Abstract

A data anomaly was observed that affected the uniformity and reproducibility of fluorescent signal across DNA microarrays. Results from experimental sets designed to identify potential causes (from microarray production to array scanning) indicated that the anomaly was linked to a batch process; further work allowed us to localize the effect to the posthybridization array stringency washes. Ozone levels were monitored and highly correlated with the batch effect. Controlled exposures of microarrays to ozone confirmed this factor as the root cause, and we present data that show susceptibility of a class of cyanine dyes (e.g., Cy5, Alexa 647) to ozone levels as low as 5-10 ppb for periods as short as 10-30 s. Other cyanine dyes (e.g., Cy3, Alexa 555) were not significantly affected until higher ozone levels (> 100 ppb). To address this environmental effect, laboratory ozone levels should be kept below 2 ppb (e.g., with filters in HVAC) to achieve high quality microarray data.

Keywords

ChemistryOzoneCyanineMicroarrayDNA microarrayEnvironmental chemistryFluorescenceAnalytical Chemistry (journal)BiochemistryGene expressionOrganic chemistryGene

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Publication Info

Year
2003
Type
article
Volume
75
Issue
17
Pages
4672-4675
Citations
221
Access
Closed

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Thomas L. Fare, Ernest M. Coffey, Hongyue Dai et al. (2003). Effects of Atmospheric Ozone on Microarray Data Quality. Analytical Chemistry , 75 (17) , 4672-4675. https://doi.org/10.1021/ac034241b

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DOI
10.1021/ac034241b