Selection of reference genes in mouse preimplantation embryos of different ploidies at various developmental stages

2014 ◽  
Author(s):  
Yanli Gu ◽  
Xinghui Shen ◽  
Dongjie Zhou ◽  
Zhendong Wang ◽  
Lei Lei
Keyword(s):  
Reference Genes ◽  
Developmental Stages ◽  
Preimplantation Embryos ◽  
Selection Of

scholarly journals Spatio-temporal selection of reference genes in the two congeneric species of Glycyrrhiza

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yuping Li ◽  
Xiaoju Liang ◽  
Xuguo Zhou ◽  
Yu An ◽  
Ming Li ◽  
...  
Keyword(s):  
Gene Expression ◽  
Developmental Stage ◽  
Reference Genes ◽  
Developmental Stages ◽  
Individual Factors ◽  
Congeneric Species ◽  
Spatio Temporal ◽  
The Stability ◽  
Different Tissues ◽  
Selection Of

AbstractGlycyrrhiza, a genus of perennial medicinal herbs, has been traditionally used to treat human diseases, including respiratory disorders. Functional analysis of genes involved in the synthesis, accumulation, and degradation of bioactive compounds in these medicinal plants requires accurate measurement of their expression profiles. Reverse transcription quantitative real-time PCR (RT-qPCR) is a primary tool, which requires stably expressed reference genes to serve as the internal references to normalize the target gene expression. In this study, the stability of 14 candidate reference genes from the two congeneric species G. uralensis and G. inflata, including ACT, CAC, CYP, DNAJ, DREB, EF1, RAN, TIF1, TUB, UBC2, ABCC2, COPS3, CS, R3HDM2, were evaluated across different tissues and throughout various developmental stages. More importantly, we investigated the impact of interactions between tissue and developmental stage on the performance of candidate reference genes. Four algorithms, including geNorm, NormFinder, BestKeeper, and Delta Ct, were used to analyze the expression stability and RefFinder, a comprehensive software, provided the final recommendation. Based on previous research and our preliminary data, we hypothesized that internal references for spatio-temporal gene expression are different from the reference genes suited for individual factors. In G. uralensis, the top three most stable reference genes across different tissues were R3HDM2, CAC and TUB, while CAC, CYP and ABCC2 were most suited for different developmental stages. CAC is the only candidate recommended for both biotic factors, which is reflected in the stability ranking for the spatio (tissue)-temporal (developmental stage) interactions (CAC, R3HDM2 and DNAJ). Similarly, in G. inflata, COPS3, R3HDM2 and DREB were selected for tissues, while RAN, COPS3 and CS were recommended for developmental stages. For the tissue-developmental stage interactions, COPS3, DREB and ABCC2 were the most suited reference genes. In both species, only one of the top three candidates was shared between the individual factors and their interactions, specifically, CAC in G. uralensis and COPS3 in G. inflata, which supports our overarching hypothesis. In summary, spatio-temporal selection of reference genes not only lays the foundation for functional genomics research in Glycyrrhiza, but also facilitates these traditional medicinal herbs to reach/maximize their pharmaceutical potential.

scholarly journals Selection of Suitable Reference Genes Based on Transcriptomic Data in Ginkgo biloba under Different Experimental Conditions

Forests ◽  
2020 ◽  
Vol 11 (11) ◽  
pp. 1217
Author(s):  
Tingting Zhou ◽  
Xiaoming Yang ◽  
Fangfang Fu ◽  
Guibin Wang ◽  
Fuliang Cao
Keyword(s):  
Gene Expression ◽  
Ginkgo Biloba ◽  
Reference Genes ◽  
Developmental Stages ◽  
Deciduous Tree ◽  
Internal Reference ◽  
Experimental Conditions ◽  
Transcriptomic Data ◽  
Suitable Reference ◽  
Selection Of

