Development and validation of a flax (Linum usitatissimum L.) gene expression oligo microarray.
Identifieur interne : 001E55 ( PubMed/Checkpoint ); précédent : 001E54; suivant : 001E56Development and validation of a flax (Linum usitatissimum L.) gene expression oligo microarray.
Auteurs : Stéphane Fenart [France] ; Yves-Placide Assoumou Ndong ; Jorge Duarte ; Nathalie Rivière ; Jeroen Wilmer ; Olivier Van Wuytswinkel ; Anca Lucau ; Emmanuelle Cariou ; Godfrey Neutelings ; Laurent Gutierrez ; Brigitte Chabbert ; Xavier Guillot ; Reynald Tavernier ; Simon Hawkins ; Brigitte ThomassetSource :
- BMC genomics [ 1471-2164 ] ; 2010.
Descripteurs français
- KwdFr :
- Analyse de profil d'expression de gènes, Analyse de séquence d'ADN, Analyse en composantes principales, Annotation de séquence moléculaire, Cartographie de contigs, Gènes de plante (génétique), Génotype, Lin (croissance et développement), Lin (génétique), RT-PCR, Reproductibilité des résultats, Régulation de l'expression des gènes au cours du développement, Régulation de l'expression des gènes végétaux, Spécificité d'organe (génétique), Séquençage par oligonucléotides en batterie (), Tiges de plante (génétique).
- MESH :
- croissance et développement : Lin.
- génétique : Gènes de plante, Lin, Spécificité d'organe, Tiges de plante.
- Analyse de profil d'expression de gènes, Analyse de séquence d'ADN, Analyse en composantes principales, Annotation de séquence moléculaire, Cartographie de contigs, Génotype, RT-PCR, Reproductibilité des résultats, Régulation de l'expression des gènes au cours du développement, Régulation de l'expression des gènes végétaux, Séquençage par oligonucléotides en batterie.
English descriptors
- KwdEn :
- Contig Mapping, Flax (genetics), Flax (growth & development), Gene Expression Profiling, Gene Expression Regulation, Developmental, Gene Expression Regulation, Plant, Genes, Plant (genetics), Genotype, Molecular Sequence Annotation, Oligonucleotide Array Sequence Analysis (methods), Organ Specificity (genetics), Plant Stems (genetics), Principal Component Analysis, Reproducibility of Results, Reverse Transcriptase Polymerase Chain Reaction, Sequence Analysis, DNA.
- MESH :
- genetics : Flax, Genes, Plant, Organ Specificity, Plant Stems.
- growth & development : Flax.
- methods : Oligonucleotide Array Sequence Analysis.
- Contig Mapping, Gene Expression Profiling, Gene Expression Regulation, Developmental, Gene Expression Regulation, Plant, Genotype, Molecular Sequence Annotation, Principal Component Analysis, Reproducibility of Results, Reverse Transcriptase Polymerase Chain Reaction, Sequence Analysis, DNA.
Abstract
Flax (Linum usitatissimum L.) has been cultivated for around 9,000 years and is therefore one of the oldest cultivated species. Today, flax is still grown for its oil (oil-flax or linseed cultivars) and its cellulose-rich fibres (fibre-flax cultivars) used for high-value linen garments and composite materials. Despite the wide industrial use of flax-derived products, and our actual understanding of the regulation of both wood fibre production and oil biosynthesis more information must be acquired in both domains. Recent advances in genomics are now providing opportunities to improve our fundamental knowledge of these complex processes. In this paper we report the development and validation of a high-density oligo microarray platform dedicated to gene expression analyses in flax.
