The effects of glass surfaces and probe GC content on signal intensities of a 60-mer diagnostic microarray
Identifieur interne : 000241 ( PascalFrancis/Checkpoint ); précédent : 000240; suivant : 000242The effects of glass surfaces and probe GC content on signal intensities of a 60-mer diagnostic microarray
Auteurs : Xiaoyang Mo [République populaire de Chine] ; Qinghua Wu [République populaire de Chine] ; Junjian Hu [République populaire de Chine] ; Wenli Ma [République populaire de Chine] ; Min Wei [République populaire de Chine] ; Wuzhou Yuan [République populaire de Chine] ; Yuequn Wang [République populaire de Chine] ; Yongqin Li [République populaire de Chine] ; Yun Deng [République populaire de Chine] ; Xiushan Wu [République populaire de Chine]Source :
- Annals of microbiology [ 1590-4261 ] ; 2008.
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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.
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en" level="a">The effects of glass surfaces and probe GC content on signal intensities of a 60-mer diagnostic microarray</title><author><name sortKey="Mo, Xiaoyang" sort="Mo, Xiaoyang" uniqKey="Mo X" first="Xiaoyang" last="Mo">Xiaoyang Mo</name><affiliation wicri:level="1"><inist:fA14 i1="01"><s1>The Center for Heart Development, Key Lab of MOE for Development Biology and Protein Chemistry, College of Life Sciences, Hunan Normal University</s1><s2>Changsha, Hunan 410081</s2><s3>CHN</s3><sZ>1 aut.</sZ><sZ>3 aut.</sZ><sZ>6 aut.</sZ><sZ>7 aut.</sZ><sZ>8 aut.</sZ><sZ>9 aut.</sZ><sZ>10 aut.</sZ></inist:fA14><country>République populaire de Chine</country><wicri:noRegion>Changsha, Hunan 410081</wicri:noRegion></affiliation></author><author><name sortKey="Wu, Qinghua" sort="Wu, Qinghua" uniqKey="Wu Q" first="Qinghua" last="Wu">Qinghua Wu</name><affiliation wicri:level="1"><inist:fA14 i1="02"><s1>Key Lab of Biochip, Southern Medical 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Development Biology and Protein Chemistry, College of Life Sciences, Hunan Normal University</s1><s2>Changsha, Hunan 410081</s2><s3>CHN</s3><sZ>1 aut.</sZ><sZ>3 aut.</sZ><sZ>6 aut.</sZ><sZ>7 aut.</sZ><sZ>8 aut.</sZ><sZ>9 aut.</sZ><sZ>10 aut.</sZ></inist:fA14><country>République populaire de Chine</country><wicri:noRegion>Changsha, Hunan 410081</wicri:noRegion></affiliation></author><author><name sortKey="Wang, Yuequn" sort="Wang, Yuequn" uniqKey="Wang Y" first="Yuequn" last="Wang">Yuequn Wang</name><affiliation wicri:level="1"><inist:fA14 i1="01"><s1>The Center for Heart Development, Key Lab of MOE for Development Biology and Protein Chemistry, College of Life Sciences, Hunan Normal University</s1><s2>Changsha, Hunan 410081</s2><s3>CHN</s3><sZ>1 aut.</sZ><sZ>3 aut.</sZ><sZ>6 aut.</sZ><sZ>7 aut.</sZ><sZ>8 aut.</sZ><sZ>9 aut.</sZ><sZ>10 aut.