RNA sequencing read depth requirement for optimal transcriptome coverage in Hevea brasiliensis.
Identifieur interne : 001769 ( PubMed/Checkpoint ); précédent : 001768; suivant : 001770RNA sequencing read depth requirement for optimal transcriptome coverage in Hevea brasiliensis.
Auteurs : Keng-See Chow [Malaisie] ; Ahmad-Kamal Ghazali ; Chee-Choong Hoh ; Zainorlina Mohd-ZainuddinSource :
- BMC research notes [ 1756-0500 ] ; 2014.
Descripteurs français
- KwdFr :
- ARN des plantes (), ARN des plantes (biosynthèse), ARN des plantes (génétique), ARN des plantes (isolement et purification), ARN messager (), ARN messager (biosynthèse), ARN messager (génétique), ARN messager (isolement et purification), Analyse de profil d'expression de gènes (), Banque de gènes, Bases de données génétiques, Cadres ouverts de lecture, Feuilles de plante (métabolisme), Gènes de plante, Hevea (), Hevea (génétique), Protéines végétales (génétique), Reproductibilité des résultats, Régulation de l'expression des gènes végétaux, Séquençage nucléotidique à haut débit, Transcriptome, Écorce (métabolisme).
- MESH :
- biosynthèse : ARN des plantes, ARN messager.
- génétique : ARN des plantes, ARN messager, Hevea, Protéines végétales.
- isolement et purification : ARN des plantes, ARN messager.
- métabolisme : Feuilles de plante, Écorce.
- ARN des plantes, ARN messager, Analyse de profil d'expression de gènes, Banque de gènes, Bases de données génétiques, Cadres ouverts de lecture, Gènes de plante, Hevea, Reproductibilité des résultats, Régulation de l'expression des gènes végétaux, Séquençage nucléotidique à haut débit, Transcriptome.
English descriptors
- KwdEn :
- Databases, Genetic, Gene Expression Profiling (methods), Gene Expression Regulation, Plant, Gene Library, Genes, Plant, Hevea (chemistry), Hevea (genetics), High-Throughput Nucleotide Sequencing, Open Reading Frames, Plant Bark (metabolism), Plant Leaves (metabolism), Plant Proteins (genetics), RNA, Messenger (biosynthesis), RNA, Messenger (chemistry), RNA, Messenger (genetics), RNA, Messenger (isolation & purification), RNA, Plant (biosynthesis), RNA, Plant (chemistry), RNA, Plant (genetics), RNA, Plant (isolation & purification), Reproducibility of Results, Transcriptome.
- MESH :
- chemical , biosynthesis : RNA, Messenger, RNA, Plant.
- chemical , chemistry : RNA, Messenger, RNA, Plant.
- chemical , genetics : Plant Proteins, RNA, Messenger, RNA, Plant.
- chemistry : Hevea.
- genetics : Hevea.
- chemical , isolation & purification : RNA, Messenger, RNA, Plant.
- metabolism : Plant Bark, Plant Leaves.
- methods : Gene Expression Profiling.
- Databases, Genetic, Gene Expression Regulation, Plant, Gene Library, Genes, Plant, High-Throughput Nucleotide Sequencing, Open Reading Frames, Reproducibility of Results, Transcriptome.
Abstract
One of the concerns of assembling de novo transcriptomes is determining the amount of read sequences required to ensure a comprehensive coverage of genes expressed in a particular sample. In this report, we describe the use of Illumina paired-end RNA-Seq (PE RNA-Seq) reads from Hevea brasiliensis (rubber tree) bark to devise a transcript mapping approach for the estimation of the read amount needed for deep transcriptome coverage.
DOI: 10.1186/1756-0500-7-69
PubMed: 24484543
Affiliations:
Links toward previous steps (curation, corpus...)
