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Effects of atmospheric ozone on microarray data quality.
Thomas L Fare1, Ernest M Coffey, Hongyue Dai
1Rosetta Inpharmatics LLC, 12040 115th Avenue NE, Kirkland, Washington 98034, USA.
Analytical Chemistry
|November 25, 2003
Summary
Ozone exposure causes data anomalies in DNA microarrays, affecting fluorescent signals. Keeping laboratory ozone levels below 2 ppb is crucial for reliable microarray results.
Area of Science:
- Molecular Biology
- Environmental Science
- Biotechnology
Background:
- Data anomalies in DNA microarray experiments can compromise fluorescent signal uniformity and reproducibility.
- Previous studies have not fully elucidated the environmental factors contributing to such anomalies.
Purpose of the Study:
- To identify the root cause of observed data anomalies in DNA microarray experiments.
- To investigate the impact of environmental factors on fluorescent signal integrity.
Main Methods:
- Experimental analysis of microarray production and scanning processes.
- Monitoring of ozone levels and correlation with batch effects.
- Controlled exposure of microarrays to varying ozone concentrations.
Main Results:
- A batch process anomaly was localized to posthybridization stringency washes.
- Ozone levels were highly correlated with the observed batch effect.
- Cyanine dyes like Cy5 and Alexa 647 are susceptible to low ozone levels (5-10 ppb), while Cy3 and Alexa 555 require higher levels (>100 ppb).
Conclusions:
- Ozone is the root cause of data anomalies affecting fluorescent signals in DNA microarrays.
- Specific cyanine dyes exhibit differential sensitivity to ozone exposure.
- Maintaining laboratory ozone levels below 2 ppb is recommended for high-quality microarray data.