Article
Biochemistry & Molecular Biology
Alice Nevone, Francesca Lattarulo, Monica Russo, Giada Panno, Paolo Milani, Marco Basset, Maria Antonietta Avanzini, Giampaolo Merlini, Giovanni Palladini, Mario Nuvolone
Summary: In the next-generation sequencing era, RT-qPCR remains widely used for quantifying nucleic acids due to its popularity, versatility, and cost-effectiveness. However, accurate measurement of transcriptional levels requires appropriate reference genes for normalization. Here, we present a strategy that utilizes publicly available transcriptomic datasets to select suitable reference genes for specific clinical or experimental settings and includes a pipeline for RT-qPCR assay design and validation. We demonstrated the efficacy of this strategy by identifying and validating reference genes for transcriptional studies of bone-marrow plasma cells in AL amyloidosis patients. This strategy can be applied to other settings with publicly available transcriptomic datasets.
Article
Environmental Sciences
Ju Mu, Yu Wang, Miao Wang, Dayi Zhang, Mingying Liu
Summary: This study constructed a mouse model exposed to poly-propylene microplastics (PP-MPs) to evaluate the bioaccumulation of PP-MPs in the kidney and explore potential reference genes using RT-qPCR. The stability and reliability of 19 candidate reference genes were assessed using four algorithms, and the top five most stable genes were determined (Cox4i1, Rps3, Rps9, Rps18, and Gapdh). Three genes associated with different biochemical processes were chosen to verify the identified reference genes, showing different expression profiles and emphasizing the importance of selecting reliable reference genes.
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
(2023)
Article
Plant Sciences
Leandro Francisco de Oliveira, Amanda Rusiska Piovezani, Dimitre A. Ivanov, Leonardo Yoshida, Eny Iochevet Segal Floh, Massuo Jorge Kato
Summary: This study identified stable reference genes for gene expression analysis in four Piper species and provided a list of recommended gene pairs for each species. These findings will facilitate further transcriptomic and functional gene research.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2022)
Article
Plant Sciences
Maria Noelia Ulrich, Esteban Muniz-Padilla, Alejandra Corach, Esteban Hopp, Daniela Tosto
Summary: This study evaluated the stability of different reference genes of glyphosate-resistant S. halepense, finding that PP2A and ARI8 were the most stable genes. The results provide valuable information for gene expression analysis under glyphosate stress and will facilitate resistance mechanism studies in this weed species.
Article
Plant Sciences
Qizhang Wang, Chunqian Guo, Shipeng Yang, Qiwen Zhong, Jie Tian
Summary: The aim of this study was to identify suitable reference genes for gene expression analysis during different growth conditions in garlic. Nine candidate reference genes were selected using garlic transcriptome sequence data and their expression levels were evaluated in specific tissues under drought and cold stress. Several statistical methods were used to assess the stability of the reference gene expression levels. The most stable reference genes were identified, and their reliability was confirmed by evaluating the expression of a stress-responsive gene. This study provides a theoretical reference for gene expression analysis in garlic under stress conditions.
Article
Biochemistry & Molecular Biology
Chaofan Jiang, Lin Zhou, Qingchen Zhao, Mengke Wang, Sirui Shen, Te Zhao, Kaidi Cui, Leiming He
Summary: This study validated the expression stability of seven candidate reference genes in Sclerotium rolfsii under different conditions and recommended suitable reference gene combinations for RT-qPCR normalization. The results showed that using one or two reference genes to normalize the expression of target genes in S. rolfsii did not significantly differ.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Agriculture, Dairy & Animal Science
Jianfei Chen, Ziwei Chen, Jilong Zhang, Wuchao Zhuang, Xiaotong Zheng
Summary: This study utilized different algorithms to evaluate the stability of internal reference genes in the gastrointestinal tract of chickens. The most suitable reference genes for each type of GI tissue were identified. Commonly used internal reference genes exhibited poor stability and are not recommended for future gene expression studies in the GI region.