Links to Exploration step
pubmed:24484543Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">RNA sequencing read depth requirement for optimal transcriptome coverage in Hevea brasiliensis.</title><author><name sortKey="Chow, Keng See" sort="Chow, Keng See" uniqKey="Chow K" first="Keng-See" last="Chow">Keng-See Chow</name><affiliation wicri:level="1"><nlm:affiliation>Biotechnology Unit, Malaysian Rubber Board, Rubber Research Institute of Malaysia, Experiment Station, Kuala Lumpur 47000, Sungai Buloh, Selangor, Malaysia. kschow@lgm.gov.my.</nlm:affiliation><country xml:lang="fr">Malaisie</country><wicri:regionArea>Biotechnology Unit, Malaysian Rubber Board, Rubber Research Institute of Malaysia, Experiment Station, Kuala Lumpur 47000, Sungai Buloh, Selangor</wicri:regionArea><wicri:noRegion>Selangor</wicri:noRegion></affiliation></author><author><name sortKey="Ghazali, Ahmad Kamal" sort="Ghazali, Ahmad Kamal" uniqKey="Ghazali A" first="Ahmad-Kamal" last="Ghazali">Ahmad-Kamal Ghazali</name></author><author><name sortKey="Hoh, Chee Choong" sort="Hoh, Chee Choong" uniqKey="Hoh C" first="Chee-Choong" last="Hoh">Chee-Choong Hoh</name></author><author><name sortKey="Mohd Zainuddin, Zainorlina" sort="Mohd Zainuddin, Zainorlina" uniqKey="Mohd Zainuddin Z" first="Zainorlina" last="Mohd-Zainuddin">Zainorlina Mohd-Zainuddin</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2014">2014</date><idno type="RBID">pubmed:24484543</idno><idno type="pmid">24484543</idno><idno type="doi">10.1186/1756-0500-7-69</idno><idno type="wicri:Area/PubMed/Corpus">001A66</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001A66</idno><idno type="wicri:Area/PubMed/Curation">001A66</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">001A66</idno><idno type="wicri:Area/PubMed/Checkpoint">001769</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">001769</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">RNA sequencing read depth requirement for optimal transcriptome coverage in Hevea brasiliensis.</title><author><name sortKey="Chow, Keng See" sort="Chow, Keng See" uniqKey="Chow K" first="Keng-See" last="Chow">Keng-See Chow</name><affiliation wicri:level="1"><nlm:affiliation>Biotechnology Unit, Malaysian Rubber Board, Rubber Research Institute of Malaysia, Experiment Station, Kuala Lumpur 47000, Sungai Buloh, Selangor, Malaysia. kschow@lgm.gov.my.</nlm:affiliation><country xml:lang="fr">Malaisie</country><wicri:regionArea>Biotechnology Unit, Malaysian Rubber Board, Rubber Research Institute of Malaysia, Experiment Station, Kuala Lumpur 47000, Sungai Buloh, Selangor</wicri:regionArea><wicri:noRegion>Selangor</wicri:noRegion></affiliation></author><author><name sortKey="Ghazali, Ahmad Kamal" sort="Ghazali, Ahmad Kamal" uniqKey="Ghazali A" first="Ahmad-Kamal" last="Ghazali">Ahmad-Kamal Ghazali</name></author><author><name sortKey="Hoh, Chee Choong" sort="Hoh, Chee Choong" uniqKey="Hoh C" first="Chee-Choong" last="Hoh">Chee-Choong Hoh</name></author><author><name sortKey="Mohd Zainuddin, Zainorlina" sort="Mohd Zainuddin, Zainorlina" uniqKey="Mohd Zainuddin Z" first="Zainorlina" last="Mohd-Zainuddin">Zainorlina Mohd-Zainuddin</name></author></analytic><series><title level="j">BMC research notes</title><idno type="eISSN">1756-0500</idno><imprint><date when="2014" type="published">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Databases, Genetic</term><term>Gene Expression Profiling (methods)</term><term>Gene Expression Regulation, Plant</term><term>Gene Library</term><term>Genes, Plant</term><term>Hevea (chemistry)</term><term>Hevea (genetics)</term><term>High-Throughput Nucleotide Sequencing</term><term>Open Reading Frames</term><term>Plant Bark (metabolism)</term><term>Plant Leaves (metabolism)</term><term>Plant Proteins (genetics)</term><term>RNA, Messenger (biosynthesis)</term><term>RNA, Messenger (chemistry)</term><term>RNA, Messenger (genetics)</term><term>RNA, Messenger (isolation & purification)</term><term>RNA, Plant (biosynthesis)</term><term>RNA, Plant (chemistry)</term><term>RNA, Plant (genetics)</term><term>RNA, Plant (isolation & purification)</term><term>Reproducibility of Results</term><term>Transcriptome</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ARN