Linear relationships between gene-expression ratios from amplified and unamplified cDNA. SMART-generated cDNA results in systematically reduced expression ratios compared to other methods. Average expression ratios (M values) comparing two different cell lines (3T3 vs OV) for unamplified cDNA (Mdna) were plotted against those calculated using cDNA/RNA amplified with each method (Msmart, SMART PCR-based amplification, Mga, global PCR amplification; Mrna, three rounds of T7-based linear isothermal amplification). Green spots indicate differentially expressed genes common to amplified and unamplified samples (see also Table 2). Scatterplot demonstrating the compression effect of SMART amplification: the M values of genes for SMART-amplified cDNA are proportionally smaller than those of unamplified cDNA. The compression was found to be linear, fitting the formula Mdna = 0.4 Msmart (red line). In contrast to SMART, coefficients of linear regression for GA and IVTIII cDNA plotted against unamplified DNA were approximately equal: -0.9 and 1.1, respectively.
Subkhankulova and Livesey Genome Biology 2006 7:R18 doi:10.1186/gb-2006-7-3-r18