| Literature DB >> 17295919 |
William S Branham1, Cathy D Melvin, Tao Han, Varsha G Desai, Carrie L Moland, Adam T Scully, James C Fuscoe.
Abstract
BACKGROUND: Environmental ozone can rapidly degrade cyanine 5 (Cy5), a fluorescent dye commonly used in microarray gene expression studies. Cyanine 3 (Cy3) is much less affected by atmospheric ozone. Degradation of the Cy5 signal relative to the Cy3 signal in 2-color microarrays will adversely reduce the Cy5/Cy3 ratio resulting in unreliable microarray data.Entities:
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Year: 2007 PMID: 17295919 PMCID: PMC1800842 DOI: 10.1186/1472-6750-7-8
Source DB: PubMed Journal: BMC Biotechnol ISSN: 1472-6750 Impact factor: 2.563
Figure 1Diurnal ozone fluctuations. The means of hourly atmospheric ozone levels measured during January and June 2005 in central Arkansas by the ADEQ along with carbon-filtered laboratory air are shown. Peak ozone concentrations averaged 56–66 ppb between 0900 and 1800. Hourly ozone levels during this period commonly reached 60–90 ppb with the highest level reaching 103 ppb. By contrast, laboratory ozone levels varied between 2.6 and 4.4 ppb after installation of the carbon-filtered air supply.
Figure 2Reduction of Cy5 signal for in-house fabricated microarrays kept in a none-ozone controlled environment. These figures show a region of two 20 K mouse microarrays, selected because of their wide range of both Cy5 and Cy3 signals. The microarray images were from scans made during a 114 minute experiment interval. While the microarrays maintained in the carbon-filtered laboratory environment (ozone ~2–4 ppb) remained relatively unchanged with time (top images), reduction in Cy5 in the uncontrolled ozone environment (ozone ~25 ppb) causes the microarray image to have a predominantly green cast (bottom images).
Figure 3Dramatic improvement of Cy5 fluorescence stability as a result of ozone depletion. Pairs of microarrays printed in-house [A] or printed by Agilent Technologies [B] were hybridized and initially scanned immediately after washing in the carbon-filtered lab. One of each of the pairs of slides was then moved to an environment in which ozone was not removed by carbon filtration (ozone ~25 ppb for the in-house produced slide and ~10 ppb for the Agilent slide). The remaining slide remained in the ozone controlled microarray laboratory (ozone ~2–4 ppb). The slides were then alternately rescanned 6 times. The data show the rapid decline in Cy5 feature intensities as early as 13 minutes in the non-ozone controlled environment. It should be noted that the "ozone-exposed" microarray was not exposed to ozone while it was being scanned.
Effects of LOWESS Normalization on Correlations.
| Effects of LOWESS Normalization | |||||||||
| Scan Interval (minutes): | 0 | 13 | 26 | 39 | 52 | 65 | 78 | 91 | |
| Non- carbon-filtered | Raw ratio data | 1.00 | 0.93 | 0.81 | 0.69 | 0.59 | 0.48 | 0.40 | 0.37 |
| Normalized ratio data | 1.00 | 0.98 | 0.96 | 0.94 | 0.92 | 0.88 | 0.84 | 0.80 | |
| Cy5 Intensity data | 1.00 | 0.98 | 0.96 | 0.94 | 0.90 | 0.85 | 0.80 | 0.76 | |
| Cy3 Intensity data | 1.00 | 0.99 | 0.99 | 0.99 | 0.98 | 0.98 | 0.98 | 0.97 | |
| Carbon-filtered | Raw ratio data | 1.00 | 0.99 | 0.99 | 0.99 | 0.98 | 0.98 | 0.97 | 0.96 |
| Normalized ratio data | 1.00 | 0.99 | 0.99 | 0.99 | 0.98 | 0.98 | 0.98 | 0.98 | |
| Cy5 Intensity data | 1.00 | 0.99 | 0.99 | 0.99 | 0.99 | 0.99 | 0.99 | 0.99 | |
| Cy3 Intensity data | 1.00 | 0.99 | 0.99 | 0.99 | 0.99 | 0.99 | 0.99 | 0.99 | |
Intensity data and Cy5/Cy3 ratio (raw) data were obtained for individual microarray features at each scan time using the Axon GenePix Pro software. LOWESS normalization was performed on the ratio data. The data shown are correlations (r-values) of the raw or normalized data at each scan interval compared to the 0-minute scan interval.