Figure 2.

Comparison of amplification protocols. (a) Comparison of the full-length amplification protocol (mRP-Amp, blue) and a 3'-biased amplification protocol (black) of the RB1 gene in the Jurkat cell line. As expected, the 3' protocol amplifies the 3' end well but probe intensities greater than 1,000 nucleotides from the 3' end are near background levels. Background is defined by the mean intensity of 10,700 probes spaced throughout RB1 introns. (b) Comparison of the mRP-Amp protocol to random-primed reverse transcription (RP-RT) alone. The plot shows the log₁₀ intensity ratios between Jurkat and K562 cell lines from 17,000 probes hybridized, where the Jurkat and K562 samples were amplified with either the mRP-Amp protocol (horizontal axis) or a 'gold standard' RP-RT protocol. (c) Two independent mRP-Amp amplifications of Jurkat and K562 cell lines demonstrate protocol reproducibility. Points show log₁₀ intensity ratios of K562 to Jurkat from the probes complementary to the RB1 mRNA sequence.