</sZ></inist:fA14><country>République populaire de Chine</country><wicri:noRegion>Changsha, Hunan 410081</wicri:noRegion></affiliation></author><author><name sortKey="Li, Yongqin" sort="Li, Yongqin" uniqKey="Li Y" first="Yongqin" last="Li">Yongqin Li</name><affiliation wicri:level="1"><inist:fA14 i1="01"><s1>The Center for Heart Development, Key Lab of MOE for Development Biology and Protein Chemistry, College of Life Sciences, Hunan Normal University</s1><s2>Changsha, Hunan 410081</s2><s3>CHN</s3><sZ>1 aut.</sZ><sZ>3 aut.</sZ><sZ>6 aut.</sZ><sZ>7 aut.</sZ><sZ>8 aut.</sZ><sZ>9 aut.</sZ><sZ>10 aut.</sZ></inist:fA14><country>République populaire de Chine</country><wicri:noRegion>Changsha, Hunan 410081</wicri:noRegion></affiliation></author><author><name sortKey="Deng, Yun" sort="Deng, Yun" uniqKey="Deng Y" first="Yun" last="Deng">Yun Deng</name><affiliation wicri:level="1"><inist:fA14 i1="01"><s1>The Center for Heart Development, Key Lab of MOE for Development Biology and Protein Chemistry, College of Life Sciences, Hunan Normal University</s1><s2>Changsha, Hunan 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when="2008">2008</date><idno type="stanalyst">PASCAL 08-0375216 INIST</idno><idno type="RBID">Pascal:08-0375216</idno><idno type="wicri:Area/PascalFrancis/Corpus">000261</idno><idno type="wicri:Area/PascalFrancis/Curation">000727</idno><idno type="wicri:Area/PascalFrancis/Checkpoint">000241</idno><idno type="wicri:explorRef" wicri:stream="PascalFrancis" wicri:step="Checkpoint">000241</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a">The effects of glass surfaces and probe GC content on signal intensities of a 60-mer diagnostic microarray</title><author><name sortKey="Mo, Xiaoyang" sort="Mo, Xiaoyang" uniqKey="Mo X" first="Xiaoyang" last="Mo">Xiaoyang Mo</name><affiliation wicri:level="1"><inist:fA14 i1="01"><s1>The Center for Heart Development, Key Lab of MOE for Development Biology and Protein Chemistry, College of Life Sciences, Hunan Normal University</s1><s2>Changsha, Hunan 410081</s2><s3>CHN</s3><sZ>1 aut.</sZ><sZ>3 aut.</sZ><sZ>6 aut.</sZ><sZ>7 aut.</sZ><sZ>8 aut.</sZ><sZ>9 aut.</sZ><sZ>10 aut.</sZ></inist:fA14><country>République populaire de Chine</country><wicri:noRegion>Changsha, Hunan 410081</wicri:noRegion></affiliation></author><author><name sortKey="Wu, Qinghua" sort="Wu, Qinghua" uniqKey="Wu Q" first="Qinghua" last="Wu">Qinghua Wu</name><affiliation wicri:level="1"><inist:fA14 i1="02"><s1>Key Lab of Biochip, Southern Medical University</s1><s2>Guangzhou, Guangdong 510515</s2><s3>CHN</s3><sZ>2 aut.</sZ><sZ>4 aut.</sZ><sZ>5 aut.</sZ></inist:fA14><country>République populaire de Chine</country><wicri:noRegion>Guangzhou, Guangdong 510515</wicri:noRegion></affiliation></author><author><name sortKey="Hu, Junjian" sort="Hu, Junjian" uniqKey="Hu J" first="Junjian" last="Hu">Junjian Hu</name><affiliation wicri:level="1"><inist:fA14 i1="01"><s1>The Center for Heart Development, Key Lab of MOE for Development Biology and Protein Chemistry, College of Life Sciences, Hunan Normal University</s1><s2>Changsha, Hunan 410081</s2><s3>CHN</s3><sZ>1 aut.</sZ><sZ>3 aut.</sZ><sZ>6 aut.</sZ><sZ>7 aut.</sZ><sZ>8 aut.</sZ><sZ>9 aut.</sZ><sZ>10 aut.