RNA-seq reveals more consistent reference genes for gene expression studies in human non-melanoma skin cancers

Hoang, Van LT; Tom, Lisa; Quek, Xiu-Cheng; Tan, Jean-Marie; Payne, Elizabeth; Lin, Lynlee L.; Sinnya, Sudipta; Raphael, Anthony P.; Lambie, Duncan; Frazer, Ian H.; Dinger, Marcel E.; Soyer, H. Peter; Prow, Tarl W.

doi:10.7287/peerj.preprints.2331v1

Cited by 5 publications

(6 citation statements)

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“…Hence, by using a large collection of RNA-Seq datasets as the one presented here, one can not only evaluate commonly used reference genes, but also propose new ones. By employing a previously developed method (Hoang et al, 2017), we inferred 452 HK genes (Table S6). We evaluated expression levels of each gene in tissues with at least 10 samples and found that HK genes had very low expression variation ( Figure 4A).…”

Section: Housekeeping Genesmentioning

confidence: 99%

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Systematic analysis of 1298 RNA‐Seq samples and construction of a comprehensive soybean (Glycine max) expression atlas

et al. 2020

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SUMMARY Soybean (Glycine max [L.] Merr.) is a major crop in animal feed and human nutrition, mainly for its rich protein and oil contents. The remarkable rise in soybean transcriptome studies over the past 5 years generated an enormous amount of RNA‐seq data, encompassing various tissues, developmental conditions and genotypes. In this study, we have collected data from 1298 publicly available soybean transcriptome samples, processed the raw sequencing reads and mapped them to the soybean reference genome in a systematic fashion. We found that 94% of the annotated genes (52 737/56 044) had detectable expression in at least one sample. Unsupervised clustering revealed three major groups, comprising samples from aerial, underground and seed/seed‐related parts. We found 452 genes with uniform and constant expression levels, supporting their roles as housekeeping genes. On the other hand, 1349 genes showed heavily biased expression patterns towards particular tissues. A transcript‐level analysis revealed that 95% (70 963 of 74 490) of the assembled transcripts have intron chains exactly matching those from known transcripts, whereas 3256 assembled transcripts represent potentially novel splicing isoforms. The dataset compiled here constitute a new resource for the community, which can be downloaded or accessed through a user‐friendly web interface at http://venanciogroup.uenf.br/resources/. This comprehensive transcriptome atlas will likely accelerate research on soybean genetics and genomics.

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Section: Housekeeping Genesmentioning

confidence: 99%

“…We selected 11 tissues with at least 10 samples, which resulted in 1225 samples. The variability in gene expression was evaluated as previously described (Hoang et al, 2017). The following criteria were applied to identify HK genes:…”

Section: Identification Of Hk Genesmentioning

confidence: 99%

Systematic analysis of 1298 RNA‐Seq samples and construction of a comprehensive soybean (Glycine max) expression atlas

et al. 2020

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“…All mRNA primer sequences and amplification efficiencies can be found in Supplementary Table 1. All gene expression was normalized to Rpl7a due to its widespread use and proven stability [29,30].…”

Section: Gene Expressionmentioning

confidence: 99%

Perinatal phthalate and high-fat diet exposure induce sex-specific changes in adipocyte size and DNA methylation

Moody¹,

Kougias

Jung³

et al. 2019

The Journal of Nutritional Biochemistry

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Environmental factors such as diet and endocrine-disrupting chemicals have individually been shown to mediate metabolic function. However, the underlying mechanism by which the combination disrupts adipocyte morphology and fat storage remains unknown. The current study evaluated early-life programming by diet and phthalate exposure. During gestation and lactation, pregnant Long-Evans hooded rat dams were fed either a control (C) or high fat (HF) diet and were orally administered one of three phthalate dosages (0, 200, or 1000 μg/kg/day), yielding 6 groups of offspring: C-0, C-200, C-1000, HF-0, HF-200, and HF-1000. On postnatal day (PND) 90, gonadal fat pads were collected and analyzed for histology, gene expression, and DNA methylation. Differences in body weight were observed only in males. H&E staining revealed larger adipocyte size in HF-0 versus C-0 females. Exposure to 200 or 1000 μg/kg/day phthalates modulated diet-induced changes in adipose morphology. Compared to C-0 females, HF-0 females also had higher expression of the adipogenesis gene Wnt receptor, frizzled 1 (Fzd1), and the triglyceride cleaving enzyme, lipoprotein lipase (Lpl). These increases in gene expression were accompanied by lower DNA methylation surrounding the transcription start sites of the two genes. Diet-driven effects were observed in unexposed females, but not in phthalate-treated rats. Results suggest a sex-specific association between perinatal HF diet and body weight, adipocyte size, and DNA methylation. Perinatal phthalate exposure appears to produce a phenotype that more closely resembles HF-fed animals.

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“…However, according to the results of a study reported by Bai, rpoD was a stable internal reference gene in Pseudomonas brassicacearum GS20 [41]. Therefore, it could be inferred that the internal reference genes exhibited specificity [42].…”

Section: Discussionmentioning

confidence: 99%

Selection and validation of reference genes for quantitative real-time polymerase chain reaction in Serratia ureilytica DW2

Bai

Jin

et al. 2022

Preprint

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Serratia ureilytica DW2 is a highly efficient phosphate-solubilizing bacterium isolated from Codonopsis pilosula rhizosphere soil that can promote the growth of C. pilosula . However, no validated reference genes from the genus Serratia for use in quantitative real-time polymerase chain reaction (RT–qPCR) normalization have been reported . To screen stable reference genes in S. ureilytica DW2, the expression of eight candidate reference genes (16S rRNA, ftsZ , ftsA , mreB , r e cA , slyD , thiC , and zipA ) under different treatment conditions (pH, temperature, culture time, and salt content) was assayed by RT–qPCR. The expression stability of these genes was analyzed with different algorithms (geNorm, NormFinder, and BestKeeper). To verify the reliability of the data , the most stably expressed reference gene was used to quantify expression of the glucose dehydrogenase ( gdh ) gene under different soluble phosphate levels. The results showed that the zipA and 16S rRNA genes were the most stable reference genes, and the least stable were thiC and recA . The expression of gdh was consistent with the phosphate solubilization ability on p lates containing National Botanical Research Institute phosphate (NBRIP) growth medium. Therefore, this study provides a stable and reliable reference gene for Serratia , which is vital for the accurate quantification of functional gene expression in future studies.

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RNA-seq reveals more consistent reference genes for gene expression studies in human non-melanoma skin cancers

Cited by 5 publications

References 0 publications

Systematic analysis of 1298 RNA‐Seq samples and construction of a comprehensive soybean (Glycine max) expression atlas

Systematic analysis of 1298 RNA‐Seq samples and construction of a comprehensive soybean (Glycine max) expression atlas

Perinatal phthalate and high-fat diet exposure induce sex-specific changes in adipocyte size and DNA methylation

Selection and validation of reference genes for quantitative real-time polymerase chain reaction in Serratia ureilytica DW2

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