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; fur...
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| Veröffentlicht in: | Analytical chemistry (Washington) 2003-09, Vol.75 (17), p.4672-4675 |
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| creator | Fare, Thomas L Coffey, Ernest M Dai, Hongyue He, Yudong D Kessler, Deborah A Kilian, Kristopher A Koch, John E LeProust, Eric Marton, Matthew J Meyer, Michael R Stoughton, Roland B Tokiwa, George Y Wang, Yanqun |
| description | 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. |
| doi_str_mv | 10.1021/ac034241b |
| format | Article |
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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.</description><identifier>ISSN: 0003-2700</identifier><identifier>EISSN: 1520-6882</identifier><identifier>DOI: 10.1021/ac034241b</identifier><identifier>PMID: 14632079</identifier><identifier>CODEN: ANCHAM</identifier><language>eng</language><publisher>Washington, DC: American Chemical Society</publisher><subject>Analytical, structural and metabolic biochemistry ; Atmosphere ; Atmosphere - chemistry ; Biological and medical sciences ; Carbocyanines - chemistry ; Desiccation ; Dna, deoxyribonucleoproteins ; Effects ; Fluorescence ; Fundamental and applied biological sciences. Psychology ; Nucleic acids ; Oligonucleotide Array Sequence Analysis - instrumentation ; Oligonucleotide Array Sequence Analysis - standards ; Ozone ; Ozone - analysis ; Ozone - chemistry ; Quality Control ; Reproducibility of Results</subject><ispartof>Analytical chemistry (Washington), 2003-09, Vol.75 (17), p.4672-4675</ispartof><rights>Copyright © 2003 American Chemical Society</rights><rights>2004 INIST-CNRS</rights><rights>Copyright American Chemical Society Sep 1, 2003</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-a472t-e245f1d11245c2f56fb2061f630a7ae09ea07ea9de097b316c50aeb1d26b32ad3</citedby><cites>FETCH-LOGICAL-a472t-e245f1d11245c2f56fb2061f630a7ae09ea07ea9de097b316c50aeb1d26b32ad3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://pubs.acs.org/doi/pdf/10.1021/ac034241b$$EPDF$$P50$$Gacs$$H</linktopdf><linktohtml>$$Uhttps://pubs.acs.org/doi/10.1021/ac034241b$$EHTML$$P50$$Gacs$$H</linktohtml><link.rule.ids>315,781,785,2766,27081,27929,27930,56743,56793</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=15097431$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/14632079$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Fare, Thomas L</creatorcontrib><creatorcontrib>Coffey, Ernest M</creatorcontrib><creatorcontrib>Dai, Hongyue</creatorcontrib><creatorcontrib>He, Yudong D</creatorcontrib><creatorcontrib>Kessler, Deborah A</creatorcontrib><creatorcontrib>Kilian, Kristopher A</creatorcontrib><creatorcontrib>Koch, John E</creatorcontrib><creatorcontrib>LeProust, Eric</creatorcontrib><creatorcontrib>Marton, Matthew J</creatorcontrib><creatorcontrib>Meyer, Michael R</creatorcontrib><creatorcontrib>Stoughton, Roland B</creatorcontrib><creatorcontrib>Tokiwa, George Y</creatorcontrib><creatorcontrib>Wang, Yanqun</creatorcontrib><title>Effects of Atmospheric Ozone on Microarray Data Quality</title><title>Analytical chemistry (Washington)</title><addtitle>Anal. Chem</addtitle><description>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.</description><subject>Analytical, structural and metabolic biochemistry</subject><subject>Atmosphere</subject><subject>Atmosphere - chemistry</subject><subject>Biological and medical sciences</subject><subject>Carbocyanines - chemistry</subject><subject>Desiccation</subject><subject>Dna, deoxyribonucleoproteins</subject><subject>Effects</subject><subject>Fluorescence</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Nucleic acids</subject><subject>Oligonucleotide Array Sequence Analysis - instrumentation</subject><subject>Oligonucleotide Array Sequence Analysis - standards</subject><subject>Ozone</subject><subject>Ozone - analysis</subject><subject>Ozone - chemistry</subject><subject>Quality Control</subject><subject>Reproducibility of Results</subject><issn>0003-2700</issn><issn>1520-6882</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2003</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNplkEFLJDEQhYOs6Kx68A9II7iwh9aqJJ3MHEXdVVRUHM-hOp1ga0_3mHTDjr_eyAwOuKdXUB-v6j3G9hGOETiekAUhucRyg42w4JCr8Zj_YCMAEDnXANvsZ4wvAIiAaotto1SCg56MmL7w3tk-Zp3PTvtZF-fPLtQ2u3vvWpd1bXZb29BRCLTIzqmn7GGgpu4Xu2zTUxPd3kp32NOfi-nZZX5z9_fq7PQmJ6l5nzsuC48VYlLLfaF8yUGhVwJIk4OJI9COJlUadSlQ2QLIlVhxVQpOldhhv5a-89C9DS72ZlZH65qGWtcN0WiUIJSQCTz8Br50Q2jTb4ajHitRSEzQ7yWUMsUYnDfzUM8oLAyC-azSfFWZ2IOV4VDOXLUmV90l4GgFULTU-ECtreOaK1IkKT6P5kuujr3797Wn8GqUFrow0_tHcz29lxNVSCPWvmTjOsT_D34AFweTjA</recordid><startdate>20030901</startdate><enddate>20030901</enddate><creator>Fare, Thomas L</creator><creator>Coffey, Ernest M</creator><creator>Dai, Hongyue</creator><creator>He, Yudong D</creator><creator>Kessler, Deborah A</creator><creator>Kilian, Kristopher A</creator><creator>Koch, John E</creator><creator>LeProust, Eric</creator><creator>Marton, Matthew J</creator><creator>Meyer, Michael R</creator><creator>Stoughton, Roland B</creator><creator>Tokiwa, George Y</creator><creator>Wang, Yanqun</creator><general>American Chemical