Intra-platform comparison of 25-mer and 60-mer oligonucleotide Nimblegen DNA microarrays.
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Auteurs : Stephane Fenart [France] ; Malika Chabi ; Sophie Gallina ; Rudy Huis ; Godfrey Neutelings ; Nathalie Riviere ; Brigitte Thomasset ; Simon Hawkins ; Anca Lucau-DanilaSource :
- BMC research notes [ 1756-0500 ] ; 2013.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : DNA.
- chemical : DNA Probes.
- Nucleic Acid Hybridization, Oligonucleotide Array Sequence Analysis, Reproducibility of Results.
Abstract
We performed a Nimblegen intra-platform microarray comparison by assessing two categories of flax target probes (short 25-mers oligonucleotides and long 60-mers oligonucleotides) in identical conditions of target production, design, labelling, hybridization, image analyses, and data filtering. We compared technical parameters of array hybridizations, precision and accuracy as well as specific gene expression profiles.
DOI: 10.1186/1756-0500-6-43
PubMed: 23375116
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uniqKey="Huis R" first="Rudy" last="Huis">Rudy Huis</name></author><author><name sortKey="Neutelings, Godfrey" sort="Neutelings, Godfrey" uniqKey="Neutelings G" first="Godfrey" last="Neutelings">Godfrey Neutelings</name></author><author><name sortKey="Riviere, Nathalie" sort="Riviere, Nathalie" uniqKey="Riviere N" first="Nathalie" last="Riviere">Nathalie Riviere</name></author><author><name sortKey="Thomasset, Brigitte" sort="Thomasset, Brigitte" uniqKey="Thomasset B" first="Brigitte" last="Thomasset">Brigitte Thomasset</name></author><author><name sortKey="Hawkins, Simon" sort="Hawkins, Simon" uniqKey="Hawkins S" first="Simon" last="Hawkins">Simon Hawkins</name></author><author><name sortKey="Lucau Danila, Anca" sort="Lucau Danila, Anca" uniqKey="Lucau Danila A" first="Anca" last="Lucau-Danila">Anca Lucau-Danila</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2013">2013</date><idno type="RBID">pubmed:23375116</idno><idno 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cedex</wicri:regionArea></affiliation></author><author><name sortKey="Chabi, Malika" sort="Chabi, Malika" uniqKey="Chabi M" first="Malika" last="Chabi">Malika Chabi</name></author><author><name sortKey="Gallina, Sophie" sort="Gallina, Sophie" uniqKey="Gallina S" first="Sophie" last="Gallina">Sophie Gallina</name></author><author><name sortKey="Huis, Rudy" sort="Huis, Rudy" uniqKey="Huis R" first="Rudy" last="Huis">Rudy Huis</name></author><author><name sortKey="Neutelings, Godfrey" sort="Neutelings, Godfrey" uniqKey="Neutelings G" first="Godfrey" last="Neutelings">Godfrey Neutelings</name></author><author><name sortKey="Riviere, Nathalie" sort="Riviere, Nathalie" uniqKey="Riviere N" first="Nathalie" last="Riviere">Nathalie Riviere</name></author><author><name sortKey="Thomasset, Brigitte" sort="Thomasset, Brigitte" uniqKey="Thomasset B" first="Brigitte" last="Thomasset">Brigitte Thomasset</name></author><author><name sortKey="Hawkins, Simon" sort="Hawkins, Simon" uniqKey="Hawkins S" first="Simon" last="Hawkins">Simon Hawkins</name></author><author><name sortKey="Lucau Danila, Anca" sort="Lucau Danila, Anca" uniqKey="Lucau Danila A" first="Anca" last="Lucau-Danila">Anca Lucau-Danila</name></author></analytic><series><title level="j">BMC research notes</title><idno type="eISSN">1756-0500</idno><imprint><date when="2013" type="published">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>DNA (chemistry)</term><term>DNA Probes</term><term>Nucleic Acid Hybridization</term><term>Oligonucleotide Array Sequence Analysis</term><term>Reproducibility of Results</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN ()</term><term>Hybridation d'acides nucléiques</term><term>Reproductibilité des résultats</term><term>Sondes d'ADN</term><term>Séquençage par oligonucléotides en batterie</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>DNA</term></keywords><keywords scheme="MESH" type="chemical" xml:lang="en"><term>DNA Probes</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Nucleic Acid Hybridization</term><term>Oligonucleotide Array Sequence Analysis</term><term>Reproducibility of Results</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>ADN</term><term>Hybridation d'acides nucléiques</term><term>Reproductibilité des résultats</term><term>Sondes d'ADN</term><term>Séquençage par oligonucléotides en batterie</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">We performed a Nimblegen intra-platform microarray comparison by assessing two categories of flax target probes (short 25-mers oligonucleotides and long 60-mers oligonucleotides) in identical conditions of target production, design, labelling, hybridization, image analyses, and data filtering. We compared technical parameters of array hybridizations, precision and accuracy as well as specific gene expression profiles.