</sZ></inist:fA14><country>République populaire de Chine</country><wicri:noRegion>Changsha, Hunan 410081</wicri:noRegion></affiliation></author><author><name sortKey="Ma, Wenli" sort="Ma, Wenli" uniqKey="Ma W" first="Wenli" last="Ma">Wenli Ma</name><affiliation wicri:level="1"><inist:fA14 i1="02"><s1>Key Lab of Biochip, Southern Medical University</s1><s2>Guangzhou, Guangdong 510515</s2><s3>CHN</s3><sZ>2 aut.</sZ><sZ>4 aut.</sZ><sZ>5 aut.</sZ></inist:fA14><country>République populaire de Chine</country><wicri:noRegion>Guangzhou, Guangdong 510515</wicri:noRegion></affiliation></author><author><name sortKey="Wei, Min" sort="Wei, Min" uniqKey="Wei M" first="Min" last="Wei">Min Wei</name><affiliation wicri:level="1"><inist:fA14 i1="02"><s1>Key Lab of Biochip, Southern Medical University</s1><s2>Guangzhou, Guangdong 510515</s2><s3>CHN</s3><sZ>2 aut.</sZ><sZ>4 aut.</sZ><sZ>5 aut.</sZ></inist:fA14><country>République populaire de Chine</country><wicri:noRegion>Guangzhou, Guangdong 510515</wicri:noRegion></affiliation></author><author><name sortKey="Yuan, Wuzhou" sort="Yuan, Wuzhou" uniqKey="Yuan W" first="Wuzhou" last="Yuan">Wuzhou Yuan</name><affiliation wicri:level="1"><inist:fA14 i1="01"><s1>The Center for Heart Development, Key Lab of MOE for Development Biology and Protein Chemistry, College of Life Sciences, Hunan Normal University</s1><s2>Changsha, Hunan 410081</s2><s3>CHN</s3><sZ>1 aut.</sZ><sZ>3 aut.</sZ><sZ>6 aut.</sZ><sZ>7 aut.</sZ><sZ>8 aut.</sZ><sZ>9 aut.</sZ><sZ>10 aut.</sZ></inist:fA14><country>République populaire de Chine</country><wicri:noRegion>Changsha, Hunan 410081</wicri:noRegion></affiliation></author><author><name sortKey="Wang, Yuequn" sort="Wang, Yuequn" uniqKey="Wang Y" first="Yuequn" last="Wang">Yuequn Wang</name><affiliation wicri:level="1"><inist:fA14 i1="01"><s1>The Center for Heart Development, Key Lab of MOE for Development Biology and Protein Chemistry, College of Life Sciences, Hunan Normal University</s1><s2>Changsha, Hunan 410081</s2><s3>CHN</s3><sZ>1 aut.</sZ><sZ>3 aut.</sZ><sZ>6 aut.</sZ><sZ>7 aut.</sZ><sZ>8 aut.</sZ><sZ>9 aut.</sZ><sZ>10 aut.</sZ></inist:fA14><country>République populaire de Chine</country><wicri:noRegion>Changsha, Hunan 410081</wicri:noRegion></affiliation></author><author><name sortKey="Li, Yongqin" sort="Li, Yongqin" uniqKey="Li Y" first="Yongqin" last="Li">Yongqin Li</name><affiliation wicri:level="1"><inist:fA14 i1="01"><s1>The Center for Heart Development, Key Lab of MOE for Development Biology and Protein Chemistry, College of Life Sciences, Hunan Normal University</s1><s2>Changsha, Hunan 410081</s2><s3>CHN</s3><sZ>1 aut.</sZ><sZ>3 aut.</sZ><sZ>6 aut.</sZ><sZ>7 aut.</sZ><sZ>8 aut.</sZ><sZ>9 aut.</sZ><sZ>10 aut.</sZ></inist:fA14><country>République populaire de Chine</country><wicri:noRegion>Changsha, Hunan 410081</wicri:noRegion></affiliation></author><author><name sortKey="Deng, Yun" sort="Deng, Yun" uniqKey="Deng Y" first="Yun" last="Deng">Yun Deng</name><affiliation wicri:level="1"><inist:fA14 i1="01"><s1>The Center for Heart Development, Key Lab of MOE for Development Biology and Protein Chemistry, College of Life Sciences, Hunan Normal University</s1><s2>Changsha, Hunan 410081</s2><s3>CHN</s3><sZ>1 aut.