Society</general><scope>BSCLL</scope><scope>IQODW</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QF</scope><scope>7QO</scope><scope>7QQ</scope><scope>7SC</scope><scope>7SE</scope><scope>7SP</scope><scope>7SR</scope><scope>7TA</scope><scope>7TB</scope><scope>7TM</scope><scope>7U5</scope><scope>7U7</scope><scope>7U9</scope><scope>8BQ</scope><scope>8FD</scope><scope>C1K</scope><scope>F28</scope><scope>FR3</scope><scope>H8D</scope><scope>H8G</scope><scope>H94</scope><scope>JG9</scope><scope>JQ2</scope><scope>KR7</scope><scope>L7M</scope><scope>L~C</scope><scope>L~D</scope><scope>P64</scope><scope>7X8</scope></search><sort><creationdate>20030901</creationdate><title>Effects of Atmospheric Ozone on Microarray Data Quality</title><author>Fare, Thomas L ; Coffey, Ernest M ; Dai, Hongyue ; He, Yudong D ; Kessler, Deborah A ; Kilian, Kristopher A ; Koch, John E ; LeProust, Eric ; Marton, Matthew J ; Meyer, Michael R ; Stoughton, Roland B ; Tokiwa, George Y ; Wang, Yanqun</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-a472t-e245f1d11245c2f56fb2061f630a7ae09ea07ea9de097b316c50aeb1d26b32ad3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2003</creationdate><topic>Analytical, structural and metabolic biochemistry</topic><topic>Atmosphere</topic><topic>Atmosphere - chemistry</topic><topic>Biological and medical sciences</topic><topic>Carbocyanines - chemistry</topic><topic>Desiccation</topic><topic>Dna, deoxyribonucleoproteins</topic><topic>Effects</topic><topic>Fluorescence</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Nucleic acids</topic><topic>Oligonucleotide Array Sequence Analysis - instrumentation</topic><topic>Oligonucleotide Array Sequence Analysis - standards</topic><topic>Ozone</topic><topic>Ozone - analysis</topic><topic>Ozone - chemistry</topic><topic>Quality Control</topic><topic>Reproducibility of Results</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Fare, Thomas L</creatorcontrib><creatorcontrib>Coffey, Ernest M</creatorcontrib><creatorcontrib>Dai, Hongyue</creatorcontrib><creatorcontrib>He, Yudong D</creatorcontrib><creatorcontrib>Kessler, Deborah A</creatorcontrib><creatorcontrib>Kilian, Kristopher A</creatorcontrib><creatorcontrib>Koch, John E</creatorcontrib><creatorcontrib>LeProust, Eric</creatorcontrib><creatorcontrib>Marton, Matthew J</creatorcontrib><creatorcontrib>Meyer, Michael R</creatorcontrib><creatorcontrib>Stoughton, Roland B</creatorcontrib><creatorcontrib>Tokiwa, George Y</creatorcontrib><creatorcontrib>Wang, Yanqun</creatorcontrib><collection>Istex</collection><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Aluminium Industry Abstracts</collection><collection>Biotechnology Research Abstracts</collection><collection>Ceramic Abstracts</collection><collection>Computer and Information Systems Abstracts</collection><collection>Corrosion Abstracts</collection><collection>Electronics & Communications Abstracts</collection><collection>Engineered Materials Abstracts</collection><collection>Materials Business File</collection><collection>Mechanical & Transportation Engineering Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Solid State and Superconductivity Abstracts</collection><collection>Toxicology Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>METADEX</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ANTE: Abstracts in New Technology & Engineering</collection><collection>Engineering Research Database</collection><collection>Aerospace Database</collection><collection>Copper Technical Reference Library</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>Materials Research Database</collection><collection>ProQuest Computer Science Collection</collection><collection>Civil Engineering Abstracts</collection><collection>Advanced Technologies Database with Aerospace</collection><collection>Computer and Information Systems Abstracts Academic</collection><collection>Computer and Information Systems Abstracts Professional</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Analytical chemistry (Washington)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Fare, Thomas L</au><au>Coffey, Ernest M</au><au>Dai, Hongyue</au><au>He, Yudong D</au><au>Kessler, Deborah A</au><au>Kilian, Kristopher A</au><au>Koch, John E</au><au>LeProust, Eric</au><au>Marton, Matthew J</au><au>Meyer, Michael R</au><au>Stoughton, Roland B</au><au>Tokiwa, George Y</au><au>Wang, Yanqun</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Effects of Atmospheric Ozone on Microarray Data Quality</atitle><jtitle>Analytical chemistry (Washington)</jtitle><addtitle>Anal. 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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.</abstract><cop>Washington, DC</cop><pub>American Chemical Society</pub><pmid>14632079</pmid><doi>10.1021/ac034241b</doi><tpages>4</tpages></addata></record> |
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| subjects | Analytical, structural and metabolic biochemistry Atmosphere Atmosphere - chemistry Biological and medical sciences Carbocyanines - chemistry Desiccation Dna, deoxyribonucleoproteins Effects Fluorescence Fundamental and applied biological sciences. Psychology Nucleic acids Oligonucleotide Array Sequence Analysis - instrumentation Oligonucleotide Array Sequence Analysis - standards Ozone Ozone - analysis Ozone - chemistry Quality Control Reproducibility of Results |
| title | Effects of Atmospheric Ozone on Microarray Data Quality |
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