Deconvolution of the confounding variations for reverse transcription quantitative real-time polymerase chain reaction by separate analysis of biological replicate data

Analytical Biochemistry

Volumn 427, Issue 1, 2012, Pages 21-25

  Ling, Daijun ^a,b   Pike, Christian J ^b   Salvaterra, Paul M ^a  

^a CITY OF HOPE NATIONAL MEDICAL CENTER   (United States)

^b UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

Author keywords

cDNA; Data analysis; Gene expression; mRNA; Normalization; Real time PCR; Replicates; Reverse transcription; RT qPCR; Variance

Indexed keywords

DATA HANDLING; DATA REDUCTION; GENE EXPRESSION; INFORMATION ANALYSIS; ITERATIVE METHODS; SEPARATION; SIGNAL TO NOISE RATIO; TRANSCRIPTION;

CDNA; MRNA; NORMALIZATION; REAL-TIME PCR; REPLICATES; REVERSE TRANSCRIPTION; RT-QPCR; VARIANCE;

POLYMERASE CHAIN REACTION;

ARTICLE; CONTROLLED STUDY; DATA ANALYSIS; DENATURATION; GENE EXPRESSION; GENE REPLICATION; GENE TARGETING; PRIORITY JOURNAL; REAL TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION;

EID: 84861404120     PISSN: 00032697     EISSN: 10960309     Source Type: Journal    
DOI: 10.1016/j.ab.2012.04.029     Document Type: Article

References (21)

1. S. Taylor, M. Wakem, G. Dijkman, M. Alsarraj, and M. Nguyen A practical approach to RT-qPCR: publishing data that conform to the MIQE guidelines Methods 50 2010 S1 S5
2. A. Tichopad, R. Kitchen, I. Riedmaier, C. Becker, A. Stahlberg, and M. Kubista Design and optimization of reverse-transcription quantitative PCR experiments Clin. Chem. 55 2009 1816 1823
3. T.T. Nguyen, R.R. Almon, D.C. DuBois, W.J. Jusko, and I.P. Androulakis Importance of replication in analyzing time-series gene expression data: corticosteroid dynamics and circadian patterns in rat liver BMC Bioinformatics 11 2010 279
4. M.W. Pfaffl, J. Vandesompele, and M. Kubista Data analysis software J. Logan, K. Edwards, N. Saunders, Real-time PCR: Current technology and applications 2009 Caister Academic Press Norfolk, UK 65 83
5. C.C. Stowers, F.R. Haselton, and E.M. Boczko An analysis of quantitative PCR reliability through replicates using the C method J. Biomed. Sci. Eng. 3 2010 459 469
6. E. Willems, L. Leyns, and J. Vandesompele Standardization of real-time PCR gene expression data from independent biological replicates Anal. Biochem. 379 2008 127 129
7. W.J. Fu, J. Hu, T. Spencer, R. Carroll, and G. Wu Statistical models in assessing fold change of gene expression in real-time RT-PCR experiments Comput. Biol. Chem. 30 2006 21 26
8. P. Cook, C. Fu, M. Hickey, E.S. Han, and K.S. Miller SAS programs for real-time RT-PCR having multiple independent samples BioTechniques 37 2004 990 995
9. M.J. Burns, G.J. Nixon, C.A. Foy, and N. Harris Standardisation of data from real-time quantitative PCR methods: evaluation of outliers and comparison of calibration curves BMC Biotechnol. 5 2005 31
10. N. Regier, and B. Frey Experimental comparison of relative RT-qPCR quantification approaches for gene expression studies in poplar BMC Mol. Biol. 11 2010 57
11. D. Ling SASqPCR: robust and rapid analysis of RT-qPCR data in SAS PLoS One 7 2012 e29788
12. R.R. Kitchen, M. Kubista, and A. Tichopad Statistical aspects of quantitative real-time PCR experiment design Methods 50 2010 231 236
13. S. Derveaux, J. Vandesompele, and J. Hellemans How to do successful gene expression analysis using real-time PCR Methods 50 2010 227 230
14. D. Ling, and P.M. Salvaterra Robust RT-qPCR data normalization: validation and selection of internal reference genes during post-experimental data analysis PLoS One 6 2011 e17762
15. J. Vandesompele, K. De Preter, F. Pattyn, B. Poppe, N. Van Roy, A. De Paepe, F. Speleman, Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes, Genome Biol. 3 (2002) RESEARCH 0034.
16. T) method Methods 25 2001 402 408
17. J. Hellemans, G. Mortier, A. De Paepe, F. Speleman, and J. Vandesompele QBase relative quantification framework and software for management and automated analysis of real-time quantitative PCR data Genome Biol. 8 2007 R19
18. M.W. Pfaffl, G.W. Horgan, and L. Dempfle Relative expression software tool (REST) for group-wise comparison and statistical analysis of relative expression results in real-time PCR Nucleic Acids Res. 30 2002 e36
19. 1-42 neurotoxicity converge via deterioration in autophagy-lysosomal system: a conditional Drosophila model linking Alzheimer's neurodegeneration with aging Acta Neuropathol. 121 2011 183 191
20. 42-induced neurodegeneration via an age-dependent autophagic-lysosomal injury in Drosophila PLoS One 4 2009 e4201
21. C.W. Wittmann, M.F. Wszolek, J.M. Shulman, P.M. Salvaterra, J. Lewis, M. Hutton, and M.B. Feany Tauopathy in Drosophila: neurodegeneration without neurofibrillary tangles Science 293 2001 711 714