Assessing unmodified 70-mer oligonucleotide probe performance on glass-slide microarrays
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Auteurs : Hong-Ying Wang [États-Unis] ; Renae L. Malek [États-Unis] ; Anne E. Kwitek [États-Unis] ; Andrew S. Greene [États-Unis] ; Truong V. Luu [États-Unis] ; Babak Behbahani [États-Unis] ; Bryan Frank [États-Unis] ; John Quackenbush [États-Unis] ; Norman H. Lee [États-Unis]Source :
- Genome Biology [ 1465-6906 ] ; 2003.
Abstract
Long oligonucleotide microarrays are potentially more cost- and management efficient than cDNA microarrays. Unmodified sense and antisense 70-mer oligonucleotides were synthesized and compared with PCR-amplified cDNA clones corresponding to the same genes. The correlation coefficient between oligonucleotide and cDNA probes for identifying differentially expressed genes was 0.80.
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PubMed: 12540297
PubMed Central: 151289
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Lee</name><affiliation wicri:level="1"><nlm:aff id="I1">The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="I3">Department of Pharmacology, The George Washington University Medical Center, 2300 Eye Street NW, Washington, DC 20037, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Pharmacology, The George Washington University Medical Center, 2300 Eye Street NW, Washington, DC 20037</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">12540297</idno><idno type="pmc">151289</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC151289</idno><idno type="RBID">PMC:151289</idno><date when="2003">2003</date><idno type="wicri:Area/Pmc/Corpus">000557</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000557</idno><idno type="wicri:Area/Pmc/Curation">000557</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000557</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Assessing unmodified 70-mer oligonucleotide probe performance on glass-slide microarrays</title><author><name sortKey="Wang, Hong Ying" sort="Wang, Hong Ying" uniqKey="Wang H" first="Hong-Ying" last="Wang">Hong-Ying Wang</name><affiliation wicri:level="1"><nlm:aff id="I1">The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850</wicri:regionArea></affiliation></author><author><name sortKey="Malek, Renae L" sort="Malek, Renae L" uniqKey="Malek R" first="Renae L" last="Malek">Renae L. Malek</name><affiliation wicri:level="1"><nlm:aff id="I1">The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850</wicri:regionArea></affiliation></author><author><name sortKey="Kwitek, Anne E" sort="Kwitek, Anne E" uniqKey="Kwitek A" first="Anne E" last="Kwitek">Anne E. Kwitek</name><affiliation wicri:level="1"><nlm:aff id="I2">Department of Physiology, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Physiology, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226</wicri:regionArea></affiliation></author><author><name sortKey="Greene, Andrew S" sort="Greene, Andrew S" uniqKey="Greene A" first="Andrew S" last="Greene">Andrew S. Greene</name><affiliation wicri:level="1"><nlm:aff id="I2">Department of Physiology, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Physiology, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226</wicri:regionArea></affiliation></author><author><name sortKey="Luu, Truong V" sort="Luu, Truong V" uniqKey="Luu T" first="Truong V" last="Luu">Truong V. Luu</name><affiliation wicri:level="1"><nlm:aff id="I1">The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850</wicri:regionArea></affiliation></author><author><name sortKey="Behbahani, Babak" sort="Behbahani, Babak" uniqKey="Behbahani B" first="Babak" last="Behbahani">Babak Behbahani</name><affiliation wicri:level="1"><nlm:aff id="I1">The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850</wicri:regionArea></affiliation></author><author><name sortKey="Frank, Bryan" sort="Frank, Bryan" uniqKey="Frank B" first="Bryan" last="Frank">Bryan Frank</name><affiliation wicri:level="1"><nlm:aff id="I1">The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850</wicri:regionArea></affiliation></author><author><name sortKey="Quackenbush, John" sort="Quackenbush, John" uniqKey="Quackenbush J" first="John" last="Quackenbush">John Quackenbush</name><affiliation wicri:level="1"><nlm:aff id="I1">The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850</wicri:regionArea></affiliation></author><author><name sortKey="Lee, Norman H" sort="Lee, Norman H" uniqKey="Lee N" first="Norman H" last="Lee">Norman H. Lee</name><affiliation wicri:level="1"><nlm:aff id="I1">The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="I3">Department of Pharmacology, The George Washington University Medical Center, 2300 Eye Street NW, Washington, DC 20037, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Pharmacology, The George Washington University Medical Center, 2300 Eye Street NW, Washington, DC 20037</wicri:regionArea></affiliation></author></analytic><series><title level="j">Genome Biology</title><idno type="ISSN">1465-6906</idno><idno type="eISSN">1465-6914</idno><imprint><date when="2003">2003</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Long oligonucleotide microarrays are potentially more cost- and management efficient than cDNA microarrays. Unmodified sense and antisense 70-mer oligonucleotides were synthesized and compared with PCR-amplified cDNA clones corresponding to the same genes. The correlation coefficient between oligonucleotide and cDNA probes for identifying differentially expressed genes was 0.80.