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Analysis of mammalian native elongating transcript sequencing (mNET-seq) high-throughput data

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dc.contributor.authorPrudêncio, Pedro
dc.contributor.authorRebelo, Kenny
dc.contributor.authorGrosso, Ana Rita
dc.contributor.authorGoncalo Martinho, Rui
dc.contributor.authorCarmo-Fonseca, Maria
dc.date.accessioned2022-01-21T16:31:32Z
dc.date.available2022-01-21T16:31:32Z
dc.date.issued2020
dc.description© 2019 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/BY-NC-ND/4.0/)pt_PT
dc.description.abstractMammalian Native Elongating Transcript sequencing (mNET-seq) is a recently developed technique that generates genome-wide profiles of nascent transcripts associated with RNA polymerase II (Pol II) elongation complexes. The ternary transcription complexes formed by Pol II, DNA template and nascent RNA are first isolated, without crosslinking, by immunoprecipitation with antibodies that specifically recognize the different phosphorylation states of the polymerase large subunit C-terminal domain (CTD). The coordinate of the 3' end of the RNA in the complexes is then identified by high-throughput sequencing. The main advantage of mNET-seq is that it provides global, bidirectional maps of Pol II CTD phosphorylation-specific nascent transcripts and coupled RNA processing at single nucleotide resolution. Here we describe the general pipeline to prepare and analyse high-throughput data from mNET-seq experiments.pt_PT
dc.description.sponsorshipM.C.-F. acknowledges funding from Fundação para a Ciência e Tecnologia (FCT)/ Ministério da Ciência, Tecnologia e Ensino Superior (MCTES) through Fundos do Orçamento de Estado (UID/BIM/50005/2019), and FCT/FEDER/POR Lisboa 2020, Programa Operacional Regional de Lisboa, PORTUGAL 2020 (LISBOA-01-0145-FEDER-016394).. R.G.M. is supported by FCT grants PTDC/BEX-BID/0395/2014, PTDC/BIA-BID/28441/2017, and UID/BIM/04773/2013 CBMR 1334.pt_PT
dc.description.versioninfo:eu-repo/semantics/publishedVersionpt_PT
dc.identifier.citationMethods 178 (2020) 89–95pt_PT
dc.identifier.doi10.1016/j.ymeth.2019.09.003pt_PT
dc.identifier.eissn1095-9130
dc.identifier.issn1046-2023
dc.identifier.urihttp://hdl.handle.net/10451/50918
dc.language.isoengpt_PT
dc.peerreviewedyespt_PT
dc.publisherElsevierpt_PT
dc.relationLISBOA-01-0145-FEDER-016394pt_PT
dc.relationInstituto de Medicina Molecular
dc.relationCBMR 1334pt_PT
dc.relation.publisherversionhttps://www.sciencedirect.com/journal/methodspt_PT
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/4.0/pt_PT
dc.subjectCo-transcriptional splicingpt_PT
dc.subjectNascent RNApt_PT
dc.subjectRNA polymerase IIpt_PT
dc.subjectmNET-seqpt_PT
dc.titleAnalysis of mammalian native elongating transcript sequencing (mNET-seq) high-throughput datapt_PT
dc.typejournal article
dspace.entity.typePublication
oaire.awardNumberUID/BIM/50005/2019
oaire.awardNumberPTDC/BEX-BID/0395/2014
oaire.awardNumberPTDC/BIA-BID/28441/2017
oaire.awardNumberUID/BIM/04773/2013
oaire.awardTitleInstituto de Medicina Molecular
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/6817 - DCRRNI ID/UID%2FBIM%2F50005%2F2019/PT
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/3599-PPCDT/PTDC%2FBEX-BID%2F0395%2F2014/PT
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/9471 - RIDTI/PTDC%2FBIA-BID%2F28441%2F2017/PT
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/5876/UID%2FBIM%2F04773%2F2013/PT
oaire.citation.endPage95pt_PT
oaire.citation.startPage89pt_PT
oaire.citation.titleMethodspt_PT
oaire.citation.volume178pt_PT
oaire.fundingStream6817 - DCRRNI ID
oaire.fundingStream3599-PPCDT
oaire.fundingStream9471 - RIDTI
oaire.fundingStream5876
person.familyNamePrudêncio
person.familyNameGrosso
person.familyNameMartinho
person.familyNameCarmo-Fonseca
person.givenNamePedro
person.givenNameAna Rita
person.givenNameRui Goncalo
person.givenNameMaria
person.identifierhttps://scholar.google.com/citations?hl=pt-PT&user=NnJJEewAAAAJ
person.identifierI-6656-2013
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project.funder.nameFundação para a Ciência e a Tecnologia
project.funder.nameFundação para a Ciência e a Tecnologia
project.funder.nameFundação para a Ciência e a Tecnologia
project.funder.nameFundação para a Ciência e a Tecnologia
rcaap.rightsopenAccesspt_PT
rcaap.typearticlept_PT
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