</sZ><sZ>3 aut.</sZ><sZ>6 aut.</sZ><sZ>7 aut.</sZ><sZ>8 aut.</sZ><sZ>9 aut.</sZ><sZ>10 aut.</sZ></inist:fA14><country>République populaire de Chine</country><wicri:noRegion>Changsha, Hunan 410081</wicri:noRegion></affiliation></author><author><name sortKey="Wu, Xiushan" sort="Wu, Xiushan" uniqKey="Wu X" first="Xiushan" last="Wu">Xiushan Wu</name><affiliation wicri:level="1"><inist:fA14 i1="01"><s1>The Center for Heart Development, Key Lab of MOE for Development Biology and Protein Chemistry, College of Life Sciences, Hunan Normal University</s1><s2>Changsha, Hunan 410081</s2><s3>CHN</s3><sZ>1 aut.</sZ><sZ>3 aut.</sZ><sZ>6 aut.</sZ><sZ>7 aut.</sZ><sZ>8 aut.</sZ><sZ>9 aut.</sZ><sZ>10 aut.</sZ></inist:fA14><country>République populaire de Chine</country><wicri:noRegion>Changsha, Hunan 410081</wicri:noRegion></affiliation></author></analytic><series><title level="j" type="main">Annals of microbiology</title><title level="j" type="abbreviated">Ann. microbiol.</title><idno type="ISSN">1590-4261</idno><imprint><date when="2008">2008</date></imprint></series></biblStruct></sourceDesc><seriesStmt><title level="j" type="main">Annals of microbiology</title><title level="j" type="abbreviated">Ann. microbiol.</title><idno type="ISSN">1590-4261</idno></seriesStmt></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Diagnosis</term><term>Glass</term><term>Microarray</term><term>Oligonucleotide</term><term>Probe</term></keywords><keywords scheme="Pascal" xml:lang="fr"><term>Verre</term><term>Sonde</term><term>Diagnostic</term><term>Microréseau</term><term>Oligonucléotide</term></keywords><keywords scheme="Wicri" type="topic" xml:lang="fr"><term>Verre</term></keywords></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><inist><standard h6="B"><pA><fA01 i1="01" i2="1"><s0>1590-4261</s0></fA01><fA03 i2="1"><s0>Ann. microbiol.</s0></fA03><fA05><s2>58</s2></fA05><fA06><s2>2</s2></fA06><fA08 i1="01" i2="1" l="ENG"><s1>The effects of glass surfaces and probe GC content on signal intensities of a 60-mer diagnostic microarray</s1></fA08><fA11 i1="01" i2="1"><s1>MO (Xiaoyang)</s1></fA11><fA11 i1="02" i2="1"><s1>WU (Qinghua)</s1></fA11><fA11 i1="03" i2="1"><s1>HU (Junjian)</s1></fA11><fA11 i1="04" i2="1"><s1>MA (Wenli)</s1></fA11><fA11 i1="05" i2="1"><s1>WEI (Min)</s1></fA11><fA11 i1="06" i2="1"><s1>YUAN (Wuzhou)</s1></fA11><fA11 i1="07" i2="1"><s1>WANG (Yuequn)</s1></fA11><fA11 i1="08" i2="1"><s1>LI (Yongqin)</s1></fA11><fA11 i1="09" i2="1"><s1>DENG (Yun)</s1></fA11><fA11 i1="10" i2="1"><s1>WU (Xiushan)</s1></fA11><fA14 i1="01"><s1>The Center for Heart Development, Key Lab of MOE for Development Biology and Protein Chemistry, College of Life Sciences, Hunan Normal University</s1><s2>Changsha, Hunan 410081</s2><s3>CHN</s3><sZ>1 aut.</sZ><sZ>3 aut.</sZ><sZ>6 aut.</sZ><sZ>7 aut.</sZ><sZ>8 aut.</sZ><sZ>9 aut.</sZ><sZ>10 aut.</sZ></fA14><fA14 i1="02"><s1>Key Lab of Biochip, Southern Medical University</s1><s2>Guangzhou, Guangdong 510515</s2><s3>CHN</s3><sZ>2 aut.