des plantes ()</term><term>ARN des plantes (biosynthèse)</term><term>ARN des plantes (génétique)</term><term>ARN des plantes (isolement et purification)</term><term>ARN messager ()</term><term>ARN messager (biosynthèse)</term><term>ARN messager (génétique)</term><term>ARN messager (isolement et purification)</term><term>Analyse de profil d'expression de gènes ()</term><term>Banque de gènes</term><term>Bases de données génétiques</term><term>Cadres ouverts de lecture</term><term>Feuilles de plante (métabolisme)</term><term>Gènes de plante</term><term>Hevea ()</term><term>Hevea (génétique)</term><term>Protéines végétales (génétique)</term><term>Reproductibilité des résultats</term><term>Régulation de l'expression des gènes végétaux</term><term>Séquençage nucléotidique à haut débit</term><term>Transcriptome</term><term>Écorce (métabolisme)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="biosynthesis" xml:lang="en"><term>RNA, Messenger</term><term>RNA, Plant</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>RNA, Messenger</term><term>RNA, Plant</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Plant Proteins</term><term>RNA, Messenger</term><term>RNA, Plant</term></keywords><keywords scheme="MESH" qualifier="biosynthèse" xml:lang="fr"><term>ARN des plantes</term><term>ARN messager</term></keywords><keywords scheme="MESH" qualifier="chemistry" xml:lang="en"><term>Hevea</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Hevea</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ARN des plantes</term><term>ARN messager</term><term>Hevea</term><term>Protéines végétales</term></keywords><keywords scheme="MESH" type="chemical" qualifier="isolation & purification" xml:lang="en"><term>RNA, Messenger</term><term>RNA, Plant</term></keywords><keywords scheme="MESH" qualifier="isolement et purification" xml:lang="fr"><term>ARN des plantes</term><term>ARN messager</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Plant Bark</term><term>Plant Leaves</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Gene Expression Profiling</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Feuilles de plante</term><term>Écorce</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Databases, Genetic</term><term>Gene Expression Regulation, Plant</term><term>Gene Library</term><term>Genes, Plant</term><term>High-Throughput Nucleotide Sequencing</term><term>Open Reading Frames</term><term>Reproducibility of Results</term><term>Transcriptome</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>ARN des plantes</term><term>ARN messager</term><term>Analyse de profil d'expression de gènes</term><term>Banque de gènes</term><term>Bases de données génétiques</term><term>Cadres ouverts de lecture</term><term>Gènes de plante</term><term>Hevea</term><term>Reproductibilité des résultats</term><term>Régulation de l'expression des gènes végétaux</term><term>Séquençage nucléotidique à haut débit</term><term>Transcriptome</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">One of the concerns of assembling de novo transcriptomes is determining the amount of read sequences required to ensure a comprehensive coverage of genes expressed in a particular sample. In this report, we describe the use of Illumina paired-end RNA-Seq (PE RNA-Seq) reads from Hevea brasiliensis (rubber tree) bark to devise a transcript mapping approach for the estimation of the read amount needed for deep transcriptome coverage.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">24484543</PMID><DateCompleted><Year>2014</Year><Month>09</Month><Day>03</Day></DateCompleted><DateRevised><Year>2019</Year><Month>12</Month><Day>10</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1756-0500</ISSN><JournalIssue CitedMedium="Internet"><Volume>7</Volume><PubDate><Year>2014</Year><Month>Feb</Month><Day>01</Day></PubDate></JournalIssue><Title>BMC research notes</Title><ISOAbbreviation>BMC Res Notes</ISOAbbreviation></Journal><ArticleTitle>RNA sequencing read depth requirement for optimal transcriptome coverage in Hevea brasiliensis.