中国水产科学研究院机构知识库

Genome-wide identification of suitable zebrafish Danio rerio reference genes for normalization of gene expression data by RT-qPCR

收藏
分享
全文链接

文献类型：外文期刊

作者： Xu, H. ¹ ; Li, C. ² ; Zeng, Q. ² ; Agrawal, I. ² ; Zhu, X. ¹ ; Gong, Z. ² ;

作者机构： 1.Chinese Acad Fishery Sci, Pearl River Fisheries Res Inst, Guangzhou 510380, Guangdong, Peoples R China

2.Natl Univ Singapore, Dept Biol Sci, Singapore 117543, Singapore

关键词： fish;gene expression;housekeeping genes;transcriptomes

期刊名称：JOURNAL OF FISH BIOLOGY （影响因子：2.051；五年影响因子：2.25 ）

ISSN：

年卷期：

页码：

收录情况： SCI

摘要： In this study, to systematically identify the most stably expressed genes for internal reference in zebrafish Danio rerio investigations, 37 D. rerio transcriptomic datasets (both RNA sequencing and microarray data) were collected from gene expression omnibus (GEO) database and unpublished data, and gene expression variations were analysed under three experimental conditions: tissue types, developmental stages and chemical treatments. Forty-four putative candidate genes were identified with the c.v. <0.2 from all datasets. Following clustering into different functional groups, 21 genes, in addition to four conventional housekeeping genes (eef1a1l1, b2m, hrpt1l and actb1), were selected from different functional groups for further quantitative real-time (qrt-)PCR validation using 25 RNA samples from different adult tissues, developmental stages and chemical treatments. The qrt-PCR data were then analysed using the statistical algorithm refFinder for gene expression stability. Several new candidate genes showed better expression stability than the conventional housekeeping genes in all three categories. It was found that sep15 and metap1 were the top two stable genes for tissue types, ube2a and tmem50a the top two for different developmental stages, and rpl13a and rp1p0 the top two for chemical treatments. Thus, based on the extensive transcriptomic analyses and qrt-PCR validation, these new reference genes are recommended for normalization of D. rerio qrt-PCR data respectively for the three different experimental conditions. (C) 2016 The Fisheries Society of the British Isles

相关文献

[1]BIRC7 gene in channel catfish (Ictalurus punctatus): Identification and expression analysis in response to Edwardsiella tarda, Streptococcus iniae and channel catfish Hemorrhage Reovirus. Li, Min,Wang, Qi-Long,Chen, Song-Lin,Sha, Zhen-Xia,Li, Min,Liu, Yang.

[2]Pathogen recognition receptors in channel catfish: I. Identification, phylogeny and expression of NOD-like receptors. Rajendran, K. V.,Zhang, Jiaren,Liu, Shikai,Kucuktas, Huseyin,Wang, Xiuli,Liu, Hong,Sha, Zhenxia,Terhune, Jeffery,Peatman, Eric,Liu, Zhanjiang,Rajendran, K. V.,Zhang, Jiaren,Liu, Shikai,Kucuktas, Huseyin,Wang, Xiuli,Liu, Hong,Sha, Zhenxia,Terhune, Jeffery,Peatman, Eric,Liu, Zhanjiang,Rajendran, K. V.,Sha, Zhenxia.

[3]Physiological responses and gene expression changes in the western mosquitofish (Gambusia affinis) exposed to progesterone at environmentally relevant concentrations. Hou, Liping,Yang, Yang,Shu, Hu,Cheng, Xuemei,Xu, Hongyan,Ying, Guangguo,Zhao, Jianliang,Ying, Guangguo,Zhao, Jianliang. 2017

[4]Identification of suitable reference genes for quantitative real-time PCR normalization in blotched snakehead Channa maculata. Mao, H.,Chen, K.,Zhu, X.,Luo, Q.,Zhao, J.,Li, W.,Wu, X.,Xu, H.,Mao, H.,Chen, K.,Wu, X.,Xu, H..

[5]Alteration of parameters of energy metabolism and ATPase enzymatic system in juvenile common carp (Cyprinus carpio) chronically exposed to tributyltin. Li, Z. -H.,Zhong, L. -Q.,Mu, W. -N.,Wu, Y. -H.,Li, Z. -H.,Mu, W. -N.,Wu, Y. -H..

