Evaluation of sense-strand mRNA amplification by comparative quantitative PCR

BMC Genomics

Table 2 Rank correlations of liver C_t values identifies effects of oligo d(T) primers vs. random hexamer primers.

	Unamplified	MessageAmp	NuGen	Version 1	Version 2	Version 1–2	2 Rounds V 1–2
MessageAmp	*0.75*	1
NuGen	*0.65*	0.83	1
Version 1	*0.61*	0.68	0.61	1
Version 2	*0.84*	0.92	0.78	0.71	1
Version 1–2	*0.84*	0.90	0.84	0.67	0.95	1
2 Rounds V1–2	*0.79*	0.89	0.81	0.67	0.93	0.92	1
Degraded V1–2	0.85	*0.85*	*0.77*	*0.71*	*0.89*	*0.91*	*0.85*

Rank cross-correlation matrix for liver C_t values. The mean cycle threshold (C_t) values obtained with liver RNA samples were rank-ordered and correlated. Results indicate the faithful reproduction of an ordered list of mRNA concentrations in liver RNA before and after amplification. Results were filtered for acceptable PCR efficiencies (see Methods), producing 138 primer pairs for this analysis. Methods using random primer (including unamplified RNA) are bold, those using oligo d(T) are italicized. Scatter plots of each rank C_t correlation are available at: http://cord.rutgers.edu/amplification/index.html

ISSN: 1471-2164