scholarly journals Selection of Reliable Reference Genes for Real-time qRT-PCR Analysis of Zi Geese (<italic>Anser anser domestica</italic>) Gene Expression

2013 ◽  
Vol 26 (3) ◽  
pp. 423-432 ◽  
Author(s):  
Hong Ji ◽  
Jianfa Wang ◽  
Juxiong Liu ◽  
Jingru Guo ◽  
Zhongwei Wang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Real Time ◽  
Reference Genes ◽  
Pcr Analysis ◽  
Anser Anser ◽  
Qrt Pcr ◽  
Selection Of

scholarly journals Selection and Validation of Appropriate Reference Genes for Real-Time Quantitative PCR Analysis in Needles of Larix olgensis under Abiotic Stresses

Forests ◽  
2020 ◽  
Vol 11 (2) ◽  
pp. 193
Author(s):  
Dandan Li ◽  
Sen Yu ◽  
Minzhen Zeng ◽  
Xiao Liu ◽  
Jia Yang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Heat Stress ◽  
Real Time ◽  
Reference Genes ◽  
Pcr Analysis ◽  
Stable Gene ◽  
Larix Olgensis ◽  
Qrt Pcr ◽  
Study Gene Expression ◽  
Selection Of

Larix olgensis Henry is an important afforestation species in northeastern China because of its fast juvenile growth, high-quality timber, and significant economic and ecological values. The selection of appropriate reference genes is necessary for the normalization of gene expression determination during quantitative real-time polymerase chain reaction (qRT-PCR) experiments. In this study, qRT-PCR was used to study gene expression. Three software packages geNorm, NormFinder, BestKeeper were used, and a comprehensive ranking of candidate reference genes was produced based on their output to evaluate the expression stability of 16 candidate reference genes from L. olgensis under drought, salt, cold, and heat stress. PP2A-1 and GAPDH ranked as the most stable reference genes under drought and cold stress, PP2A-1 and UBQ10 were most stable under salt stress, and TIP41 and ACT2 were most stable under heat stress. The least stable gene was ADP, which ranked the last under all treatments. Expression profile analysis of the antioxidant gene CAT using the two most stable and the single least stable reference genes under each stress further verified that the selected reference genes were suitable for gene expression normalization. This study provides an important foundation for the selection of suitable reference genes for the normalization and quantification of L. olgensis gene expression under abiotic stress conditions.

scholarly journals Selection of Reference Genes for qRT-PCR Analysis of Gene Expression in Stipa grandis during Environmental Stresses

PLoS ONE ◽  
2017 ◽  
Vol 12 (1) ◽  
pp. e0169465 ◽  
Author(s):  
Dongli Wan ◽  
Yongqing Wan ◽  
Qi Yang ◽  
Bo Zou ◽  
Weibo Ren ◽  
...  
Keyword(s):  
Gene Expression ◽  
Reference Genes ◽  
Environmental Stresses ◽  
Pcr Analysis ◽  
Qrt Pcr ◽  
Selection Of

scholarly journals Standardization of Gene Expression Quantification by Absolute Real-Time qRT-PCR System Using a Single Standard for Marker and Reference Genes

2010 ◽  
Vol 5 ◽  
pp. BMI.S5596 ◽  
Author(s):  
Yi-Hong Zhou ◽  
Vinay R. Raj ◽  
Eric Siegel ◽  
Liping Yu
Keyword(s):  
Gene Expression ◽  
Real Time ◽  
Gene Expression Data ◽  
Reference Genes ◽  
Pcr Analysis ◽  
Expression Data ◽  
Internal Reference ◽  
Expression Ratio ◽  
Qrt Pcr ◽  
Single Standard

In the last decade, genome-wide gene expression data has been collected from a large number of cancer specimens. In many studies utilizing either microarray-based or knowledge-based gene expression profiling, both the validation of candidate genes and the identification and inclusion of biomarkers in prognosis-modeling has employed real-time quantitative PCR on reverse transcribed mRNA (qRT-PCR) because of its inherent sensitivity and quantitative nature. In qRT-PCR data analysis, an internal reference gene is used to normalize the variation in input sample quantity. The relative quantification method used in current real-time qRT-PCR analysis fails to ensure data comparability pivotal in identification of prognostic biomarkers. By employing an absolute qRT-PCR system that uses a single standard for marker and reference genes (SSMR) to achieve absolute quantification, we showed that the normalized gene expression data is comparable and independent of variations in the quantities of sample as well as the standard used for generating standard curves. We compared two sets of normalized gene expression data with same histological diagnosis of brain tumor from two labs using relative and absolute real-time qRT-PCR. Base-10 logarithms of the gene expression ratio relative to ACTB were evaluated for statistical equivalence between tumors processed by two different labs. The results showed an approximate comparability for normalized gene expression quantified using a SSMR-based qRT-PCR. Incomparable results were seen for the gene expression data using relative real-time qRT-PCR, due to inequality in molar concentration of two standards for marker and reference genes. Overall results show that SSMR-based real-time qRT-PCR ensures comparability of gene expression data much needed in establishment of prognostic/predictive models for cancer patients–-a process that requires large sample sizes by combining independent sets of data.

scholarly journals Selection of reference genes for quantitative real-time PCR analysis in halophytic plantRhizophora apiculata

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5226 ◽  
Author(s):  
Ankush Ashok Saddhe ◽  
Manali Ramakant Malvankar ◽  
Kundan Kumar
Keyword(s):  
Gene Expression ◽  
Salt Stress ◽  
Real Time ◽  
Reference Gene ◽  
Reference Genes ◽  
Candidate Reference Gene ◽  
Expression Level ◽  
Bisphosphate Carboxylase ◽  
Qrt Pcr ◽  
Selection Of

