A general framework for designing and validating oligomer-based DNA microarrays and its application to Clostridium acetobutylicum.
Identifieur interne : 002184 ( PubMed/Curation ); précédent : 002183; suivant : 002185A general framework for designing and validating oligomer-based DNA microarrays and its application to Clostridium acetobutylicum.
Auteurs : Carlos J. Paredes [États-Unis] ; Ryan S. Senger ; Iwona S. Spath ; Jacob R. Borden ; Ryan Sillers ; Eleftherios T. PapoutsakisSource :
- Applied and environmental microbiology [ 0099-2240 ] ; 2007.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : Oligonucleotide Probes.
- genetics : Clostridium acetobutylicum.
- methods : Gene Expression Profiling, Oligonucleotide Array Sequence Analysis.
- Nucleic Acid Hybridization, Sensitivity and Specificity.
Abstract
While DNA microarray analysis is widely accepted as an essential tool for modern biology, its use still eludes many researchers for several reasons, especially when microarrays are not commercially available. In that case, the design, construction, and use of microarrays for a sequenced organism constitute substantial, time-consuming, and expensive tasks. Recently, it has become possible to construct custom microarrays using industrial manufacturing processes, which offer several advantages, including speed of manufacturing, quality control, no up-front setup costs, and need-based microarray ordering. Here, we describe a strategy for designing and validating DNA microarrays manufactured using a commercial process. The 22K microarrays for the solvent producer Clostridium acetobutylicum ATCC 824 are based on in situ-synthesized 60-mers employing the Agilent technology. The strategy involves designing a large library of possible oligomer probes for each target (i.e., gene or DNA sequence) and experimentally testing and selecting the best probes for each target. The degenerate C. acetobutylicum strain M5 lacking the pSOL1 megaplasmid (with 178 annotated open reading frames [genes]) was used to estimate the level of probe cross-hybridization in the new microarrays and to establish the minimum intensity for a gene to be considered expressed. Results obtained using this microarray design were consistent with previously reported results from spotted cDNA-based microarrays. The proposed strategy is applicable to any sequenced organism.
DOI: 10.1128/AEM.00144-07
PubMed: 17526797
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Borden</name></author><author><name sortKey="Sillers, Ryan" sort="Sillers, Ryan" uniqKey="Sillers R" first="Ryan" last="Sillers">Ryan Sillers</name></author><author><name sortKey="Papoutsakis, Eleftherios T" sort="Papoutsakis, Eleftherios T" uniqKey="Papoutsakis E" first="Eleftherios T" last="Papoutsakis">Eleftherios T. Papoutsakis</name></author></analytic><series><title level="j">Applied and environmental microbiology</title><idno type="ISSN">0099-2240</idno><imprint><date when="2007" type="published">2007</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Clostridium acetobutylicum (genetics)</term><term>Gene Expression Profiling (methods)</term><term>Nucleic Acid Hybridization</term><term>Oligonucleotide Array Sequence Analysis (methods)</term><term>Oligonucleotide Probes (genetics)</term><term>Sensitivity and Specificity</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de profil d'expression de gènes ()</term><term>Clostridium acetobutylicum (génétique)</term><term>Hybridation d'acides nucléiques</term><term>Sensibilité et spécificité</term><term>Sondes oligonucléotidiques (génétique)</term><term>Séquençage par oligonucléotides en batterie ()</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Oligonucleotide Probes</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Clostridium acetobutylicum</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Clostridium acetobutylicum</term><term>Sondes oligonucléotidiques</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Gene Expression Profiling</term><term>Oligonucleotide Array Sequence Analysis</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Nucleic Acid Hybridization</term><term>Sensitivity and Specificity</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de profil d'expression de gènes</term><term>Hybridation d'acides nucléiques</term><term>Sensibilité et spécificité</term><term>Séquençage par oligonucléotides en batterie</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">While DNA microarray analysis is widely accepted as an essential tool for modern biology, its use still eludes many researchers for several reasons, especially when microarrays are not commercially available. In that case, the design, construction, and use of microarrays for a sequenced organism constitute substantial, time-consuming, and expensive tasks. Recently, it has become possible to construct custom microarrays using industrial manufacturing processes, which offer several advantages, including speed of manufacturing, quality control, no up-front setup costs, and need-based microarray ordering. Here, we describe a strategy for designing and validating DNA microarrays manufactured using a commercial process. The 22K microarrays for the solvent producer Clostridium acetobutylicum ATCC 824 are based on in situ-synthesized 60-mers employing the Agilent technology. The strategy involves designing a large library of possible oligomer probes for each target (i.e., gene or DNA sequence) and experimentally testing and selecting the best probes for each target. The degenerate C. acetobutylicum strain M5 lacking the pSOL1 megaplasmid (with 178 annotated open reading frames [genes]) was used to estimate the level of probe cross-hybridization in the new microarrays and to establish the minimum intensity for a gene to be considered expressed. Results obtained using this microarray design were consistent with previously reported results from spotted cDNA-based microarrays. The proposed strategy is applicable to any sequenced organism.