Toward enhanced MIQE compliance: Reference residual normalization of qPCR gene expression data

Journal of Biomolecular Techniques

Volumn 25, Issue 2, 2014, Pages 54-60

  Edmunds, Richard C ^a   McIntyre, Jenifer K ^b   Adam Luckenbach, J ^c,d   Baldwin, David H ^a   Incardona, John P ^a  

^a Environmental Conservation Division   (United States)

^b WASHINGTON STATE UNIVERSITY   (United States)

^c NORTHWEST FISHERIES SCIENCE CENTER   (United States)

^d WASHINGTON STATE UNIVERSITY   (United States)

Author keywords

ANOVA; Normalization; Reference genes; Threshold cycle; Treatment effect

Indexed keywords

ANALYSIS OF VARIANCE; ARTICLE; GENE; GENE EXPRESSION; MEASUREMENT ACCURACY; REAL TIME POLYMERASE CHAIN REACTION; REFERENCE GENE; REFERENCE RESIDUAL; STATISTICAL PARAMETERS; PROCEDURES; STANDARD; STANDARDS; STATISTICAL ANALYSIS; STATISTICS AND NUMERICAL DATA;

ANALYSIS OF VARIANCE; DATA INTERPRETATION, STATISTICAL; GENE EXPRESSION; REAL-TIME POLYMERASE CHAIN REACTION; REFERENCE STANDARDS;

EID: 84903741179     PISSN: 15240215     EISSN: 19434731     Source Type: Journal    
DOI: 10.7171/jbt.14-2502-003     Document Type: Article

References (13)

1. Bustin SA, Benes V, Garson JA, et al. The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin Chem 2009;55:611-622.
2. Bustin SA. Whythe need forqPCRpublication guidelines?-Thecase for MIQE. Methods 2010;50:217-226.
3. Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2-Ct method. Methods 2001;25:402-408.
4. Schmittgen TD, Livak KJ. Analyzing real-time PCR data by the comparative Ct method. Nat Protoc 2008;3:1101-1108.
5. Linbo TL, Baldwin DH, McIntyre JK, Scholz NL. Effects of water hardness, alkalinity, and dissolved organic carbon on the toxicity of copper to the lateral line of developing fish. Environ Toxicol 2009;28:1455-1461.
6. Metzger DC, Luckenbach JA, Shimizu M, Beckman BR. Normalizing for biology: accounting for technical and biological variation in levels of reference gene and insulin-like growth factor 1 (igf1) transcripts in fish livers. Comp Biochem Physiol A 2010;163:7-14.
7. Tang R, Dodd A, Lai D, McNabb WC, Love DR. Validation of zebrafish (Danio rerio) reference genes for quantitative real-time RT-PCR normalization. Acta Biochim Biophys Sin (Shanghai) 2007;39:384-390.
8. McCurley AT, Callard GV. Characterization of housekeeping genes in zebrafish: male-female differences and effects of tissue type, developmental stage and chemical treatment. BMC Mol Biol 2008;9:102.
9. Pfaffl MW, Tichopad A, Prgomet C, Neuvians TP. Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper-Excel-based tool using pair-wise correlations. Biotechnol Lett 2004;26:509-515.
10. Vandesompele J, De Preter, K, Pattyn F, et al. Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol 2002; 3:RESEARCH0034.
11. Etheridge A, Gomes CP, Pereira RW, Galas D, Wang K. The complexity, function, and applications of RNA in circulation. Front Genet 2013;4:115.
12. Mattick JS. The genetic signatures of noncoding RNAs. PLoS Genet 2009;5:e1000459.
13. Mattick JS, Makunin IV. Small regulatory RNAs in mammals. Hum Mol Genet 2005;14(Spec No 1):R121-R132.