Enchytraeus albidus Microarray: Enrichment, Design, Annotation and Database (EnchyBASE)
Identifieur interne : 000613 ( Main/Exploration ); précédent : 000612; suivant : 000614Enchytraeus albidus Microarray: Enrichment, Design, Annotation and Database (EnchyBASE)
Auteurs : Sara C. Novais [Portugal] ; Joel Arrais [Portugal] ; Pedro Lopes [Portugal] ; Tine Vandenbrouck [Belgique] ; Wim De Coen [Belgique] ; Dick Roelofs [Pays-Bas] ; Amadeu M. V. M. Soares [Portugal] ; M Nica J. B. Amorim [Portugal]Source :
- PLoS ONE [ 1932-6203 ] ; 2012.
Abstract
Url:
DOI: 10.1371/journal.pone.0034266
PubMed: 22558086
PubMed Central: 3338728
Affiliations:
Links toward previous steps (curation, corpus...)
- to stream Pmc, to step Corpus: 000517
- to stream Pmc, to step Curation: 000517
- to stream Pmc, to step Checkpoint: 000337
- to stream Ncbi, to step Merge: 000805
- to stream Ncbi, to step Curation: 000805
- to stream Ncbi, to step Checkpoint: 000805
- to stream Main, to step Merge: 000613
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Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en"><italic>Enchytraeus albidus</italic> Microarray: Enrichment, Design, Annotation and Database (EnchyBASE)</title><author><name sortKey="Novais, Sara C" sort="Novais, Sara C" uniqKey="Novais S" first="Sara C." last="Novais">Sara C. Novais</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Department of Biology & CESAM, University of Aveiro, Aveiro, Portugal</addr-line></nlm:aff><country xml:lang="fr">Portugal</country><wicri:regionArea>Department of Biology & CESAM, University of Aveiro, Aveiro</wicri:regionArea><wicri:noRegion>Aveiro</wicri:noRegion></affiliation></author><author><name sortKey="Arrais, Joel" sort="Arrais, Joel" uniqKey="Arrais J" first="Joel" last="Arrais">Joel Arrais</name><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Department of Electronics, Telecommunications and Informatics (DETI), Institute of Electronics and Telematics Engineering of Aveiro (IEETA), University of Aveiro, Aveiro, Portugal</addr-line></nlm:aff><country xml:lang="fr">Portugal</country><wicri:regionArea>Department of Electronics, Telecommunications and Informatics (DETI), Institute of Electronics and Telematics Engineering of Aveiro (IEETA), University of Aveiro, Aveiro</wicri:regionArea><wicri:noRegion>Aveiro</wicri:noRegion></affiliation></author><author><name sortKey="Lopes, Pedro" sort="Lopes, Pedro" uniqKey="Lopes P" first="Pedro" last="Lopes">Pedro Lopes</name><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Department of Electronics, Telecommunications and Informatics (DETI), Institute of Electronics and Telematics Engineering of Aveiro (IEETA), University of Aveiro, Aveiro, Portugal</addr-line></nlm:aff><country xml:lang="fr">Portugal</country><wicri:regionArea>Department of Electronics, Telecommunications and Informatics (DETI), Institute of Electronics and Telematics Engineering of Aveiro (IEETA), University of Aveiro, Aveiro</wicri:regionArea><wicri:noRegion>Aveiro</wicri:noRegion></affiliation></author><author><name sortKey="Vandenbrouck, Tine" sort="Vandenbrouck, Tine" uniqKey="Vandenbrouck T" first="Tine" last="Vandenbrouck">Tine Vandenbrouck</name><affiliation wicri:level="4"><nlm:aff id="aff3"><addr-line>University of Antwerp, Department of Biology - E.B.T., Groenenborgerlaan, Antwerp, Belgium</addr-line></nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>University of Antwerp, Department of Biology - E.B.T., Groenenborgerlaan, Antwerp</wicri:regionArea><orgName type="university">Université d'Anvers</orgName><placeName><settlement type="city">Anvers</settlement><region>Région flamande</region><region type="district" nuts="2">Province d'Anvers</region></placeName></affiliation></author><author><name sortKey="De Coen, Wim" sort="De Coen, Wim" uniqKey="De Coen W" first="Wim" last="De Coen">Wim De Coen</name><affiliation wicri:level="4"><nlm:aff id="aff3"><addr-line>University of Antwerp, Department of Biology - E.B.T., Groenenborgerlaan, Antwerp, Belgium</addr-line></nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>University