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">17526797</PMID><DateCompleted><Year>2007</Year><Month>09</Month><Day>04</Day></DateCompleted><DateRevised><Year>2019</Year><Month>12</Month><Day>10</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">0099-2240</ISSN><JournalIssue CitedMedium="Print"><Volume>73</Volume><Issue>14</Issue><PubDate><Year>2007</Year><Month>Jul</Month></PubDate></JournalIssue><Title>Applied and environmental microbiology</Title><ISOAbbreviation>Appl. Environ. Microbiol.</ISOAbbreviation></Journal><ArticleTitle>A general framework for designing and validating oligomer-based DNA microarrays and its application to Clostridium acetobutylicum.</ArticleTitle><Pagination><MedlinePgn>4631-8</MedlinePgn></Pagination><Abstract><AbstractText>While DNA microarray analysis is widely accepted as an essential tool for modern biology, its use still eludes many researchers for several reasons, especially when microarrays are not commercially available. In that case, the design, construction, and use of microarrays for a sequenced organism constitute substantial, time-consuming, and expensive tasks. Recently, it has become possible to construct custom microarrays using industrial manufacturing processes, which offer several advantages, including speed of manufacturing, quality control, no up-front setup costs, and need-based microarray ordering. Here, we describe a strategy for designing and validating DNA microarrays manufactured using a commercial process. The 22K microarrays for the solvent producer Clostridium acetobutylicum ATCC 824 are based on in situ-synthesized 60-mers employing the Agilent technology. The strategy involves designing a large library of possible oligomer probes for each target (i.e., gene or DNA sequence) and experimentally testing and selecting the best probes for each target. The degenerate C. acetobutylicum strain M5 lacking the pSOL1 megaplasmid (with 178 annotated open reading frames [genes]) was used to estimate the level of probe cross-hybridization in the new microarrays and to establish the minimum intensity for a gene to be considered expressed. Results obtained using this microarray design were consistent with previously reported results from spotted cDNA-based microarrays. The proposed strategy is applicable to any sequenced organism.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Paredes</LastName><ForeName>Carlos J</ForeName><Initials>CJ</Initials><AffiliationInfo><Affiliation>Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Senger</LastName><ForeName>Ryan S</ForeName><Initials>RS</Initials></Author><Author ValidYN="Y"><LastName>Spath</LastName><ForeName>Iwona S</ForeName><Initials>IS</Initials></Author><Author ValidYN="Y"><LastName>Borden</LastName><ForeName>Jacob R</ForeName><Initials>JR</Initials></Author><Author ValidYN="Y"><LastName>Sillers</LastName><ForeName>Ryan</ForeName><Initials>R</Initials></Author><Author ValidYN="Y"><LastName>Papoutsakis</LastName><ForeName>Eleftherios T</ForeName><Initials>ET</Initials></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>T32 GM008449</GrantID><Acronym>GM</Acronym><Agency>NIGMS NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>T32-GM08449-11</GrantID><Acronym>GM</Acronym><Agency>NIGMS NIH HHS</Agency><Country>United States</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D052061">Research Support, N.I.H., Extramural</PublicationType><PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType><PublicationType UI="D023361">Validation Study</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2007</Year><Month>05</Month><Day>25</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Appl Environ Microbiol</MedlineTA><NlmUniqueID>7605801</NlmUniqueID><ISSNLinking>0099-2240</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D015345">Oligonucleotide Probes</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D046969" MajorTopicYN="N">Clostridium acetobutylicum</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020869" MajorTopicYN="N">Gene Expression Profiling</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D009693" MajorTopicYN="N">Nucleic Acid Hybridization</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020411" MajorTopicYN="N">Oligonucleotide Array Sequence Analysis</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D015345" MajorTopicYN="N">Oligonucleotide Probes</DescriptorName><QualifierName UI="Q000235" 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