</ArticleTitle><Pagination><MedlinePgn>69</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/1756-0500-7-69</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">One of the concerns of assembling de novo transcriptomes is determining the amount of read sequences required to ensure a comprehensive coverage of genes expressed in a particular sample. In this report, we describe the use of Illumina paired-end RNA-Seq (PE RNA-Seq) reads from Hevea brasiliensis (rubber tree) bark to devise a transcript mapping approach for the estimation of the read amount needed for deep transcriptome coverage.</AbstractText><AbstractText Label="FINDINGS" NlmCategory="RESULTS">We optimized the assembly of a Hevea bark transcriptome based on 16 Gb Illumina PE RNA-Seq reads using the Oases assembler across a range of k-mer sizes. We then assessed assembly quality based on transcript N50 length and transcript mapping statistics in relation to (a) known Hevea cDNAs with complete open reading frames, (b) a set of core eukaryotic genes and (c) Hevea genome scaffolds. This was followed by a systematic transcript mapping process where sub-assemblies from a series of incremental amounts of bark transcripts were aligned to transcripts from the entire bark transcriptome assembly. The exercise served to relate read amounts to the degree of transcript mapping level, the latter being an indicator of the coverage of gene transcripts expressed in the sample. As read amounts or datasize increased toward 16 Gb, the number of transcripts mapped to the entire bark assembly approached saturation. A colour matrix was subsequently generated to illustrate sequencing depth requirement in relation to the degree of coverage of total sample transcripts.</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">We devised a procedure, the "transcript mapping saturation test", to estimate the amount of RNA-Seq reads needed for deep coverage of transcriptomes. For Hevea de novo assembly, we propose generating between 5-8 Gb reads, whereby around 90% transcript coverage could be achieved with optimized k-mers and transcript N50 length. The principle behind this methodology may also be applied to other non-model plants, or with reads from other second generation sequencing platforms.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Chow</LastName><ForeName>Keng-See</ForeName><Initials>KS</Initials><AffiliationInfo><Affiliation>Biotechnology Unit, Malaysian Rubber Board, Rubber Research Institute of Malaysia, Experiment Station, Kuala Lumpur 47000, Sungai Buloh, Selangor, Malaysia. kschow@lgm.gov.my.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ghazali</LastName><ForeName>Ahmad-Kamal</ForeName><Initials>AK</Initials></Author><Author ValidYN="Y"><LastName>Hoh</LastName><ForeName>Chee-Choong</ForeName><Initials>CC</Initials></Author><Author ValidYN="Y"><LastName>Mohd-Zainuddin</LastName><ForeName>Zainorlina</ForeName><Initials>Z</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D003160">Comparative Study</PublicationType><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>2014</Year><Month>02</Month><Day>01</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="D010940">Plant Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D012333">RNA, Messenger</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D018749">RNA, Plant</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D030541" MajorTopicYN="N">Databases, Genetic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020869" MajorTopicYN="N">Gene Expression Profiling</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018506" MajorTopicYN="Y">Gene Expression Regulation, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D015723" MajorTopicYN="N">Gene Library</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017343" MajorTopicYN="N">Genes, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D028482" MajorTopicYN="N">Hevea</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D059014" MajorTopicYN="N">High-Throughput Nucleotide Sequencing</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016366" MajorTopicYN="N">Open Reading Frames</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D024301" MajorTopicYN="N">Plant Bark</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018515" MajorTopicYN="N">Plant