Ginkgo biloba, a deciduous tree species in the Ginkgo family, has a long history of cultivation in China and is widely used in garden landscapes, medicine, food, and health products. However, few reports have focused on the systematic selection of optimal reference genes based on transcriptomic data in G. biloba. The purpose of our research was to select an internal reference gene suitable for different experimental conditions from thirteen candidate reference genes by the delta cycle threshold (ΔCt) method, geNorm, BestKeeper, NormFinder, and RefFinder programs. The reference genes were used for gene expression analyses of Ginkgo biloba. These results showed that elongation factor 1(EF1) and ubiquitin (UBI) were the best choices for samples of different ginkgo genotypes. The expression of UBI and HAS28 presented the most stable at different developmental stages of ginkgo, and EIF3I and RPII were considered as suitable reference genes in different tissues of ginkgo. For methyl jasmonate (MeJA) treatment, ACA and ACT were identified as the optimal reference genes. For cold stress treatment, RPII and EIF4E were chosen for the gene expression normalizations. HAS28 and GAPDH presented the most stable expression for the heat treatment. To validate the above results, a chalcone synthase gene (GbCHS) in ginkgo was amplified by quantitative real-time polymerase chain reaction (qRT-PCR). Our results provide different suitable reference genes for further gene expression studies in ginkgo.

scholarly journals Selection and Expression Profiles of Reference Genes in Mouse Preimplantation Embryos of Different Ploidies at Various Developmental Stages

PLoS ONE ◽  
2014 ◽  
Vol 9 (6) ◽  
pp. e98956 ◽  
Author(s):  
Yanli Gu ◽  
Xinghui Shen ◽  
Dongjie Zhou ◽  
Zhendong Wang ◽  
Na Zhang ◽  
...  
Keyword(s):  
Reference Genes ◽  
Developmental Stages ◽  
Expression Profiles ◽  
Preimplantation Embryos

scholarly journals Selection of reliable reference genes for RT-qPCR analysis during developmental stages and abiotic stress in Setaria viridis

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Polyana Kelly Martins ◽  
Valéria Mafra ◽  
Wagner Rodrigo de Souza ◽  
Ana Paula Ribeiro ◽  
Felipe Vinecky ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Reference Genes ◽  
Developmental Stages ◽  
Setaria Viridis ◽  
Qpcr Analysis ◽  
Selection Of

scholarly journals Selection of reliable reference genes for normalization of quantitative RT-PCR from different developmental stages and tissues in amphioxus

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Qi-Lin Zhang ◽  
Qian-Hua Zhu ◽  
Xin Liao ◽  
Xiu-Qiang Wang ◽  
Tao Chen ◽  
...  
Keyword(s):  
Reference Genes ◽  
Developmental Stages ◽  
Rt Pcr ◽  
Selection Of

Selection of appropriate reference genes for qPCR in the Chinese mitten crab, Eriocheir sinensis (Decapoda, Varunidae)

Crustaceana ◽  
2017 ◽  
Vol 90 (3) ◽  
pp. 275-296 ◽  
Author(s):  
Shu Huang ◽  
Xiaowen Chen ◽  
Jun Wang ◽  
Jiao Chen ◽  
Wucheng Yue ◽  
...  
Keyword(s):  
Reference Gene ◽  
Reference Genes ◽  
Developmental Stages ◽  
Receptor Gene ◽  
Eriocheir Sinensis ◽  
Chinese Mitten Crab ◽  
Experimental Conditions ◽  
Mitten Crab ◽  
The Stability ◽  
Selection Of

The accuracy of qPCR depends on the stability of the reference gene used for data normalization. However, the stably expressed reference genes in the Chinese mitten crab,Eriocheir sinensis, have not been well identified under different experimental conditions. In this study, the stabilities of the expressions of 10 candidate reference genes were evaluated in different developmental stages, tissues, and moulting stages ofE. sinensis. Our results indicated thatUBEandS27were the most stable reference genes. To validate the suitability of the reference genes, theEcR(ecdysone receptor) gene was analysed among different moulting stages. The results showed that the expression level ofEcRwas elevated using the least stable reference gene,GST, compared with using the three most stable reference genes. Taken together, our results indicate that reference genes should be assessed and selected in accordance with the experimental conditions, and more than one reference gene should be selected.

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