Effects of atmospheric ozone on microarray data quality.
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.
Fare
Thomas L
TL
Rosetta Inpharmatics LLC, 12040 115th Avenue NE, Kirkland, Washington 98034, USA.
Coffey
Ernest M
EM
Dai
Hongyue
H
He
Yudong D
YD
Kessler
Deborah A
DA
Kilian
Kristopher A
KA
Koch
John E
JE
LeProust
Eric
E
Marton
Matthew J
MJ
Meyer
Michael R
MR
Stoughton
Roland B
RB
Tokiwa
George Y
GY
Wang
Yanqun
Y
D016477:Artifacts; D001272:Atmosphere / Q000737:chemistry*; D002232:Carbocyanines / Q000737:chemistry*; D003890:Desiccation; D005453:Fluorescence; D020411:Oligonucleotide Array Sequence Analysis / Q000295:instrumentation* / Q000592:standards*; D010126:Ozone / Q000032:analysis* / Q000737:chemistry*; D011786:Quality Control; D015203:Reproducibility of Results
D002232:Carbocyanines; C089187:cyanine dye 3; C085321:cyanine dye 5; D010126:Ozone