The effects of glass surfaces and probe GC content on signal intensities of a 60-mer diagnostic microarray.
Identifieur interne : 003625 ( Ncbi/Merge ); précédent : 003624; suivant : 003626The effects of glass surfaces and probe GC content on signal intensities of a 60-mer diagnostic microarray.
Auteurs : Xiaoyang Mo ; Qinghua Wu [République populaire de Chine] ; Junjian Hu ; Wenli Ma [République populaire de Chine] ; Min Wei [République populaire de Chine] ; Wuzhou Yuan ; Yuequn Wang ; Yongqin Li ; Yun Deng ; Xiushan WuSource :
- Annals of microbiology [ 1590-4261 ] ; 2008.
Abstract
The effects of glass surfaces and probe GC content on signal intensities of a 60-mer diagnostic microarray were studied. Twelve virus-specific oligonucleotide probes for severe acute respiratory syndrome coronavirus (SARS-CoV) were divided into a high GC content group (≥ 50%) and a low GC content group (< 50%), and spotted onto four different chemically-modified glass surfaces: a poly-amine coating activated by 1,4-phenylene diisothiocyanate (Poly-Amine surface), an acrylic acid-co-acrylamide copolymer coating activated by 1-(3-dimethylamino propyl)-3-ethylcarbodiimide hydrochloride and N-hydroxysuccinimide (AACA-Copolymer surface), a commercial Corning CMT-GAPS amino surface, and a Telechem SuperAmine amino surface. RNA samples from cultured SARS-CoV strain were labelled using direct cDNA labelling with restriction display in a single colour format. The background-subtracted signal intensities were analysed using two-way analysis of variance. The effects of glass surfaces on background-subtracted signal intensities were significant (p=0.003). Multiple comparisons showed that differences existed mainly between the AACA-Copolymer surface and the other glass surfaces, and that the AACA-Copolymer surface had the highest background-subtracted signal intensity. The probe GC content had no significant effect on signal intensities in the narrow range of GC content represented (p=0.07). The results suggested that the AACA-Copolymer surface may be a novel choice of microorganism survey based on long oligonucleotide microarray.
DOI: 10.1007/BF03175336
PubMed: 32226355
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sortKey="Yuan, Wuzhou" sort="Yuan, Wuzhou" uniqKey="Yuan W" first="Wuzhou" last="Yuan">Wuzhou Yuan</name><affiliation><nlm:affiliation>1The Center for Heart Development, Key Lab of MOE for Development Biology and Protein Chemistry, College of Life Sciences, Hunan Normal University, 410081 Changsha, Human.</nlm:affiliation><wicri:noCountry code="subField">Human</wicri:noCountry></affiliation></author><author><name sortKey="Wang, Yuequn" sort="Wang, Yuequn" uniqKey="Wang Y" first="Yuequn" last="Wang">Yuequn Wang</name><affiliation><nlm:affiliation>1The Center for Heart Development, Key Lab of MOE for Development Biology and Protein Chemistry, College of Life Sciences, Hunan Normal University, 410081 Changsha, Human.</nlm:affiliation><wicri:noCountry code="subField">Human</wicri:noCountry></affiliation></author><author><name sortKey="Li, Yongqin" sort="Li, Yongqin" uniqKey="Li Y" first="Yongqin" last="Li">Yongqin Li</name><affiliation><nlm:affiliation>1The Center for Heart Development, Key Lab of MOE for Development Biology and Protein Chemistry, College of Life Sciences, Hunan Normal University, 410081 Changsha, Human.</nlm:affiliation><wicri:noCountry code="subField">Human</wicri:noCountry></affiliation></author><author><name sortKey="Deng, Yun" sort="Deng, Yun" uniqKey="Deng Y" first="Yun" last="Deng">Yun Deng</name><affiliation><nlm:affiliation>1The Center for Heart Development, Key Lab of MOE for Development Biology and Protein Chemistry, College of Life Sciences, Hunan Normal University, 410081 Changsha, Human.</nlm:affiliation><wicri:noCountry code="subField">Human</wicri:noCountry></affiliation></author><author><name sortKey="Wu, Xiushan" sort="Wu, Xiushan" uniqKey="Wu X" first="Xiushan" last="Wu">Xiushan Wu</name><affiliation><nlm:affiliation>1The Center for Heart Development, Key Lab of MOE for Development Biology and Protein Chemistry, College of Life Sciences, Hunan Normal University, 410081 Changsha, Human.