Correction of RT-qPCR data for genomic DNA-derived signals with ValidPrime

Nucleic Acids Research

Volumn 40, Issue 7, 2012, Pages

  Laurell, Henrik ^a   Iacovoni, Jason S ^a   Abot, Anne ^a   Svec, David ^b,c   Maoret, Jean José ^a,d   Arnal, Jean François ^a,e   Kubista, Mikael ^b,c  

^a University Hospital of Toulouse   (France)

^b INSTITUTE OF BIOTECHNOLOGY   (Czech Republic)

^c TATAA Biocenter AB   (Sweden)

^d Parc Scientifique de Luminy   (France)

^e UNIVERSITÉ PAUL SABATIER   (France)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA; GENOMIC DNA; RNA;

ACCURACY; ANIMAL TISSUE; ARTICLE; ASSAY; CONTROLLED STUDY; DNA CONTAMINATION; DNA CONTENT; GENE AMPLIFICATION; MOUSE; NONHUMAN; PRIORITY JOURNAL; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA PURIFICATION; SENSITIVITY AND SPECIFICITY; SIGNAL PROCESSING;

ANIMALS; DNA; DNA CONTAMINATION; DNA PRIMERS; GENOMICS; MICE; MICE, INBRED C57BL; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION;

EID: 84860196602     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr1259     Document Type: Article

References (25)

1. Bustin, S.A. (2002) Quantification of mRNA using real-time reverse transcription PCR (RT-PCR): trends and problems. J. Mol. Endocrinol., 29, 23-39. (Pubitemid 34965744)
2. Peccoud, J. and Jacob, C. (1996) Theoretical uncertainty of measurements using quantitative polymerase chain reaction. Biophys. J., 71, 101-108. (Pubitemid 26227296)
3. Nordgä rd, O., Kvaloy, J.T., Farmen, R.K. and Heikkila, R. (2006) Error propagation in relative real-time reverse transcription polymerase chain reaction quantification models: the balance between accuracy and precision. Anal. Biochem., 356, 182-193. (Pubitemid 44389680)
4. Bengtsson, M., Hemberg, M., Rorsman, P. and Stä hlberg, A. (2008) Quantification of mRNA in single cells and modelling of RT-qPCR induced noise. BMC Mol. Biol., 9, 63.
5. Calippe, B., Douin-Echinard, V., Laffargue, M., Laurell, H., Rana-Poussine, V., Pipy, B., Guery, J.C., Bayard, F., Arnal, J.F. and Gourdy, P. (2008) Chronic estradiol administration in vivo promotes the proinflammatory response of macrophages to TLR4 activation: involvement of the phosphatidylinositol 3-kinase pathway. J. Immunol., 180, 7980-7988.
6. Hofstetter, J.R., Zhang, A., Mayeda, A.R., Guscar, T., Nurnberger, J.I. Jr and Lahiri, D.K. (1997) Genomic DNA from mice: a comparison of recovery methods and tissue sources. Biochem. Mol. Med., 62, 197-202. (Pubitemid 28063398)
7. Spurgeon, S.L., Jones, R.C. and Ramakrishnan, R. (2008) High throughput gene expression measurement with real time PCR in a microfluidic dynamic array. PLoS One, 3, e1662.
8. Riant, E., Waget, A., Cogo, H., Arnal, J.F., Burcelin, R. and Gourdy, P. (2009) Estrogens protect against high-fat diet-induced insulin resistance and glucose intolerance in mice. Endocrinology, 150, 2109-2117.
9. Giulietti, A., Overbergh, L., Valckx, D., Decallonne, B., Bouillon, R. and Mathieu, C. (2001) An overview of real-time quantitative PCR: applications to quantify cytokine gene expression. Methods, 25, 386-401. (Pubitemid 34164011)
10. Livak, K.J. and Schmittgen, T.D. (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods, 25, 402-408. (Pubitemid 34164012)
11. Bustin, S.A. and Nolan, T. (2004) Pitfalls of quantitative real-time reverse-transcription polymerase chain reaction. J. Biomol. Tech., 15, 155-166.
12. Nolan, T., Hands, R.E. and Bustin, S.A. (2006) Quantification of mRNA using real-time RT-PCR. Nat. Protoc., 1, 1559-1582.
13. Higuchi, R., Fockler, C., Dollinger, G. and Watson, R. (1993) Kinetic PCR analysis: real-time monitoring of DNA amplification reactions. Biotechnology, 11, 1026-1030. (Pubitemid 23254023)
14. Gibson, U.E., Heid, C.A. and Williams, P.M. (1996) A novel method for real time quantitative RT-PCR. Genome Res., 6, 995-1001. (Pubitemid 26388092)
15. Pfaffl, M.W. (2010) The ongoing evolution of qPCR. Methods, 50, 215-216.
16. Roy, S.W. and Gilbert, W. (2006) The evolution of spliceosomal introns: patterns, puzzles and progress. Nat. Rev. Genet., 7, 211-221. (Pubitemid 43361532)
17. Bustin, S.A., Benes, V., Garson, J.A., Hellemans, J., Huggett, J., Kubista, M., Mueller, R., Nolan, T., Pfaffl, M.W., Shipley, G.L. et al. (2009) The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin. Chem., 55, 611-622.
18. Yun, J.J., Heisler, L.E., Hwang, I.I.L., Wilkins, O., Lau, S.K., Hyrcza, M., Jayabalasingham, B., Jin, J., McLaurin, J., Tsao, M.S. et al. (2006) Genomic DNA functions as a universal external standard in quantitative real-time PCR. Nucleic Acids Res., 34, e85.
19. Kubista, M., Sindelka, R., Tichopad, A., Bergkvist, A., Lindh, D. and Forootan, A. (2007) The Prime Technique. Real-time PCR data analysis. GIT Lab. J., 9-10, 33-35.
20. Pfaffl, M.W. (2001) A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res., 29, e45.
21. Tholen, D.W., Kroll, M., Astles, J.R., Caffo, A.L., Happe, T.M., Krouwer, J. and Lasky, F. (2003) Evaluation of the Linearity of Quantitative Measurement Procedures: a Statistical Approach; Approved Guideline, Vol. 23, CLSI EP6-A. Clinical and Laboratory Standards Institute, Wayne, PA, pp. 1-60.
22. Vandesompele, J., De Preter, K., Pattyn, F., Poppe, B., Van Roy, N., De Paepe, A. and Speleman, F. (2002) Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol., 3, RESEARCH0034.
23. Andersen, C.L., Jensen, J.L. and Orntoft, T.F. (2004) Normalization of real-time quantitative reverse transcription-PCR data: a model-based variance estimation approach to identify genes suited for normalization, applied to bladder and colon cancer data sets. Cancer Res., 64, 5245-5250. (Pubitemid 39006544)
24. Hellemans, J., Mortier, G., De Paepe, A., Speleman, F. and Vandesompele, J. (2007) qBase relative quantification framework and software for management and automated analysis of real-time quantitative PCR data. Genome Biol., 8, R19.
25. Liu, Y.J., Zheng, D., Balasubramanian, S., Carriero, N., Khurana, E., Robilotto, R. and Gerstein, M.B. (2009) Comprehensive analysis of the pseudogenes of glycolytic enzymes in vertebrates: the anomalously high number of GAPDH pseudogenes highlights a recent burst of retrotrans-positional activity. BMC Genomics, 10, 480.