Rhizophora apiculatais a halophytic, small mangrove tree distributed along the coastal regions of the tropical and subtropical areas of the world. They are natural genetic reservoirs of salt adaptation genes and offer a unique system to explore adaptive mechanisms under salinity stress. However, there are no reliable studies available on selection and validation of reference genes for quantitative real-time polymerase chain reaction (qRT-PCR) inR. apiculataphysiological tissues and in salt stress conditions. The selection of appropriate candidate reference gene for normalization of qRT-PCR data is a crucial step towards relative analysis of gene expression. In the current study, seven genes such as elongation factor 1α (EF1α), Ubiquitin (UBQ), β-tubulin (β-TUB), Actin (ACT), Ribulose1,5-bisphosphate carboxylase/oxygenase (rbcL), Glyceraldehyde 3-phosphate dehydrogenase (GAPDH), and 18S rRNA (18S) were selected and analyzed for their expression stability. Physiological tissues such as leaf, root, stem, and flower along with salt stress leaf samples were used for selection of candidate reference genes. The high-quality expression data was obtained from biological replicates and further analyzed using five different programs such as geNorm, NormFinder, BestKeeper, Delta Ct and RefFinder. All algorithms comprehensively rankedEF1α followed byACTas the most stable candidate reference genes inR. apiculataphysiological tissues. Moreover, β-TUBand 18S were ranked as moderately stable candidate reference genes, while GAPDH andrbcLwere least stable reference genes. Under salt stress,EF1α was comprehensively recommended top-ranked candidate reference gene followed byACTand 18S. In order to validate the identified most stable candidate reference genes,EF1α,ACT, 18S andUBQwere used for relative gene expression level of sodium/proton antiporter (NHX) gene under salt stress. The expression level ofNHXvaried according to the internal control which showed the importance of selection of appropriate reference gene. Taken together, this is the first ever systematic attempt of selection and validation of reference gene for qRT-PCR inR. apiculataphysiological tissues and in salt stress. This study would promote gene expression profiling of salt stress tolerance related genes inR. apiculata.

Selection of Stable Reference Genes for Real-Time Quantitative PCR Analysis in Edwardsiella tarda

2017 ◽  
Vol 27 (1) ◽  
pp. 112-121 ◽  
Author(s):  
Zhongyang Sun ◽  
Jia Deng ◽  
Haizhen Wu ◽  
Qiyao Wang ◽  
Yuanxing Zhang
Keyword(s):  
Real Time ◽  
Quantitative Pcr ◽  
Reference Genes ◽  
Edwardsiella Tarda ◽  
Pcr Analysis ◽  
Real Time Quantitative Pcr ◽  
Selection Of

scholarly journals Comparison of Reliable Reference Genes Following Different Hormone Treatments by Various Algorithms for qRT-PCR Analysis of Metasequoia

2018 ◽  
Vol 20 (1) ◽  
pp. 34 ◽  
Author(s):  
Jing-Jing Wang ◽  
Shuo Han ◽  
Weilun Yin ◽  
Xinli Xia ◽  
Chao Liu
Keyword(s):  
Gene Expression ◽  
Reference Genes ◽  
Elongation Factor ◽  
Pcr Analysis ◽  
Qrt Pcr ◽  
Gene Normalization ◽  
Accurate Normalization ◽  
Suitable Reference ◽  
Different Tissues ◽  
Gene Expression Levels

Quantitative reverse transcription polymerase chain reaction (qRT-PCR) is the most sensitive technique for evaluating gene expression levels. Choosing appropriate reference genes for normalizing target gene expression is important for verifying expression changes. Metasequoia is a high-quality and economically important wood species. However, few systematic studies have examined reference genes in Metasequoia. Here, the expression stability of 14 candidate reference genes in different tissues and following different hormone treatments were analyzed using six algorithms. Candidate reference genes were used to normalize the expression pattern of FLOWERING LOCUS T and pyrabactin resistance-like 8. Analysis using the GrayNorm algorithm showed that ACT2 (Actin 2), HIS (histone superfamily protein H3) and TATA (TATA binding protein) were stably expressed in different tissues. ACT2, EF1α (elongation factor-1 alpha) and HIS were optimal for leaves treated with the flowering induction hormone solution, while Cpn60β (60-kDa chaperonin β-subunit), GAPDH (glyceraldehyde-3-phosphate dehydrogenase) and HIS were the best reference genes for treated buds. EF1α, HIS and TATA were useful reference genes for accurate normalization in abscisic acid-response signaling. Our results emphasize the importance of validating reference genes for qRT-PCR analysis in Metasequoia. To avoid errors, suitable reference genes should be used for different tissues and hormone treatments to increase normalization accuracy. Our study provides a foundation for reference gene normalization when analyzing gene expression in Metasequoia.

Evaluation of reference genes for quantitative real-time PCR analysis of gene expression in Hainan medaka (Oryzias curvinotus)

Gene Reports ◽  
2019 ◽  
Vol 14 ◽  
pp. 94-99 ◽  
Author(s):  
Zhongdian Dong ◽  
Pushun Chen ◽  
Ning Zhang ◽  
Shunkai Huang ◽  
Hairui Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Real Time ◽  
Real Time Pcr ◽  
Reference Genes ◽  
Pcr Analysis ◽  
Quantitative Real Time Pcr ◽  
Oryzias Curvinotus
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