[6]Ontogenetic behavior and migration of Chinese sturgeon, Acipenser sinensis. Zhuang, P,Kynard, B,Zhang, LZ,Zhang, T,Cao, WX.

[7]Multiple biomarkers responses in juvenile rainbow trout, Oncorhynchus mykiss, after acute exposure to a fungicide propiconazole. Li, Zhi-Hua,Zlabek, Vladimir,Velisek, Josef,Grabic, Roman,Machova, Jana,Kolarova, Jitka,Li, Ping,Randak, Tomas,Li, Zhi-Hua,Li, Ping.

[8]Derivation of a pluripotent embryonic cell line from red sea bream blastulas. Chen, SL,Ye, HQ,Sha, ZX,Hong, Y.

[9]Faunal utilization of constructed intertidal oyster (Crassostrea rivularis) reef in the Yangtze River estuary, China. Quan, Wei-min,Zhu, Jiang-xing,Ni, Yong,Shi, Li-yan,Chen, Ya-qu.

[10]Effects of chronic exposure to tributyltin on tissue-specific cytochrome P450 1 regulation in juvenile common carp. Li, Zhi-Hua,Zhong, Li-Qiao,Mu, Wei-Na,Wu, Yan-Hua,Li, Zhi-Hua,Mu, Wei-Na,Wu, Yan-Hua.

[11]Alteration of cytochrome P450 1 regulation and HSP 70 level in brain of juvenile common carp (Cyprinus carpio) after chronic exposure to tributyltin. Li, Zhi-Hua,Zhong, Li-Qiao,Wu, Yan-Hua,Mu, Wei-Na,Li, Zhi-Hua,Wu, Yan-Hua,Mu, Wei-Na.

[12]Swimming ability and physiological response to swimming fatigue in whiteleg shrimp, Litopenaeus vannamei. Zhang, Peidong,Zhang, Xiumei,Li, Jian,Huang, Guoqiang.

[13]In Vitro Protective Efficacy of Clostridium butyricum Against Fish Pathogen Infections. Gao, Quanxin,Sun, Peng,Peng, Shiming,Yin, Fei,Shi, Zhaohong,Gao, Quanxin,Xiao, Yingping,Ma, Xiangming.

[14]Comparison of Nekton Use for Cordgrass Spartina alterniflora and Bulrush Scirpus mariqueter Marshes in the Yangtze River Estuary, China. Quan, Weimin,Shi, Liyan,Chen, Yaqu.

[15]Fish ES Cells and Applications to Biotechnology. Alvarez, M. Carmen,Bejar, Julia,Chen, Songlin,Hong, Yunhan.

[16]Chronic toxicity of verapamil on juvenile rainbow trout (Oncorhynchus mykiss): Effects on morphological indices, hematological parameters and antioxidant responses. Li, Zhi-Hua,Velisek, Josef,Zlabek, Vladimir,Grabic, Roman,Machova, Jana,Kolarova, Jitka,Li, Ping,Randak, Tomas,Li, Zhi-Hua,Li, Ping.

[17]The two channel catfish intelectin genes exhibit highly differential patterns of tissue expression and regulation after infection with Edwardsiella ictaluri. Takano, Tomokazu,Sha, Zhenxia,Peatman, Eric,Terhune, Jeffery,Li, Hong,Kucuktas, Huseyin,Li, Ping,Liu, Zhanjiang,Sha, Zhenxia,Edholm, Eva-Stina,Wilson, Melanie.

[18]Responses of the hepatic glutathione antioxidant defense system and related gene expression in juvenile common carp after chronic treatment with tributyltin. Li, Zhi-Hua,Li, Ping,Shi, Ze-Chao,Li, Zhi-Hua,Li, Ping. 2015

[19]Modulation of glutathione-related antioxidant defense system of fish chronically treated by the fungicide propiconazole. Li, Zhi-Hua,Zlabek, Vladimir,Grabic, Roman,Li, Ping,Randak, Tomas,Li, Zhi-Hua,Li, Ping,Grabic, Roman. 2010

[20]The warm temperature acclimation protein Wap65 as an immune response gene: Its duplicates are differentially regulated by temperature and bacterial infections. Sha, Zhenxia,Yu, Peng,Takano, Tomokazu,Liu, Hong,Terhune, Jeffrey,Liu, Zhanjiang,Sha, Zhenxia,Liu, Hong. 2008

作者其他论文更多>>

Decorating local Li plus solvation structure and optimizing solid electrolyte interphase with potassium trifluoroacetate for dendrites-free lithium metal anodes

作者：Zeng, T.;Shu, C.;Yan, Y.;Du, D.;Xu, H.;Wen, X.;Liu, S.;Tian, G.;Wang, X.;Zeng, Y.;Wu, L.