Leaves</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010940" MajorTopicYN="N">Plant Proteins</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012333" MajorTopicYN="N">RNA, Messenger</DescriptorName><QualifierName UI="Q000096" MajorTopicYN="N">biosynthesis</QualifierName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000302" MajorTopicYN="N">isolation & purification</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018749" MajorTopicYN="N">RNA, Plant</DescriptorName><QualifierName UI="Q000096" MajorTopicYN="N">biosynthesis</QualifierName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000302" MajorTopicYN="N">isolation & purification</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D015203" MajorTopicYN="N">Reproducibility of Results</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D059467" MajorTopicYN="Y">Transcriptome</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2013</Year><Month>09</Month><Day>11</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2014</Year><Month>01</Month><Day>17</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2014</Year><Month>2</Month><Day>4</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2014</Year><Month>2</Month><Day>4</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2014</Year><Month>9</Month><Day>4</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">24484543</ArticleId><ArticleId IdType="pii">1756-0500-7-69</ArticleId><ArticleId IdType="doi">10.1186/1756-0500-7-69</ArticleId><ArticleId IdType="pmc">PMC3926681</ArticleId></ArticleIdList><ReferenceList><Reference><Citation>Nat Rev Genet. 2009 Jan;10(1):57-63</Citation><ArticleIdList><ArticleId IdType="pubmed">19015660</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Plant Biol. 2012;12:244</Citation><ArticleIdList><ArticleId IdType="pubmed">23268714</ArticleId></ArticleIdList></Reference><Reference><Citation>J Exp Bot. 2007;58(10):2429-40</Citation><ArticleIdList><ArticleId IdType="pubmed">17545224</ArticleId></ArticleIdList></Reference><Reference><Citation>J Exp Bot. 2012 Mar;63(5):1863-71</Citation><ArticleIdList><ArticleId IdType="pubmed">22162870</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Bioinformatics. 2005;6:31</Citation><ArticleIdList><ArticleId IdType="pubmed">15713233</ArticleId></ArticleIdList></Reference><Reference><Citation>DNA Res. 2011 Dec;18(6):471-82</Citation><ArticleIdList><ArticleId IdType="pubmed">22086998</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2011 Aug 1;27(15):2031-7</Citation><ArticleIdList><ArticleId IdType="pubmed">21636596</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Genomics. 2010;11:681</Citation><ArticleIdList><ArticleId IdType="pubmed">21122097</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2012 Apr 15;28(8):1086-92</Citation><ArticleIdList><ArticleId IdType="pubmed">22368243</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Bioinformatics. 2011;12 Suppl 14:S2</Citation><ArticleIdList><ArticleId IdType="pubmed">22373417</ArticleId></ArticleIdList></Reference><Reference><Citation>Tree Physiol. 2000 Apr;20(8):503-510</Citation><ArticleIdList><ArticleId IdType="pubmed">12651430</ArticleId></ArticleIdList></Reference><Reference><Citation>Proc Natl Acad Sci U S A. 1990 Mar;87(5):1787-90</Citation><ArticleIdList><ArticleId IdType="pubmed">11607069</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Biotechnol. 2010 May;28(5):421-3</Citation><ArticleIdList><ArticleId IdType="pubmed">20458303</ArticleId></ArticleIdList></Reference><Reference><Citation>PLoS One. 2011;6(6):e21220</Citation><ArticleIdList><ArticleId IdType="pubmed">21731678</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Res. 2008 May;18(5):821-9</Citation><ArticleIdList><ArticleId IdType="pubmed">18349386</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Genomics. 2011;12:30</Citation><ArticleIdList><ArticleId IdType="pubmed">21232141</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Genomics. 2010;11:726</Citation><ArticleIdList><ArticleId IdType="pubmed">21182800</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Rev Genet. 2011 Feb;12(2):87-98</Citation><ArticleIdList><ArticleId IdType="pubmed">21191423</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Genomics. 