a. Ozone treatments of HyPer5 and Cy5 arrays lead to only Cy5 signal loss. These figures show sections of Cy3/HyPer5 and Cy3/Cy5 hybridized microarrays before (top) and after (bottom) 300 ppb ozone treatments. The ozone readings were monitored using a meter throughout the course of treatments. The first scan (no treatment) was set as time zero and the ozone images shown are following 10 minutes of total (two exposure of 5 minutes each) ozone exposure. Cy5 or HyPer5 signals appear as red spots and Cy3 signal as green spots. Near equal signal intensities of Cy3 and Cy5 or HyPer5 from individual features are observed as yellow spots. The signal from HyPer5 arrays remains unchanged following ozone treatments (compare top image to bottom). In contrast, sudden drop in Cy5 signal (red or yellow spots) is seen as conversion of yellow or red (top) features to green spots. b. Ozone stability of HyPer5 dye. Two separate in-house printed mouse arrays were hybridized with Cy3/Cy5 and Cy3/HyPer5 labelled cDNAs. Following initial scan (time zero), the arrays were exposed to 300 ppb of ozone for 5, 10, and 15 minute intervals. After each exposure, the slides were removed from the box and scanned. The slides were then immediately placed back inside the box again for longer exposures. The signal intensities were quantified and reported as the percentage of total Cy5 or HyPer5 signal following each ozone exposure relative to the total signal intensities at time zero. The data shows the sudden decline in Cy5 signal to 50% from 5 minutes of ozone exposure and drops to low level of 17% at 15 minute interval. In contrast, the HyPer5 signal remains completely intact following three 300 ppb ozone exposures demonstrating the resistance of dye signal to ozone in the chamber.