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Deciphering the RNA landscape by RNAome sequencing

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dc.creatorDerks, Kasper WJspa
dc.creatorMisovic, Branislavspa
dc.creatorvan den Hout, Mirjam CGNspa
dc.creatorKockx, Christel EMspa
dc.creatorGomez, Cesar Payanspa
dc.creatorBrouwer, Rutger WWspa
dc.creatorVrieling, Harryspa
dc.creatorHoeijmakers, Jan HJspa
dc.creatorvan IJcken, Wilfred FJspa
dc.creatorPothof, Jorisspa
dc.date.accessioned2020-05-26T00:00:41Z
dc.date.available2020-05-26T00:00:41Z
dc.date.created2015spa
dc.description.abstractCurrent RNA expression profiling methods rely on enrichment steps for specific RNA classes, thereby not detecting all RNA species in an unperturbed manner. We report strand-specific RNAome sequencing that determines expression of small and large RNAs from rRNA-depleted total RNA in a single sequence run. Since current analysis pipelines cannot reliably analyze small and large RNAs simultaneously, we developed TRAP, Total Rna Analysis Pipeline, a robust interface that is also compatible with existing RNA sequencing protocols. RNAome sequencing quantitatively preserved all RNA classes, allowing cross-class comparisons that facilitates the identification of relationships between different RNA classes. We demonstrate the strength of RNAome sequencing in mouse embryonic stem cells treated with cisplatin. MicroRNA and mRNA expression in RNAome sequencing significantly correlated between replicates and was in concordance with both existing RNA sequencing methods and gene expression arrays generated from the same samples. Moreover, RNAome sequencing also detected additional RNA classes such as enhancer RNAs, anti-sense RNAs, novel RNA species and numerous differentially expressed RNAs undetectable by other methods. At the level of complete RNA classes, RNAome sequencing also identified a specific global repression of the microRNA and microRNA isoform classes after cisplatin treatment whereas all other classes such as mRNAs were unchanged. These characteristics of RNAome sequencing will significantly improve expression analysis as well as studies on RNA biology not covered by existing methods. © Kasper WJ Derks, Branislav Misovic, Mirjam CGN van den Hout, Christel EM Kockx, Cesar Payan Gomez, Rutger WW Brouwer, Harry Vrieling, Jan HJ Hoeijmakers, Wilfred FJ van IJcken, and Joris Pothof.eng
dc.format.mimetypeapplication/pdf
dc.identifier.doihttps://doi.org/10.1080/15476286.2015.1017202
dc.identifier.issn15558584
dc.identifier.issn15476286
dc.identifier.urihttps://repository.urosario.edu.co/handle/10336/23257
dc.language.isoengspa
dc.publisherTaylor and Francis Inc.spa
dc.relation.citationEndPage42
dc.relation.citationIssueNo. 1
dc.relation.citationStartPage30
dc.relation.citationTitleRNA Biology
dc.relation.citationVolumeVol. 12
dc.relation.ispartofRNA Biology, ISSN:15558584, 15476286, Vol.12, No.1 (2015); pp. 30-42spa
dc.relation.urihttps://www.scopus.com/inward/record.uri?eid=2-s2.0-84928229123&doi=10.1080%2f15476286.2015.1017202&partnerID=40&md5=bbcb72448f90253529d286cd520f1bdcspa
dc.rights.accesRightsinfo:eu-repo/semantics/openAccess
dc.rights.accesoAbierto (Texto Completo)spa
dc.source.instnameinstname:Universidad del Rosariospa
dc.source.reponamereponame:Repositorio Institucional EdocURspa
dc.subject.keywordCisplatinspa
dc.subject.keywordLong untranslated rnaspa
dc.subject.keywordMessenger rnaspa
dc.subject.keywordMicrornaspa
dc.subject.keywordPolyadenylated rnaspa
dc.subject.keywordRibosome rnaspa
dc.subject.keywordRnaspa
dc.subject.keywordSmall nucleolar rnaspa
dc.subject.keywordRnaspa
dc.subject.keywordTranscriptomespa
dc.subject.keywordAlgorithmspa
dc.subject.keywordAnimal cellspa
dc.subject.keywordApoptosisspa
dc.subject.keywordArticlespa
dc.subject.keywordControlled studyspa
dc.subject.keywordDna libraryspa
dc.subject.keywordEmbryospa
dc.subject.keywordEmbryonic stem cellspa
dc.subject.keywordEnhancer regionspa
dc.subject.keywordGene expressionspa
dc.subject.keywordGene repressionspa
dc.subject.keywordGenetic codespa
dc.subject.keywordGenetic transcriptionspa
dc.subject.keywordMicroarray analysisspa
dc.subject.keywordMousespa
dc.subject.keywordNonhumanspa
dc.subject.keywordQuantitative analysisspa
dc.subject.keywordRna analysisspa
dc.subject.keywordRna isolationspa
dc.subject.keywordRna sequencespa
dc.subject.keywordRna synthesisspa
dc.subject.keywordAnimalspa
dc.subject.keywordHigh throughput sequencingspa
dc.subject.keywordHumanspa
dc.subject.keywordMetabolismspa
dc.subject.keywordProceduresspa
dc.subject.keywordSequence analysisspa
dc.subject.keywordAnimalsspa
dc.subject.keywordHigh-throughput nucleotide sequencingspa
dc.subject.keywordHumansspa
dc.subject.keywordMicespa
dc.subject.keywordRnaspa
dc.subject.keywordSequence analysiseng
dc.subject.keywordTranscriptomespa
dc.subject.keywordNon-coding rnaspa
dc.subject.keywordRna abundancespa
dc.subject.keywordRna expressionspa
dc.subject.keywordRnaomespa
dc.subject.keywordStrand-specific rna-sequencingspa
dc.subject.keywordWhole transcriptomespa
dc.titleDeciphering the RNA landscape by RNAome sequencingspa
dc.typearticleeng
dc.type.hasVersioninfo:eu-repo/semantics/publishedVersion
dc.type.spaArtículospa
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