Article
Fisheries
Shuaijie Sun, Zhitong Wang, Dongdong Yuan, Mengke Ni, Huifen Xu, Wanliang Wang, Chi Zhang, Meiqun Chen, Lamu ZhaXi, Jianshe Zhou, Ming Li
Summary: This study used RT-qPCR technology to investigate the expression of eight candidate genes in different tissues, developmental stages, and under bacterial stress in Salmo trutta. The stability of these genes was ranked using comprehensive analysis software. The results showed that the expression of the hprt1 gene was relatively stable under different conditions.
AQUACULTURE REPORTS
(2022)
Article
Multidisciplinary Sciences
Ruoyu Song, Shijun He, Yongbin Wu, Wanxin Chen, Jie Song, Yaxi Zhu, Huan Chen, Qianlu Wang, Shouman Wang, Sichuang Tan, Sipin Tan
Summary: Objective of this study was to screen and validate reference genes suitable for gene mRNA expression study in peripheral blood mononuclear cells (PBMCs) between septic patients and healthy controls (HC). Results showed that YWHAZ was the most stable gene among the 9 candidate genes. The combination of ACTB, PKG1, and YWHAZ improved RT-qPCR accuracy in septic patients. These findings provide valuable guidance for the selection of reference genes in PBMC of sepsis patients and serve as a useful tool for gene function exploration in the future.
Article
Plant Sciences
Judit Tajti, Magda Pal, Tibor Janda
Summary: Oat, a widely cultivated cereal with high nutritional value, shows different stability of reference gene expression under diverse abiotic stress conditions. ADPR was identified as the top-rated reference gene for all samples, while TUB and EF1 were most affected by the treatments.
Article
Agriculture, Dairy & Animal Science
Juan Zhao, Cheng Wang, Lin Zhang, Aiai Lei, Linjie Wang, Lili Niu, Siyuan Zhan, Jiazhong Guo, Jiaxue Cao, Li Li, Hongping Zhang, Tao Zhong
Summary: The rumen is essential for the absorption of energy substrate in ruminants, and understanding the gene expression profiles is crucial for exploring the regulatory mechanisms of rumen development in goats. This study identified 16 candidate reference genes from transcriptome sequencing of goat rumen tissues, and demonstrated that RPS4X and RPS6 were the most stable reference genes for quantifying gene expression in rumen tissues via RT-qPCR analysis.
Article
Genetics & Heredity
Dongxiao Ma, Qin Zhang, Jintao Zhou, Yu Lu, Xiaomeng Duan, Chengzhong He, Jinde Yu
Summary: In this study, the expression stability of 10 candidate reference genes was analyzed in Toxicodendron succedaneum using RT-qPCR. The results showed that TsRG03 and ACT were recommended as suitable reference genes for all samples. These findings provide alternative reference genes for gene function studies, correction and normalization of target gene expression, and directed molecular breeding in T. succedaneum.
Article
Plant Sciences
Francisca Valenzuela, Vivian D'Afonseca, Ricardo Hernandez, Aleydis Gomez, Ariel D. Arencibia
Summary: This study validates the reference genes in blueberry plants cultured in vitro on a colchicine-supplemented medium for the first time. The results show that colchicine treatments can cause genomic changes in blueberry plants and affect gene expression at the molecular level. The study also identifies potential reference genes for gene expression assays in Vaccinium.
Article
Physiology
Wei Na, Yuxiang Wang, Pengfei Gong, Xinyang Zhang, Ke Zhang, Hui Zhang, Ning Wang, Hui Li
Summary: The study utilized the GeNorm algorithm to analyze the expression stability of 14 candidate reference genes in the abdominal adipose tissue of broilers, finding that TBP and HMBS genes exhibited the highest stability at each stage.
FRONTIERS IN PHYSIOLOGY
(2021)
Article
Agriculture, Dairy & Animal Science
Qi Min, Lu Yang, Yu Wang, Yili Liu, Mingfeng Jiang
Summary: In this study, 15 candidate reference genes (CRGs) were identified based on transcriptome sequencing and literature review. Four algorithms were used to evaluate the stability of these CRGs in the yak stomach. RPS15, MRPL39, and RPS23 were found to be the most stable genes throughout the growth cycle. This study provides suitable reference genes for gene expression analysis in the yak stomach.