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The effects of glass surfaces and probe GC content on signal intensities of a 60-mer diagnostic microarray

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 gr...

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Autores principales: Mo, Xiaoyang, Wu, Qinghua, Hu, Junjian, Ma, Wenli, Wei, Min, Yuan, Wuzhou, Wang, Yuequn, Li, Yongqin, Deng, Yun, Wu, Xiushan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer-Verlag 2008
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7097383/
https://www.ncbi.nlm.nih.gov/pubmed/32226355
http://dx.doi.org/10.1007/BF03175336
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author Mo, Xiaoyang
Wu, Qinghua
Hu, Junjian
Ma, Wenli
Wei, Min
Yuan, Wuzhou
Wang, Yuequn
Li, Yongqin
Deng, Yun
Wu, Xiushan
author_facet Mo, Xiaoyang
Wu, Qinghua
Hu, Junjian
Ma, Wenli
Wei, Min
Yuan, Wuzhou
Wang, Yuequn
Li, Yongqin
Deng, Yun
Wu, Xiushan
author_sort Mo, Xiaoyang
collection PubMed
description 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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spelling pubmed-70973832020-03-26 The effects of glass surfaces and probe GC content on signal intensities of a 60-mer diagnostic microarray Mo, Xiaoyang Wu, Qinghua Hu, Junjian Ma, Wenli Wei, Min Yuan, Wuzhou Wang, Yuequn Li, Yongqin Deng, Yun Wu, Xiushan Ann Microbiol Methods 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. Springer-Verlag 2008 /pmc/articles/PMC7097383/ /pubmed/32226355 http://dx.doi.org/10.1007/BF03175336 Text en © University of Milan and Springer 2008 This article is made available via the PMC Open Access Subset for unrestricted research re-use and secondary analysis in any form or by any means with acknowledgement of the original source. These permissions are granted for the duration of the World Health Organization (WHO) declaration of COVID-19 as a global pandemic.
spellingShingle Methods
Mo, Xiaoyang
Wu, Qinghua
Hu, Junjian
Ma, Wenli
Wei, Min
Yuan, Wuzhou
Wang, Yuequn
Li, Yongqin
Deng, Yun
Wu, Xiushan
The effects of glass surfaces and probe GC content on signal intensities of a 60-mer diagnostic microarray
title The effects of glass surfaces and probe GC content on signal intensities of a 60-mer diagnostic microarray
title_full The effects of glass surfaces and probe GC content on signal intensities of a 60-mer diagnostic microarray
title_fullStr The effects of glass surfaces and probe GC content on signal intensities of a 60-mer diagnostic microarray
title_full_unstemmed The effects of glass surfaces and probe GC content on signal intensities of a 60-mer diagnostic microarray
title_short The effects of glass surfaces and probe GC content on signal intensities of a 60-mer diagnostic microarray
title_sort effects of glass surfaces and probe gc content on signal intensities of a 60-mer diagnostic microarray
topic Methods
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7097383/
https://www.ncbi.nlm.nih.gov/pubmed/32226355
http://dx.doi.org/10.1007/BF03175336
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