DOI: 10.1186/1471-2164-11-592
PubMed: 20964859
Affiliations:
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type="published">2010</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Contig Mapping</term><term>Flax (genetics)</term><term>Flax (growth & development)</term><term>Gene Expression Profiling</term><term>Gene Expression Regulation, Developmental</term><term>Gene Expression Regulation, Plant</term><term>Genes, Plant (genetics)</term><term>Genotype</term><term>Molecular Sequence Annotation</term><term>Oligonucleotide Array Sequence Analysis (methods)</term><term>Organ Specificity (genetics)</term><term>Plant Stems (genetics)</term><term>Principal Component Analysis</term><term>Reproducibility of Results</term><term>Reverse Transcriptase Polymerase Chain Reaction</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de profil d'expression de gènes</term><term>Analyse de séquence d'ADN</term><term>Analyse en composantes principales</term><term>Annotation de séquence moléculaire</term><term>Cartographie de contigs</term><term>Gènes de plante (génétique)</term><term>Génotype</term><term>Lin (croissance et développement)</term><term>Lin (génétique)</term><term>RT-PCR</term><term>Reproductibilité des résultats</term><term>Régulation de l'expression des gènes au cours du développement</term><term>Régulation de l'expression des gènes végétaux</term><term>Spécificité d'organe (génétique)</term><term>Séquençage par oligonucléotides en batterie ()</term><term>Tiges de plante (génétique)</term></keywords><keywords scheme="MESH" qualifier="croissance et développement" xml:lang="fr"><term>Lin</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Flax</term><term>Genes, Plant</term><term>Organ Specificity</term><term>Plant Stems</term></keywords><keywords scheme="MESH" qualifier="growth & development" xml:lang="en"><term>Flax</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Gènes de plante</term><term>Lin</term><term>Spécificité d'organe</term><term>Tiges de plante</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Oligonucleotide Array Sequence Analysis</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Contig Mapping</term><term>Gene Expression Profiling</term><term>Gene Expression Regulation, Developmental</term><term>Gene Expression Regulation, Plant</term><term>Genotype</term><term>Molecular Sequence Annotation</term><term>Principal Component Analysis</term><term>Reproducibility of Results</term><term>Reverse Transcriptase Polymerase Chain Reaction</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de profil d'expression de gènes</term><term>Analyse de séquence d'ADN</term><term>Analyse en composantes principales</term><term>Annotation de séquence moléculaire</term><term>Cartographie de contigs</term><term>Génotype</term><term>RT-PCR</term><term>Reproductibilité des résultats</term><term>Régulation de l'expression des gènes au cours du développement</term><term>Régulation de l'expression des gènes végétaux</term><term>Séquençage par oligonucléotides en batterie</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Flax (Linum usitatissimum L.) has been cultivated for around 9,000 years and is therefore one of the oldest cultivated species. Today, flax is still grown for its oil (oil-flax or linseed cultivars) and its cellulose-rich fibres (fibre-flax cultivars) used for high-value linen garments and composite materials. Despite the wide industrial use of flax-derived products, and our actual understanding of the regulation of both wood fibre production and oil biosynthesis more information must be acquired in both domains. Recent advances in genomics are now providing opportunities to improve our fundamental knowledge of these complex processes. In this paper we report the development and validation of a high-density oligo microarray platform dedicated to gene expression analyses in flax.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">20964859</PMID><DateCompleted><Year>2010</Year><Month>12</Month><Day>27</Day></DateCompleted><DateRevised><Year>2019</Year><Month>12</Month><Day>10</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2164</ISSN><JournalIssue CitedMedium="Internet"><Volume>11</Volume><PubDate><Year>2010</Year><Month>Oct</Month><Day>21</Day></PubDate></JournalIssue><Title>BMC genomics</Title><ISOAbbreviation>BMC Genomics</ISOAbbreviation></Journal><ArticleTitle>Development and validation of a flax (Linum usitatissimum L.) gene expression oligo microarray.