</nlm:affiliation><wicri:noCountry code="subField">Human</wicri:noCountry></affiliation></author></analytic><series><title level="j">Annals of microbiology</title><idno type="ISSN">1590-4261</idno><imprint><date when="2008" type="published">2008</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The effects of glass surfaces and probe GC content on signal intensities of a 60-mer diagnostic microarray were studied. Twelve virus-specific oligonucleotide probes for severe acute respiratory syndrome coronavirus (SARS-CoV) were divided into a high GC content group (≥ 50%) and a low GC content group (< 50%), and spotted onto four different chemically-modified glass surfaces: a poly-amine coating activated by 1,4-phenylene diisothiocyanate (Poly-Amine surface), an acrylic acid-co-acrylamide copolymer coating activated by 1-(3-dimethylamino propyl)-3-ethylcarbodiimide hydrochloride and N-hydroxysuccinimide (AACA-Copolymer surface), a commercial Corning CMT-GAPS amino surface, and a Telechem SuperAmine amino surface. RNA samples from cultured SARS-CoV strain were labelled using direct cDNA labelling with restriction display in a single colour format. The background-subtracted signal intensities were analysed using two-way analysis of variance. The effects of glass surfaces on background-subtracted signal intensities were significant (p=0.003). Multiple comparisons showed that differences existed mainly between the AACA-Copolymer surface and the other glass surfaces, and that the AACA-Copolymer surface had the highest background-subtracted signal intensity. The probe GC content had no significant effect on signal intensities in the narrow range of GC content represented (p=0.07). The results suggested that the AACA-Copolymer surface may be a novel choice of microorganism survey based on long oligonucleotide microarray.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">32226355</PMID><DateRevised><Year>2020</Year><Month>04</Month><Day>03</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Print">1590-4261</ISSN><JournalIssue CitedMedium="Print"><Volume>58</Volume><Issue>2</Issue><PubDate><Year>2008</Year></PubDate></JournalIssue><Title>Annals of microbiology</Title><ISOAbbreviation>Ann. Microbiol.</ISOAbbreviation></Journal><ArticleTitle>The effects of glass surfaces and probe GC content on signal intensities of a 60-mer diagnostic microarray.</ArticleTitle><Pagination><MedlinePgn>313</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1007/BF03175336</ELocationID><Abstract><AbstractText>The effects of glass surfaces and probe GC content on signal intensities of a 60-mer diagnostic microarray were studied. Twelve virus-specific oligonucleotide probes for severe acute respiratory syndrome coronavirus (SARS-CoV) were divided into a high GC content group (≥ 50%) and a low GC content group (< 50%), and spotted onto four different chemically-modified glass surfaces: a poly-amine coating activated by 1,4-phenylene diisothiocyanate (Poly-Amine surface), an acrylic acid-co-acrylamide copolymer coating activated by 1-(3-dimethylamino propyl)-3-ethylcarbodiimide hydrochloride and N-hydroxysuccinimide (AACA-Copolymer surface), a commercial Corning CMT-GAPS amino surface, and a Telechem SuperAmine amino surface. RNA samples from cultured SARS-CoV strain were labelled using direct cDNA labelling with restriction display in a single colour format. The background-subtracted signal intensities were analysed using two-way analysis of variance. The effects of glass surfaces on background-subtracted signal intensities were significant (p=0.003). Multiple comparisons showed that differences existed mainly between the AACA-Copolymer surface and the other glass surfaces, and that the AACA-Copolymer surface had the highest background-subtracted signal intensity. The probe GC content had no significant effect on signal intensities in the narrow range of GC content represented (p=0.07). The results suggested that the AACA-Copolymer surface may be a novel choice of microorganism survey based on long oligonucleotide microarray.</AbstractText><CopyrightInformation>© University of Milan and Springer 2008.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Mo</LastName><ForeName>Xiaoyang</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>1The Center for Heart Development, Key Lab of MOE for Development Biology and Protein Chemistry, College of Life Sciences, Hunan Normal University, 410081 Changsha, Human.</Affiliation><Identifier Source="GRID">grid.411427.5</Identifier><Identifier Source="ISNI">0000000100893695</Identifier></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wu</LastName><ForeName>Qinghua</ForeName><Initials>Q</Initials><AffiliationInfo><Affiliation>2Key Lab of Biochip, Southern Medical University, 510515 Guangzhou, Guangdong, China.