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Intra-platform comparison of 25-mer and 60-mer oligonucleotide Nimblegen DNA microarrays

Identifieur interne : 001F73 ( Main/Exploration ); précédent : 001F72; suivant : 001F74

Intra-platform comparison of 25-mer and 60-mer oligonucleotide Nimblegen DNA microarrays

Auteurs : Stephane Fenart [France] ; Malika Chabi [France] ; Sophie Gallina [France] ; Rudy Huis [France] ; Godfrey Neutelings [France] ; Nathalie Riviere [France] ; Brigitte Thomasset [France] ; Simon Hawkins [France] ; Anca Lucau-Danila [France]

Source :

RBID : PMC:3608165

Descripteurs français

English descriptors

Abstract

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.

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.

Conclusion

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.


Url:
DOI: 10.1186/1756-0500-6-43
PubMed: 23375116
PubMed Central: 3608165


Affiliations:


Links toward previous steps (curation, corpus...)


Le document en format XML

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<term>DNA (chemistry)</term>
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<term>Nucleic Acid Hybridization</term>
<term>Oligonucleotide Array Sequence Analysis</term>
<term>Reproducibility of Results</term>
</keywords>
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<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>
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<term>DNA</term>
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<keywords scheme="MESH" type="chemical" xml:lang="en">
<term>DNA Probes</term>
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<keywords scheme="MESH" xml:lang="en">
<term>Nucleic Acid Hybridization</term>
<term>Oligonucleotide Array Sequence Analysis</term>
<term>Reproducibility of Results</term>
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<term>ADN</term>
<term>Hybridation d'acides nucléiques</term>
<term>Reproductibilité des résultats</term>
<term>Sondes d'ADN</term>
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<sec>
<title>Background</title>
<p>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.</p>
</sec>
<sec>
<title>Results</title>
<p>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.</p>
</sec>
<sec>
<title>Conclusion</title>
<p>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.</p>
</sec>
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<name sortKey="Deyholos, Mk" uniqKey="Deyholos M">MK Deyholos</name>
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<list>
<country>
<li>France</li>
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<li>Auvergne (région administrative)</li>
<li>Auvergne-Rhône-Alpes</li>
<li>Hauts-de-France</li>
<li>Nord-Pas-de-Calais</li>
<li>Picardie</li>
<li>Rhône-Alpes</li>
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<name sortKey="Huis, Rudy" sort="Huis, Rudy" uniqKey="Huis R" first="Rudy" last="Huis">Rudy Huis</name>
<name sortKey="Lucau Danila, Anca" sort="Lucau Danila, Anca" uniqKey="Lucau Danila A" first="Anca" last="Lucau-Danila">Anca Lucau-Danila</name>
<name sortKey="Neutelings, Godfrey" sort="Neutelings, Godfrey" uniqKey="Neutelings G" first="Godfrey" last="Neutelings">Godfrey Neutelings</name>
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<name sortKey="Thomasset, Brigitte" sort="Thomasset, Brigitte" uniqKey="Thomasset B" first="Brigitte" last="Thomasset">Brigitte Thomasset</name>
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</record>

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