of Antwerp, Department of Biology - E.B.T., Groenenborgerlaan, Antwerp</wicri:regionArea><orgName type="university">Université d'Anvers</orgName><placeName><settlement type="city">Anvers</settlement><region>Région flamande</region><region type="district" nuts="2">Province d'Anvers</region></placeName></affiliation></author><author><name sortKey="Roelofs, Dick" sort="Roelofs, Dick" uniqKey="Roelofs D" first="Dick" last="Roelofs">Dick Roelofs</name><affiliation wicri:level="1"><nlm:aff id="aff4"><addr-line>VU University Amsterdam, Institute of Ecological Sciences, De Boelelaan, The Netherlands</addr-line></nlm:aff><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>VU University Amsterdam, Institute of Ecological Sciences, De Boelelaan</wicri:regionArea><wicri:noRegion>De Boelelaan</wicri:noRegion></affiliation></author><author><name sortKey="Soares, Amadeu M V M" sort="Soares, Amadeu M V M" uniqKey="Soares A" first="Amadeu M. 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Amorim</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Department of Biology & CESAM, University of Aveiro, Aveiro, Portugal</addr-line></nlm:aff><country xml:lang="fr">Portugal</country><wicri:regionArea>Department of Biology & CESAM, University of Aveiro, Aveiro</wicri:regionArea><wicri:noRegion>Aveiro</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">22558086</idno><idno type="pmc">3338728</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3338728</idno><idno type="RBID">PMC:3338728</idno><idno type="doi">10.1371/journal.pone.0034266</idno><date when="2012">2012</date><idno type="wicri:Area/Pmc/Corpus">000517</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000517</idno><idno type="wicri:Area/Pmc/Curation">000517</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000517</idno><idno type="wicri:Area/Pmc/Checkpoint">000337</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">000337</idno><idno type="wicri:Area/Ncbi/Merge">000805</idno><idno type="wicri:Area/Ncbi/Curation">000805</idno><idno type="wicri:Area/Ncbi/Checkpoint">000805</idno><idno type="wicri:Area/Main/Merge">000613</idno><idno type="wicri:Area/Main/Curation">000613</idno><idno type="wicri:Area/Main/Exploration">000613</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main"><italic>Enchytraeus albidus</italic> Microarray: Enrichment, Design, Annotation and Database (EnchyBASE)</title><author><name sortKey="Novais, Sara C" sort="Novais, Sara C" uniqKey="Novais S" first="Sara C." last="Novais">Sara C. Novais</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Department of Biology & CESAM, University of Aveiro, Aveiro, Portugal</addr-line></nlm:aff><country xml:lang="fr">Portugal</country><wicri:regionArea>Department of Biology & CESAM, University of Aveiro, Aveiro</wicri:regionArea><wicri:noRegion>Aveiro</wicri:noRegion></affiliation></author><author><name sortKey="Arrais, Joel" sort="Arrais, Joel" uniqKey="Arrais J" first="Joel" last="Arrais">Joel Arrais</name><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Department of Electronics, Telecommunications and Informatics (DETI), Institute of Electronics and Telematics Engineering of Aveiro (IEETA), University of Aveiro, Aveiro, Portugal</addr-line></nlm:aff><country xml:lang="fr">Portugal</country><wicri:regionArea>Department of Electronics, Telecommunications and Informatics (DETI), Institute of Electronics and Telematics Engineering of Aveiro (IEETA), University of Aveiro, Aveiro</wicri:regionArea><wicri:noRegion>Aveiro</wicri:noRegion></affiliation></author><author><name sortKey="Lopes, Pedro" sort="Lopes, Pedro" uniqKey="Lopes P" first="Pedro" last="Lopes">Pedro Lopes</name><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Department of Electronics, Telecommunications and Informatics (DETI), Institute of Electronics and Telematics Engineering of Aveiro (IEETA), University of Aveiro, Aveiro, Portugal</addr-line></nlm:aff><country xml:lang="fr">Portugal</country><wicri:regionArea>Department of