Figure 3

Effects of probe size, GC probe content and position relative to stop codon on signal intensities. Cy3- and Cy5-labelled cDNA targets were prepared from the total RNA isolated from the wild-type strain BY4742 and Δymr011w, respectively. Hybridization was performed as described in "Methods" with microarray from Batch616. For the Cy5 channel, normalized signals of each spot were computed as a function of probe size (panel A), GC probe content (panel B) and the distance from 3'end of the probe to stop codon of the CDS (panel C). Panel A includes PCR probes only, panels B and C include both PCR and oligonucleotide probes. Red curves represent running averages of the signal intensities.