</ArticleTitle><Pagination><MedlinePgn>592</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/1471-2164-11-592</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">Flax (Linum usitatissimum L.) has been cultivated for around 9,000 years and is therefore one of the oldest cultivated species. Today, flax is still grown for its oil (oil-flax or linseed cultivars) and its cellulose-rich fibres (fibre-flax cultivars) used for high-value linen garments and composite materials. Despite the wide industrial use of flax-derived products, and our actual understanding of the regulation of both wood fibre production and oil biosynthesis more information must be acquired in both domains. Recent advances in genomics are now providing opportunities to improve our fundamental knowledge of these complex processes. In this paper we report the development and validation of a high-density oligo microarray platform dedicated to gene expression analyses in flax.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">Nine different RNA samples obtained from flax inner- and outer-stems, seeds, leaves and roots were used to generate a collection of 1,066,481 ESTs by massive parallel pyrosequencing. Sequences were assembled into 59,626 unigenes and 48,021 sequences were selected for oligo design and high-density microarray (Nimblegen 385K) fabrication with eight, non-overlapping 25-mers oligos per unigene. 18 independent experiments were used to evaluate the hybridization quality, precision, specificity and accuracy and all results confirmed the high technical quality of our microarray platform. Cross-validation of microarray data was carried out using quantitative qRT-PCR. Nine target genes were selected on the basis of microarray results and reflected the whole range of fold change (both up-regulated and down-regulated genes in different samples). A statistically significant positive correlation was obtained comparing expression levels for each target gene across all biological replicates both in qRT-PCR and microarray results. Further experiments illustrated the capacity of our arrays to detect differential gene expression in a variety of flax tissues as well as between two contrasted flax varieties.</AbstractText><AbstractText Label="CONCLUSION" NlmCategory="CONCLUSIONS">All results suggest that our high-density flax oligo-microarray platform can be used as a very sensitive tool for analyzing gene expression in a large variety of tissues as well as in different cultivars. Moreover, this highly reliable platform can also be used for the quantification of mRNA transcriptional profiling in different flax tissues.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Fenart</LastName><ForeName>Stéphane</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>Ndong</LastName><ForeName>Yves-Placide Assoumou</ForeName><Initials>YP</Initials></Author><Author ValidYN="Y"><LastName>Duarte</LastName><ForeName>Jorge</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Rivière</LastName><ForeName>Nathalie</ForeName><Initials>N</Initials></Author><Author ValidYN="Y"><LastName>Wilmer</LastName><ForeName>Jeroen</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>van Wuytswinkel</LastName><ForeName>Olivier</ForeName><Initials>O</Initials></Author><Author ValidYN="Y"><LastName>Lucau</LastName><ForeName>Anca</ForeName><Initials>A</Initials></Author><Author ValidYN="Y"><LastName>Cariou</LastName><ForeName>Emmanuelle</ForeName><Initials>E</Initials></Author><Author ValidYN="Y"><LastName>Neutelings</LastName><ForeName>Godfrey</ForeName><Initials>G</Initials></Author><Author ValidYN="Y"><LastName>Gutierrez</LastName><ForeName>Laurent</ForeName><Initials>L</Initials></Author><Author ValidYN="Y"><LastName>Chabbert</LastName><ForeName>Brigitte</ForeName><Initials>B</Initials></Author><Author ValidYN="Y"><LastName>Guillot</LastName><ForeName>Xavier</ForeName><Initials>X</Initials></Author><Author ValidYN="Y"><LastName>Tavernier</LastName><ForeName>Reynald</ForeName><Initials>R</Initials></Author><Author ValidYN="Y"><LastName>Hawkins</LastName><ForeName>Simon</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><LastName>Thomasset</LastName><ForeName>Brigitte</ForeName><Initials>B</Initials></Author></AuthorList><Language>eng</Language><DataBankList CompleteYN="Y"><DataBank><DataBankName>GEO</DataBankName><AccessionNumberList><AccessionNumber>GPL10419</AccessionNumber></AccessionNumberList></DataBank></DataBankList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType><PublicationType