Electronics, Telecommunications and Informatics (DETI), Institute of Electronics and Telematics Engineering of Aveiro (IEETA), University of Aveiro, Aveiro</wicri:regionArea><wicri:noRegion>Aveiro</wicri:noRegion></affiliation></author><author><name sortKey="Vandenbrouck, Tine" sort="Vandenbrouck, Tine" uniqKey="Vandenbrouck T" first="Tine" last="Vandenbrouck">Tine Vandenbrouck</name><affiliation wicri:level="4"><nlm:aff id="aff3"><addr-line>University of Antwerp, Department of Biology - E.B.T., Groenenborgerlaan, Antwerp, Belgium</addr-line></nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>University of Antwerp, Department of Biology - E.B.T., Groenenborgerlaan, Antwerp</wicri:regionArea><orgName type="university">Université d'Anvers</orgName><placeName><settlement type="city">Anvers</settlement><region>Région flamande</region><region type="district" nuts="2">Province d'Anvers</region></placeName></affiliation></author><author><name sortKey="De Coen, Wim" sort="De Coen, Wim" uniqKey="De Coen W" first="Wim" last="De Coen">Wim De Coen</name><affiliation wicri:level="4"><nlm:aff id="aff3"><addr-line>University of Antwerp, Department of Biology - E.B.T., Groenenborgerlaan, Antwerp, Belgium</addr-line></nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>University of Antwerp, Department of Biology - E.B.T., Groenenborgerlaan, Antwerp</wicri:regionArea><orgName type="university">Université d'Anvers</orgName><placeName><settlement type="city">Anvers</settlement><region>Région flamande</region><region type="district" nuts="2">Province d'Anvers</region></placeName></affiliation></author><author><name sortKey="Roelofs, Dick" sort="Roelofs, Dick" uniqKey="Roelofs D" first="Dick" last="Roelofs">Dick Roelofs</name><affiliation wicri:level="1"><nlm:aff id="aff4"><addr-line>VU University Amsterdam, Institute of Ecological Sciences, De Boelelaan, The Netherlands</addr-line></nlm:aff><country xml:lang="fr">Pays-Bas</country><wicri:regionArea>VU University Amsterdam, Institute of Ecological Sciences, De Boelelaan</wicri:regionArea><wicri:noRegion>De Boelelaan</wicri:noRegion></affiliation></author><author><name sortKey="Soares, Amadeu M V M" sort="Soares, Amadeu M V M" uniqKey="Soares A" first="Amadeu M. V. M." last="Soares">Amadeu M. V. M. Soares</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Department of Biology & CESAM, University of Aveiro, Aveiro, Portugal</addr-line></nlm:aff><country xml:lang="fr">Portugal</country><wicri:regionArea>Department of Biology & CESAM, University of Aveiro, Aveiro</wicri:regionArea><wicri:noRegion>Aveiro</wicri:noRegion></affiliation></author><author><name sortKey="Amorim, M Nica J B" sort="Amorim, M Nica J B" uniqKey="Amorim M" first="M Nica J. B." last="Amorim">M Nica J. B. Amorim</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Department of Biology & CESAM, University of Aveiro, Aveiro, Portugal</addr-line></nlm:aff><country xml:lang="fr">Portugal</country><wicri:regionArea>Department of Biology & CESAM, University of Aveiro, Aveiro</wicri:regionArea><wicri:noRegion>Aveiro</wicri:noRegion></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2012">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><italic>Enchytraeus albidus</italic> (Oligochaeta) is an ecologically relevant species used as standard test organisms for risk assessment. Effects of stressors in this species are commonly determined at the population level using reproduction and survival as endpoints. The assessment of transcriptomic responses can be very useful e.g. to understand underlying mechanisms of toxicity with gene expression fingerprinting. In the present paper the following is being addressed: 1) development of suppressive subtractive hybridization (SSH) libraries enriched for differentially expressed genes after metal and pesticide exposures; 2) sequencing and characterization of all generated cDNA inserts; 3) development of a publicly available genomic database on <italic>E. albidus</italic>. A total of 2100 Expressed Sequence Tags (ESTs) were isolated, sequenced