti-Mendonc A, Gustavo Rodrigues Alves, Pedro Takao Yamamoto, Francisco de Assis Alves Moura O Filho
The Asian citrus psyllid, Diaphorina citri Kuwayama (Hemiptera: Liviidae), is considered the main vector of the bacteria associated with huanglongbing, a very serious disease that has threatened the world citrus industry. The absence of efficient control management protocols, including a lack of resistant cultivars, has led to the development of different approaches to study this pathosystem. The production of resistant genotypes relies on D. citri gene expression analyses by RT-qPCR to assess control of the vector population...
September 27, 2017: Journal of Economic Entomology
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