UI="D023361">Validation Study</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2010</Year><Month>10</Month><Day>21</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>BMC Genomics</MedlineTA><NlmUniqueID>100965258</NlmUniqueID><ISSNLinking>1471-2164</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D020451" MajorTopicYN="N">Contig Mapping</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D019597" MajorTopicYN="N">Flax</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000254" MajorTopicYN="N">growth & development</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020869" MajorTopicYN="N">Gene Expression Profiling</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018507" MajorTopicYN="N">Gene Expression Regulation, Developmental</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018506" MajorTopicYN="Y">Gene Expression Regulation, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017343" MajorTopicYN="N">Genes, Plant</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D005838" MajorTopicYN="N">Genotype</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D058977" MajorTopicYN="N">Molecular Sequence Annotation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020411" MajorTopicYN="N">Oligonucleotide Array Sequence Analysis</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D009928" MajorTopicYN="N">Organ Specificity</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018547" MajorTopicYN="N">Plant Stems</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D025341" MajorTopicYN="N">Principal Component Analysis</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D015203" MajorTopicYN="N">Reproducibility of Results</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020133" MajorTopicYN="N">Reverse Transcriptase Polymerase Chain Reaction</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017422" 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IdType="pubmed">11301307</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed><affiliations><list><country><li>France</li></country><region><li>Hauts-de-France</li><li>Nord-Pas-de-Calais</li></region><settlement><li>Villeneuve d'Ascq</li></settlement></list><tree><noCountry><name sortKey="Cariou, Emmanuelle" sort="Cariou, Emmanuelle" uniqKey="Cariou E" first="Emmanuelle" last="Cariou">Emmanuelle Cariou</name><name sortKey="Chabbert, Brigitte" sort="Chabbert, Brigitte" uniqKey="Chabbert B" first="Brigitte" last="Chabbert">Brigitte Chabbert</name><name sortKey="Duarte, Jorge" sort="Duarte, Jorge" uniqKey="Duarte J" first="Jorge" last="Duarte">Jorge Duarte</name><name sortKey="Guillot, Xavier" sort="Guillot, Xavier" uniqKey="Guillot X" first="Xavier" last="Guillot">Xavier Guillot</name><name sortKey="Gutierrez, Laurent" sort="Gutierrez, Laurent" uniqKey="Gutierrez L" first="Laurent" last="Gutierrez">Laurent Gutierrez</name><name sortKey="Hawkins, Simon" sort="Hawkins, Simon" uniqKey="Hawkins S" first="Simon" last="Hawkins">Simon Hawkins</name><name sortKey="Lucau, Anca" sort="Lucau, Anca" uniqKey="Lucau A" first="Anca" last="Lucau">Anca Lucau</name><name sortKey="Ndong, Yves Placide Assoumou" sort="Ndong, Yves Placide Assoumou" uniqKey="Ndong Y" first="Yves-Placide Assoumou" last="Ndong">Yves-Placide Assoumou Ndong</name><name sortKey="Neutelings, Godfrey" sort="Neutelings, Godfrey" uniqKey="Neutelings G" first="Godfrey" last="Neutelings">Godfrey Neutelings</name><name sortKey="Riviere, Nathalie" sort="Riviere, Nathalie" uniqKey="Riviere N" first="Nathalie" last="Rivière">Nathalie Rivière</name><name sortKey="Tavernier, Reynald" sort="Tavernier, Reynald" uniqKey="Tavernier R" first="Reynald" last="Tavernier">Reynald Tavernier</name><name sortKey="Thomasset, Brigitte" sort="Thomasset, Brigitte" uniqKey="Thomasset B" first="Brigitte" last="Thomasset">Brigitte Thomasset</name><name sortKey="Van Wuytswinkel, Olivier" sort="Van Wuytswinkel, Olivier" uniqKey="Van Wuytswinkel O" first="Olivier" last="Van Wuytswinkel">Olivier Van Wuytswinkel</name><name sortKey="Wilmer, Jeroen" sort="Wilmer, Jeroen" uniqKey="Wilmer J" first="Jeroen" last="Wilmer">Jeroen Wilmer</name></noCountry><country name="France"><region name="Hauts-de-France"><name sortKey="Fenart, Stephane" sort="Fenart, Stephane" uniqKey="Fenart S" first="Stéphane" last="Fenart">Stéphane Fenart</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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