关键词：Electrolyte additive; Potassium tri fluoroacetate; Li plus solvation environment; Electrode -electrolyte interphase; Dendrites -free Li deposition
Characterization of a Novel C-type Lectin against OsHV-1 infection in Scapharca broughtonii

作者：Wang, D.;Zhou, H.;Wang, D.;Huang, B.;Yu, J.;Bai, C.;Li, C.;Wang, C.;Xin, L.;Wang, D.;Huang, B.;Yu, J.;Bai, C.;Li, C.;Wang, C.;Xin, L.;Yu, J.

关键词：Scapharca broughtonii; C-type lectin; PAMP binding; OsHV-1 infection
Pharmacokinetics of enrofloxacin after oral, intramuscular and bath administration in crucian carp (Carassius auratus gibelio)

作者：Shan, Q.;Fan, J.;Zhu, X.;Yin, Y.;Zheng, G.;Wang, J.

关键词：ciprofloxacin; crucian carp; enrofloxacin; pharmacokinetic
The effect of ultrafiltered fish protein hydrolysate level on growth performance, protein digestibility and mRNA expression of PepT1 in juvenile turbot (Scophthalmus maximus L.)

作者：Wei, Y.;Wei, Y.;Liang, M.;Mu, Y.;Zheng, K.;Xu, H.

关键词：digestibility; peptide transporter 1; plant protein; turbot; ultrafiltered fish protein hydrolysate
Comparison of genetic diversity and growth traits among Fangzheng silver crucian carp (Carassius auratus gibelio) gynogenetic clones

作者：Lu, C. Y.;Cheng, L.;Li, C.;Zheng, X. H.;Cao, D. C.;Sun, X. W.

关键词：Silver crucian carp;Gynogenetic clone;Polymorphism;Growth traits;Genetic diversity
THE RELATIONSHIP BETWEEN THERMAL REGIME ALTERATION AND SPAWNING DELAY OF THE FOUR MAJOR CHINESE CARPS IN THE YANGTZE RIVER BELOW THE THREE GORGES DAM

作者：Wang, J. -N.;Luo, H. -H.;Feng, S. -X.;Peng, Q. -D.;Li, C.;Duan, X. -B.;Liao, W. -G.

关键词：thermal regime alteration;fish spawning delay;the four major Chinese carps;Three Gorges Dam;a middle reach of the Yangtze River
Effects of high water level on the river residence period of juvenile Chinese sturgeon Acipenser sinensis in the Yangtze River

作者：Zhang, H.;Wei, Q. W.;Du, H.;Li, C.

关键词：Acipenser sinensis;downstream migration;water level;Three Gorges Project

Genome-wide identification of suitable zebrafish Danio rerio reference genes for normalization of gene expression data by RT-qPCR

作者其他论文 更多>>

Decorating local Li plus solvation structure and optimizing solid electrolyte interphase with potassium trifluoroacetate for dendrites-free lithium metal anodes

Characterization of a Novel C-type Lectin against OsHV-1 infection in Scapharca broughtonii

Pharmacokinetics of enrofloxacin after oral, intramuscular and bath administration in crucian carp (Carassius auratus gibelio)

The effect of ultrafiltered fish protein hydrolysate level on growth performance, protein digestibility and mRNA expression of PepT1 in juvenile turbot (Scophthalmus maximus L.)

Comparison of genetic diversity and growth traits among Fangzheng silver crucian carp (Carassius auratus gibelio) gynogenetic clones

THE RELATIONSHIP BETWEEN THERMAL REGIME ALTERATION AND SPAWNING DELAY OF THE FOUR MAJOR CHINESE CARPS IN THE YANGTZE RIVER BELOW THE THREE GORGES DAM

Effects of high water level on the river residence period of juvenile Chinese sturgeon Acipenser sinensis in the Yangtze River

意 见 箱

作者其他论文更多>>

意见箱