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">23375116</PMID><DateCompleted><Year>2013</Year><Month>06</Month><Day>24</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1756-0500</ISSN><JournalIssue CitedMedium="Internet"><Volume>6</Volume><PubDate><Year>2013</Year><Month>Feb</Month><Day>04</Day></PubDate></JournalIssue><Title>BMC research notes</Title><ISOAbbreviation>BMC Res Notes</ISOAbbreviation></Journal><ArticleTitle>Intra-platform comparison of 25-mer and 60-mer oligonucleotide Nimblegen DNA microarrays.</ArticleTitle><Pagination><MedlinePgn>43</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/1756-0500-6-43</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">We performed a Nimblegen intra-platform microarray comparison by assessing two categories of flax target probes (short 25-mers oligonucleotides and long 60-mers oligonucleotides) in identical conditions of target production, design, labelling, hybridization, image analyses, and data filtering. We compared technical parameters of array hybridizations, precision and accuracy as well as specific gene expression profiles.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">Comparison of the hybridization quality, precision and accuracy of expression measurements, as well as an interpretation of differential gene expression in flax tissues were performed. Both array types yielded reproducible, accurate and comparable data that are coherent for expression measurements and identification of differentially expressed genes. 60-mers arrays gave higher hybridization efficiencies and therefore were more sensitive allowing the detection of a higher number of unigenes involved in the same biological process and/or belonging to the same multigene family.</AbstractText><AbstractText Label="CONCLUSION" NlmCategory="CONCLUSIONS">The two flax arrays provide a good resolution of expressed functions; however the 60-mers arrays are more sensitive and provide a more in-depth coverage of candidate genes potentially involved in different biological processes.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Fenart</LastName><ForeName>Stephane</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Université Lille Nord de France, Lille 1, UMR INRA 1281, SADV, F- 59650 Villeneuve d'Ascq cedex, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chabi</LastName><ForeName>Malika</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Gallina</LastName><ForeName>Sophie</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><LastName>Huis</LastName><ForeName>Rudy</ForeName><Initials>R</Initials></Author><Author ValidYN="Y"><LastName>Neutelings</LastName><ForeName>Godfrey</ForeName><Initials>G</Initials></Author><Author ValidYN="Y"><LastName>Riviere</LastName><ForeName>Nathalie</ForeName><Initials>N</Initials></Author><Author ValidYN="Y"><LastName>Thomasset</LastName><ForeName>Brigitte</ForeName><Initials>B</Initials></Author><Author ValidYN="Y"><LastName>Hawkins</LastName><ForeName>Simon</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><LastName>Lucau-Danila</LastName><ForeName>Anca</ForeName><Initials>A</Initials></Author></AuthorList><Language>eng</Language><DataBankList CompleteYN="Y"><DataBank><DataBankName>GEO</DataBankName><AccessionNumberList><AccessionNumber>GSE37980</AccessionNumber></AccessionNumberList></DataBank></DataBankList><PublicationTypeList><PublicationType UI="D003160">Comparative Study</PublicationType><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2013</Year><Month>02</Month><Day>04</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>BMC Res Notes</MedlineTA><NlmUniqueID>101462768</NlmUniqueID><ISSNLinking>1756-0500</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D015342">DNA Probes</NameOfSubstance></Chemical><Chemical><RegistryNumber>9007-49-2</RegistryNumber><NameOfSubstance 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