and assembled into 1124 clusters (947 singletons and 177 contigs). From these sequences, 41% matched known proteins in GenBank (BLASTX, e-value≤10<sup>-5</sup>) and 37% had at least one Gene Ontology (GO) term assigned. In total, 5.5% of the sequences were assigned to a metabolic pathway, based on KEGG. With this new sequencing information, an Agilent custom oligonucleotide microarray was designed, representing a potential tool for transcriptomic studies. EnchyBASE (<ext-link ext-link-type="uri" xlink:href="http://bioinformatics.ua.pt/enchybase/">http://bioinformatics.ua.pt/enchybase/</ext-link>) was developed as a web freely available database containing genomic information on <italic>E. albidus</italic> and will be further extended in the near future for other enchytraeid species. The database so far includes all ESTs generated for <italic>E. albidus</italic> from three cDNA libraries. This information can be downloaded and applied in functional genomics and transcription studies.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Jeffrey, S" uniqKey="Jeffrey S">S Jeffrey</name></author><author><name sortKey="Gardi, C" uniqKey="Gardi C">C Gardi</name></author><author><name sortKey="Jones, A" uniqKey="Jones A">A Jones</name></author><author><name sortKey="Montanarella, L" uniqKey="Montanarella L">L Montanarella</name></author><author><name sortKey="Marmo, L" uniqKey="Marmo L">L Marmo</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Iso" uniqKey="Iso">ISO</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Oecd" uniqKey="Oecd">OECD</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Oecd" uniqKey="Oecd">OECD</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Amorim, Mjb" uniqKey="Amorim 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Boer</name></author><author><name sortKey="Birlutiu, A" uniqKey="Birlutiu A">A Birlutiu</name></author><author><name sortKey="Bochdanovits, Z" uniqKey="Bochdanovits Z">Z Bochdanovits</name></author><author><name sortKey="Timmermans, Mjtn" uniqKey="Timmermans M">MJTN Timmermans</name></author><author><name sortKey="Dijkstra, Tmh" uniqKey="Dijkstra T">TMH Dijkstra</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Amorim, Mjb" uniqKey="Amorim M">MJB Amorim</name></author><author><name sortKey="Novais, S" uniqKey="Novais S">S Novais</name></author><author><name sortKey="Rombke, J" uniqKey="Rombke J">J Römbke</name></author><author><name sortKey="Soares, Amvm" uniqKey="Soares A">AMVM Soares</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Belgique</li><li>Pays-Bas</li><li>Portugal</li></country><region><li>Province d'Anvers</li><li>Région flamande</li></region><settlement><li>Anvers</li></settlement><orgName><li>Université d'Anvers</li></orgName></list><tree><country name="Portugal"><noRegion><name sortKey="Novais, Sara C" sort="Novais, Sara C" uniqKey="Novais S" first="Sara C." last="Novais">Sara C. Novais</name></noRegion><name sortKey="Amorim, M Nica J B" sort="Amorim, M Nica J B" uniqKey="Amorim M" first="M Nica J. B." last="Amorim">M Nica J. B. Amorim</name><name sortKey="Arrais, Joel" sort="Arrais, Joel" uniqKey="Arrais J" first="Joel" last="Arrais">Joel Arrais</name><name sortKey="Lopes, Pedro" sort="Lopes, Pedro" uniqKey="Lopes P" first="Pedro" last="Lopes">Pedro Lopes</name><name sortKey="Soares, Amadeu M V M" sort="Soares, Amadeu M V M" uniqKey="Soares A" first="Amadeu M. V. M." last="Soares">Amadeu M. V. M. Soares</name></country><country name="Belgique"><region name="Région flamande"><name sortKey="Vandenbrouck, Tine" sort="Vandenbrouck, Tine" uniqKey="Vandenbrouck T" first="Tine" last="Vandenbrouck">Tine Vandenbrouck</name></region><name sortKey="De Coen, Wim" sort="De Coen, Wim" uniqKey="De Coen W" first="Wim" last="De Coen">Wim De Coen</name></country><country name="Pays-Bas"><noRegion><name sortKey="Roelofs, Dick" sort="Roelofs, Dick" uniqKey="Roelofs D" first="Dick" last="Roelofs">Dick Roelofs</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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