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct></listBibl></div1></back></TEI><pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Genome Biol</journal-id><journal-title>Genome Biology</journal-title><issn pub-type="ppub">1465-6906</issn><issn pub-type="epub">1465-6914</issn><publisher><publisher-name>BioMed Central</publisher-name><publisher-loc>London</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">12540297</article-id><article-id pub-id-type="pmc">151289</article-id><article-id pub-id-type="publisher-id">gb-2003-4-1-r5</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research</subject></subj-group></article-categories><title-group><article-title>Assessing unmodified 70-mer oligonucleotide probe performance on glass-slide microarrays</article-title></title-group><contrib-group><contrib id="A1" contrib-type="author"><name><surname>Wang</surname><given-names>Hong-Ying</given-names></name><xref ref-type="aff" rid="I1">1</xref></contrib><contrib id="A2" contrib-type="author"><name><surname>Malek</surname><given-names>Renae L</given-names></name><xref ref-type="aff" rid="I1">1</xref></contrib><contrib id="A3" contrib-type="author"><name><surname>Kwitek</surname><given-names>Anne E</given-names></name><xref ref-type="aff" rid="I2">2</xref></contrib><contrib id="A4" contrib-type="author"><name><surname>Greene</surname><given-names>Andrew S</given-names></name><xref ref-type="aff" rid="I2">2</xref></contrib><contrib id="A5" contrib-type="author"><name><surname>Luu</surname><given-names>Truong V</given-names></name><xref ref-type="aff" rid="I1">1</xref></contrib><contrib id="A6" contrib-type="author"><name><surname>Behbahani</surname><given-names>Babak</given-names></name><xref ref-type="aff" rid="I1">1</xref></contrib><contrib id="A7" contrib-type="author"><name><surname>Frank</surname><given-names>Bryan</given-names></name><xref ref-type="aff" rid="I1">1</xref></contrib><contrib id="A8" contrib-type="author"><name><surname>Quackenbush</surname><given-names>John</given-names></name><xref ref-type="aff" rid="I1">1</xref></contrib><contrib id="A9" corresp="yes" contrib-type="author"><name><surname>Lee</surname><given-names>Norman H</given-names></name><xref ref-type="aff" rid="I1">1</xref><xref ref-type="aff" rid="I3">3</xref><email>nhlee@tigr.org</email></contrib></contrib-group><aff id="I1"><label>1</label>The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA</aff><aff id="I2"><label>2</label>Department of Physiology, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA</aff><aff id="I3"><label>3</label>Department of Pharmacology, The George Washington University Medical Center, 2300 Eye Street NW, Washington, DC 20037, USA</aff><aff>Correspondence: Norman H Lee. E-mail: nhlee@tigr.org</aff><pub-date pub-type="ppub"><year>2003</year></pub-date><pub-date pub-type="epub"><day>6</day><month>1</month><year>2003</year></pub-date><volume>4</volume><issue>1</issue><fpage>R5</fpage><lpage>R5</lpage><ext-link ext-link-type="uri" xlink:href="http://genomebiology.com/2003/4/1/R5"></ext-link><history><date date-type="received"><day>14</day><month>8</month><year>2002</year></date><date date-type="rev-recd"><day>17</day><month>10</month><year>2002</year></date><date date-type="accepted"><day>8</day><month>11</month><year>2002</year></date></history><copyright-statement>Copyright © 2003 Wang et al.; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original URL.</copyright-statement><abstract abstract-type="short"><p>Long oligonucleotide microarrays are potentially more cost- and management efficient than cDNA microarrays. Unmodified sense and antisense 70-mer oligonucleotides were synthesized and compared with PCR-amplified cDNA clones corresponding to the same genes. The correlation coefficient between oligonucleotide and cDNA probes for identifying differentially expressed genes was 0.80.</p></abstract><abstract><sec><title>Background</title><p>Long oligonucleotide microarrays are potentially more cost- and management-efficient than cDNA microarrays, but there is little information on the relative performance of these two probe types. The feasibility of using unmodified oligonucleotides to accurately measure changes in gene expression is also unclear.</p></sec><sec><title>Results</title><p>Unmodified sense and antisense 70-mer oligonucleotides representing 75 known rat genes and 10 <italic>Arabidopsis </italic>control genes were synthesized, printed and UV cross-linked onto glass slides. Printed alongside were PCR-amplified cDNA clones corresponding to the same genes, enabling us to compare the two probe types simultaneously. Our study was designed to evaluate the mRNA profiles of heart and brain, along with <italic>Arabidopsis </italic>cRNA spiked into the labeling reaction at different relative copy number. Hybridization signal intensity did not correlate with probe type but depended on the extent of UV irradiation. To determine the effect of oligonucleotide concentration on hybridization signal, 70-mers were serially diluted. No significant change in gene-expression ratio or loss in hybridization signal was detected, even at the lowest concentration tested (6.25 μm). In many instances, signal intensity actually increased with decreasing concentration. The correlation coefficient between oligonucleotide and cDNA probes for identifying differentially expressed genes was 0.80, with an average coefficient of variation of 13.4%. Approximately 8% of the genes showed discordant results with the two probe types, and in each case the cDNA results were more accurate, as determined by real-time PCR.</p></sec><sec><title>Conclusions</title><p>Microarrays of UV cross-linked unmodified oligonucleotides provided sensitive and specific measurements for most of the genes studied.</p></sec></abstract></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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