2011;12:600</Citation><ArticleIdList><ArticleId IdType="pubmed">22151917</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Genomics. 2013;14:75</Citation><ArticleIdList><ArticleId IdType="pubmed">23375136</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Plant Biol. 2012;12:222</Citation><ArticleIdList><ArticleId IdType="pubmed">23171377</ArticleId></ArticleIdList></Reference><Reference><Citation>Plant Cell Physiol. 2013 May;54(5):673-85</Citation><ArticleIdList><ArticleId IdType="pubmed">23493402</ArticleId></ArticleIdList></Reference><Reference><Citation>DNA Res. 2011 Feb;18(1):53-63</Citation><ArticleIdList><ArticleId IdType="pubmed">21217129</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Ecol Resour. 2012 Mar;12(2):333-43</Citation><ArticleIdList><ArticleId IdType="pubmed">21999839</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Rev Genet. 2011 Oct;12(10):671-82</Citation><ArticleIdList><ArticleId IdType="pubmed">21897427</ArticleId></ArticleIdList></Reference><Reference><Citation>Am J Bot. 2012 Feb;99(2):267-76</Citation><ArticleIdList><ArticleId IdType="pubmed">22301897</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Plant Biol. 2012;12:168</Citation><ArticleIdList><ArticleId IdType="pubmed">22984782</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Biotechnol. 2011 Jul;29(7):644-52</Citation><ArticleIdList><ArticleId IdType="pubmed">21572440</ArticleId></ArticleIdList></Reference><Reference><Citation>Plant Mol Biol. 2012 Jul;79(4-5):413-27</Citation><ArticleIdList><ArticleId IdType="pubmed">22580955</ArticleId></ArticleIdList></Reference><Reference><Citation>Plant Cell Physiol. 2013 Jul;54(7):1132-51</Citation><ArticleIdList><ArticleId IdType="pubmed">23624675</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 2009 Jan;37(1):289-97</Citation><ArticleIdList><ArticleId IdType="pubmed">19042974</ArticleId></ArticleIdList></Reference><Reference><Citation>PLoS One. 2012;7(6):e38653</Citation><ArticleIdList><ArticleId IdType="pubmed">22723874</ArticleId></ArticleIdList></Reference><Reference><Citation>Am J Bot. 2011 Nov;98(11):e337-8</Citation><ArticleIdList><ArticleId IdType="pubmed">22025294</ArticleId></ArticleIdList></Reference><Reference><Citation>Plant Cell Physiol. 2011 Sep;52(9):1501-14</Citation><ArticleIdList><ArticleId IdType="pubmed">21771864</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Genomics. 2011;12:389</Citation><ArticleIdList><ArticleId IdType="pubmed">21810238</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Genomics. 2011;12:342</Citation><ArticleIdList><ArticleId IdType="pubmed">21729267</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Genomics. 2013;14:279</Citation><ArticleIdList><ArticleId IdType="pubmed">23617896</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Res. 2009 Jun;19(6):1117-23</Citation><ArticleIdList><ArticleId IdType="pubmed">19251739</ArticleId></ArticleIdList></Reference><Reference><Citation>Plant Sci. 2012 Feb;183:149-58</Citation><ArticleIdList><ArticleId IdType="pubmed">22195588</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Genomics. 2010;11:180</Citation><ArticleIdList><ArticleId IdType="pubmed">20233449</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Genomics. 2012;13:92</Citation><ArticleIdList><ArticleId IdType="pubmed">22417298</ArticleId></ArticleIdList></Reference><Reference><Citation>J Mol Biol. 1990 Oct 5;215(3):403-10</Citation><ArticleIdList><ArticleId IdType="pubmed">2231712</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Genomics. 2011;12:227</Citation><ArticleIdList><ArticleId IdType="pubmed">21569327</ArticleId></ArticleIdList></Reference><Reference><Citation>Plant Mol Biol. 2011 Oct;77(3):299-308</Citation><ArticleIdList><ArticleId IdType="pubmed">21811850</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Res. 2010 Oct;20(10):1432-40</Citation><ArticleIdList><ArticleId IdType="pubmed">20693479</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Genomics. 