Choosing between RT-qPCR and RNA-seq: a back-of-the-envelope estimate towards the definition of the break-even-point

Nonis, Alberto; Nardi, Barbara De; Nonis, Alessandro

doi:10.1007/s00216-014-7687-x

Cited by 16 publications

(14 citation statements)

References 20 publications

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“…The median Ct values were in the range of 17.23 and 25.22, which indicated that they conformed to the basic requirements for qualified reference genes (Fig 1). The evaluation of reference genes is an important procedure for data normalization [35][36][37]. Tribolium castaneum was the first coleopteran insect in which reference genes were validated [2,26].…”

Section: Discussionmentioning

confidence: 99%

Evaluation of reference genes for quantitative real-time PCR normalization in the scarab beetle Holotrichia oblita

et al. 2020

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Quantitative real-time polymerase chain reaction (qPT-PCR) is commonly used to analyze gene expression, however, the accuracy of the normalized results is affected by the expression stability of reference genes. Holotrichia oblita (Coleoptera: Scarabaeidae) causes serious damage to crops. Reliable reference genes in H. oblita are needed for qRT-PCR analysis. Therefore, we evaluated 13 reference genes under biotic and abiotic conditions. RefFinder provided a comprehensive stability ranking, and geNorm suggested the optimal number of reference genes for normalization. RPL13a and RPL18 were the most suitable reference genes for developmental stages, tissues, and temperature treatments; RPL13a and RPS3 were the most suitable for pesticide and photoperiod treatments; RPS18 and RPL18 were the most suitable for the two sexes. We validated the normalized results using odorant-binding protein genes as target genes in different tissues. Compared with the selected suitable reference genes, the expression of OBP1 in antennae, abdomen, and wings, and OBP2 in antennae and wings were overestimated due to the instability of ACTb. These results identified several reliable reference genes in H. oblita for normalization, and are valuable for future molecular studies.

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Section: Discussionmentioning

confidence: 99%

Evaluation of reference genes for quantitative real-time PCR normalization in the scarab beetle Holotrichia oblita

et al. 2020

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“…General good-practice guidelines for RT-qPCR ( Udvardi et al , 2008 ; Remans et al , 2014 ) were adopted and primers efficiencies ( Supplementary Table S1 ) were calculated and considered for differentially expressed genes as described by Nonis et al (2012) . The choice of RT-qPCR for gene expression analyses was based on suggestions reported by Nonis et al (2014) . All analyses were carried out on three independent biological replicates for each time point and experimental condition.…”

Section: Methodsmentioning

confidence: 99%

Ethylene negatively regulates transcript abundance of ROP-GAP rheostat-encoding genes and affects apoplastic reactive oxygen species homeostasis in epicarps of cold stored apple fruits

Zermiani

Zonin

Nonis

et al. 2015

EXBOTJ

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“…Homeopathic rules are selected consecutively as a positive example for prediction, then the current recall and accuracy rates are calculated. The BEP (Break-Even Point) [17] is also defined for "rate of recall = recall rate value." The advantages and disadvantages of learners A and B can be compared based on BEP.…”

Section: Evaluation and Selectionmentioning

confidence: 99%

Steelmaking-Casting of Molten Steel by Decarburization Ladle Matching

Liu

Pang

et al. 2018

Mathematical Problems in Engineering

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Steelmaking-continuous casting is a complex process. The method of selecting a ladle, which also functions as a storage device, follows a specific process of the production plan. In ladle matching, several ladle attributes are considered. However, matching objectives are difficult to achieve simultaneously. Different molten steel properties have contributed to the complexity of matching constraints, and, thus, matching optimization is regarded a multiconflict goal problem. In the process of optimization, the first-order rule learning method is first used to extract key ladle attributes (performance indicators), including highest temperature, usage frequency, lowest-level material, and outlet. On the basis of a number of indicators, such as ladle temperature, quantity, material, and usage frequency, as well as skateboard quantity, the ladle matching model is established. Second, the rule of ladle selection is determined by the method of least-generalization rule learning. Third, a simulation experiment is carried out according to various scheduling order strategies and matching priority combinations. Finally, the heuristic ladle matching method based on the rule priority (RP) is determined for possible industrial applications. Results show that the accuracy of ladle selection can be improved. In particular, the numbers of ladles and maintenance times are reduced. Consequently, furnace production efficiency is also enhanced.

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Choosing between RT-qPCR and RNA-seq: a back-of-the-envelope estimate towards the definition of the break-even-point

Cited by 16 publications

References 20 publications

Evaluation of reference genes for quantitative real-time PCR normalization in the scarab beetle Holotrichia oblita

Evaluation of reference genes for quantitative real-time PCR normalization in the scarab beetle Holotrichia oblita

Ethylene negatively regulates transcript abundance of ROP-GAP rheostat-encoding genes and affects apoplastic reactive oxygen species homeostasis in epicarps of cold stored apple fruits

Steelmaking-Casting of Molten Steel by Decarburization Ladle Matching

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