</Affiliation><Identifier Source="GRID">grid.284723.8</Identifier><Identifier Source="ISNI">0000000088777471</Identifier></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hu</LastName><ForeName>Junjian</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>1The Center for Heart Development, Key Lab of MOE for Development Biology and Protein Chemistry, College of Life Sciences, Hunan Normal University, 410081 Changsha, Human.</Affiliation><Identifier Source="GRID">grid.411427.5</Identifier><Identifier Source="ISNI">0000000100893695</Identifier></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ma</LastName><ForeName>Wenli</ForeName><Initials>W</Initials><AffiliationInfo><Affiliation>2Key Lab of Biochip, Southern Medical University, 510515 Guangzhou, Guangdong, China.</Affiliation><Identifier Source="GRID">grid.284723.8</Identifier><Identifier Source="ISNI">0000000088777471</Identifier></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wei</LastName><ForeName>Min</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>2Key Lab of Biochip, Southern Medical University, 510515 Guangzhou, Guangdong, China.</Affiliation><Identifier Source="GRID">grid.284723.8</Identifier><Identifier Source="ISNI">0000000088777471</Identifier></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yuan</LastName><ForeName>Wuzhou</ForeName><Initials>W</Initials><AffiliationInfo><Affiliation>1The Center for Heart Development, Key Lab of MOE for Development Biology and Protein Chemistry, College of Life Sciences, Hunan Normal University, 410081 Changsha, Human.</Affiliation><Identifier Source="GRID">grid.411427.5</Identifier><Identifier Source="ISNI">0000000100893695</Identifier></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Yuequn</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>1The Center for Heart Development, Key Lab of MOE for Development Biology and Protein Chemistry, College of Life Sciences, Hunan Normal University, 410081 Changsha, Human.</Affiliation><Identifier Source="GRID">grid.411427.5</Identifier><Identifier Source="ISNI">0000000100893695</Identifier></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Yongqin</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>1The Center for Heart Development, Key Lab of MOE for Development Biology and Protein Chemistry, College of Life Sciences, Hunan Normal University, 410081 Changsha, Human.</Affiliation><Identifier Source="GRID">grid.411427.5</Identifier><Identifier Source="ISNI">0000000100893695</Identifier></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Deng</LastName><ForeName>Yun</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>1The Center for Heart Development, Key Lab of MOE for Development Biology and Protein Chemistry, College of Life Sciences, Hunan Normal University, 410081 Changsha, Human.</Affiliation><Identifier Source="GRID">grid.411427.5</Identifier><Identifier Source="ISNI">0000000100893695</Identifier></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wu</LastName><ForeName>Xiushan</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>1The Center for Heart Development, Key Lab of MOE for Development Biology and Protein Chemistry, College of Life Sciences, Hunan Normal University, 410081 Changsha, Human.</Affiliation><Identifier Source="GRID">grid.411427.5</Identifier><Identifier Source="ISNI">0000000100893695</Identifier></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>Italy</Country><MedlineTA>Ann Microbiol</MedlineTA><NlmUniqueID>100959580</NlmUniqueID><ISSNLinking>1590-4261</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">ANOVA</Keyword><Keyword MajorTopicYN="N">diagnostic microarray</Keyword><Keyword MajorTopicYN="N">glass surfaces</Keyword><Keyword MajorTopicYN="N">oligonucleotide probe</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>4</Month><Day>1</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2008</Year><Month>1</Month><Day>1</Day><Hour>0</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2008</Year><Month>1</Month><Day>1</Day><Hour>0</Hour><Minute>1</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">32226355</ArticleId><ArticleId IdType="doi">10.1007/BF03175336</ArticleId><ArticleId IdType="pii">BF03175336</ArticleId><ArticleId IdType="pmc">PMC7097383</ArticleId></ArticleIdList><pmc-dir>pmcsd</pmc-dir>
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