2012;13:192</Citation><ArticleIdList><ArticleId IdType="pubmed">22607098</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Biol. 2011;12(10):R102</Citation><ArticleIdList><ArticleId IdType="pubmed">22014239</ArticleId></ArticleIdList></Reference><Reference><Citation>PLoS One. 2012;7(2):e31410</Citation><ArticleIdList><ArticleId IdType="pubmed">22384018</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Genomics. 2013;14:30</Citation><ArticleIdList><ArticleId IdType="pubmed">23324139</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Genomics. 2011;12:191</Citation><ArticleIdList><ArticleId IdType="pubmed">21492485</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Plant. 2012 Sep;5(5):1020-8</Citation><ArticleIdList><ArticleId IdType="pubmed">22241453</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Inform. 2008;21:3-14</Citation><ArticleIdList><ArticleId IdType="pubmed">19425143</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Genomics. 2012;13:392</Citation><ArticleIdList><ArticleId IdType="pubmed">22891638</ArticleId></ArticleIdList></Reference><Reference><Citation>Plant Cell Physiol. 2013 May;54(5):697-710</Citation><ArticleIdList><ArticleId IdType="pubmed">23589666</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Res. 2004 Jun;14(6):1147-59</Citation><ArticleIdList><ArticleId IdType="pubmed">15140833</ArticleId></ArticleIdList></Reference><Reference><Citation>Plant Cell Physiol. 2013 Feb;54(2):244-69</Citation><ArticleIdList><ArticleId IdType="pubmed">23292600</ArticleId></ArticleIdList></Reference><Reference><Citation>Trends Plant Sci. 2013 Apr;18(4):175-9</Citation><ArticleIdList><ArticleId IdType="pubmed">23481128</ArticleId></ArticleIdList></Reference><Reference><Citation>Plant Physiol. 2013 Feb;161(2):705-24</Citation><ArticleIdList><ArticleId IdType="pubmed">23197803</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Genomics. 2012;13:99</Citation><ArticleIdList><ArticleId IdType="pubmed">22429863</ArticleId></ArticleIdList></Reference><Reference><Citation>Plant Mol Biol. 2003 Nov;53(4):479-92</Citation><ArticleIdList><ArticleId IdType="pubmed">15010614</ArticleId></ArticleIdList></Reference><Reference><Citation>Plant Physiol Biochem. 2011 Jul;49(7):729-37</Citation><ArticleIdList><ArticleId IdType="pubmed">21530287</ArticleId></ArticleIdList></Reference><Reference><Citation>J Exp Bot. 2011 May;62(9):3093-102</Citation><ArticleIdList><ArticleId IdType="pubmed">21398430</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Genomics. 2011;12:539</Citation><ArticleIdList><ArticleId IdType="pubmed">22047182</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Res. 2010 Feb;20(2):265-72</Citation><ArticleIdList><ArticleId IdType="pubmed">20019144</ArticleId></ArticleIdList></Reference><Reference><Citation>PLoS One. 2012;7(8):e42082</Citation><ArticleIdList><ArticleId IdType="pubmed">22916120</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed><affiliations><list><country><li>Malaisie</li></country></list><tree><noCountry><name sortKey="Ghazali, Ahmad Kamal" sort="Ghazali, Ahmad Kamal" uniqKey="Ghazali A" first="Ahmad-Kamal" last="Ghazali">Ahmad-Kamal Ghazali</name><name sortKey="Hoh, Chee Choong" sort="Hoh, Chee Choong" uniqKey="Hoh C" first="Chee-Choong" last="Hoh">Chee-Choong Hoh</name><name sortKey="Mohd Zainuddin, Zainorlina" sort="Mohd Zainuddin, Zainorlina" uniqKey="Mohd Zainuddin Z" first="Zainorlina" last="Mohd-Zainuddin">Zainorlina Mohd-Zainuddin</name></noCountry><country name="Malaisie"><noRegion><name sortKey="Chow, Keng See" sort="Chow, Keng See" uniqKey="Chow K" first="Keng-See" last="Chow">Keng-See Chow</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/PubMed/Checkpoint
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 001769 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/PubMed/Checkpoint/biblio.hfd -nk 001769 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Sante
|area= MersV1
|flux= PubMed
|étape= Checkpoint
|type= RBID
|clé= pubmed:24484543
|texte= RNA sequencing read depth requirement for optimal transcriptome coverage in Hevea brasiliensis.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/PubMed/Checkpoint/RBID.i -Sk "pubmed:24484543" \
| HfdSelect -Kh $EXPLOR_AREA/Data/PubMed/Checkpoint/biblio.hfd \
| NlmPubMed2Wicri -a MersV1
| This area was generated with Dilib version V0.6.33. |  |