Figure 2

Strand specificity of in situ produced sense/antisense cDNA microarray features. (a) Histogram showing the distribution of log₂ ratios after hybridization to single stranded C (blue), N (red), and double stranded CN (gray) capture probes with labelled Cy3- M13 forward and Cy5 – reverse sequencing primers (The log₂ ratios for C and N probes from cDNA clones of plate IRAT3 were centered around -5 and 5 respectively, as expected since their cloning sites were reversed compared to the other clones, but to simplify the presentation the values are inverted). (b) log₂ ratios for probes shown in panel matched on cDNA clone ID and sorted on ascending log₂ ratio for the respective CN probe. (c) Mean log2ratios for β-lactamase spike-in sense (blue) and antisense (red) control features for hybridizations A to I. For individual features, log₂ ratios were calculated using untransformed background corrected data (Median FG – Median BG). For mean log₂ ratio calculations, only features where MedianFG > MedianBG in both channels, i.e. Cy3 and Cy5, and where SNR > = 3 in either channel, were included. Error bars denote +/-1SD. Mean log2ratio were calculated using values from between 66 and 70 replicated control spots.