</sZ><sZ>4 aut.</sZ><sZ>5 aut.</sZ></fA14><fA20><s1>313-318</s1></fA20><fA21><s1>2008</s1></fA21><fA23 i1="01"><s0>ENG</s0></fA23><fA43 i1="01"><s1>INIST</s1><s2>5126</s2><s5>354000197674750240</s5></fA43><fA44><s0>0000</s0><s1>© 2008 INIST-CNRS. All rights reserved.</s1></fA44><fA45><s0>1/2 p.</s0></fA45><fA47 i1="01" i2="1"><s0>08-0375216</s0></fA47><fA60><s1>P</s1></fA60><fA61><s0>A</s0></fA61><fA64 i1="01" i2="1"><s0>Annals of microbiology</s0></fA64><fA66 i1="01"><s0>ITA</s0></fA66><fC01 i1="01" l="ENG"><s0>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.</s0></fC01><fC02 i1="01" i2="X"><s0>002A05</s0></fC02><fC03 i1="01" i2="X" l="FRE"><s0>Verre</s0><s5>01</s5></fC03><fC03 i1="01" i2="X" l="ENG"><s0>Glass</s0><s5>01</s5></fC03><fC03 i1="01" i2="X" l="SPA"><s0>Vidrio</s0><s5>01</s5></fC03><fC03 i1="02" i2="X" l="FRE"><s0>Sonde</s0><s5>02</s5></fC03><fC03 i1="02" i2="X" l="ENG"><s0>Probe</s0><s5>02</s5></fC03><fC03 i1="02" i2="X" l="SPA"><s0>Sonda</s0><s5>02</s5></fC03><fC03 i1="03" i2="X" l="FRE"><s0>Diagnostic</s0><s5>10</s5></fC03><fC03 i1="03" i2="X" l="ENG"><s0>Diagnosis</s0><s5>10</s5></fC03><fC03 i1="03" i2="X" l="SPA"><s0>Diagnóstico</s0><s5>10</s5></fC03><fC03 i1="04" i2="X" l="FRE"><s0>Microréseau</s0><s5>11</s5></fC03><fC03 i1="04" i2="X" l="ENG"><s0>Microarray</s0><s5>11</s5></fC03><fC03 i1="04" i2="X" l="SPA"><s0>Microarreglo</s0><s5>11</s5></fC03><fC03 i1="05" i2="X" l="FRE"><s0>Oligonucléotide</s0><s5>12</s5></fC03><fC03 i1="05" i2="X" l="ENG"><s0>Oligonucleotide</s0><s5>12</s5></fC03><fC03 i1="05" i2="X" l="SPA"><s0>Oligonucleótido</s0><s5>12</s5></fC03><fN21><s1>238</s1></fN21><fN44 i1="01"><s1>OTO</s1></fN44><fN82><s1>OTO</s1></fN82></pA></standard></inist><affiliations><list><country><li>République populaire de Chine</li></country></list><tree><country name="République populaire de Chine"><noRegion><name sortKey="Mo, Xiaoyang" sort="Mo, Xiaoyang" uniqKey="Mo X" first="Xiaoyang" last="Mo">Xiaoyang Mo</name></noRegion><name sortKey="Deng, Yun" sort="Deng, Yun" uniqKey="Deng Y" first="Yun" last="Deng">Yun Deng</name><name sortKey="Hu, Junjian" sort="Hu, Junjian" uniqKey="Hu J" first="Junjian" last="Hu">Junjian Hu</name><name sortKey="Li, Yongqin" sort="Li, Yongqin" uniqKey="Li Y" first="Yongqin" last="Li">Yongqin Li</name><name sortKey="Ma, Wenli" sort="Ma, Wenli" uniqKey="Ma W" first="Wenli" last="Ma">Wenli Ma</name><name sortKey="Wang, Yuequn" sort="Wang, Yuequn" uniqKey="Wang Y" first="Yuequn" last="Wang">Yuequn Wang</name><name sortKey="Wei, Min" sort="Wei, Min" uniqKey="Wei M" first="Min" last="Wei">Min Wei</name><name sortKey="Wu, Qinghua" sort="Wu, Qinghua" uniqKey="Wu Q" first="Qinghua" last="Wu">Qinghua Wu</name><name sortKey="Wu, Xiushan" sort="Wu, Xiushan" uniqKey="Wu X" first="Xiushan" last="Wu">Xiushan Wu</name><name sortKey="Yuan, Wuzhou" sort="Yuan, Wuzhou" uniqKey="Yuan W" first="Wuzhou" last="Yuan">Wuzhou Yuan</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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