BROWSE

Related Scientist

rna's photo.

rna
rna연구단
more info

ITEM VIEW & DOWNLOAD

Partitioning RNAs by length improves transcriptome reconstruction from short-read RNA-seq data

DC Field Value Language
dc.contributor.authorRingeling, Francisca Rojas-
dc.contributor.authorChakraborty, Shounak-
dc.contributor.authorVissers, Caroline-
dc.contributor.authorReiman, Derek-
dc.contributor.authorPatel, Akshay M.-
dc.contributor.authorLee, Ki-Heon-
dc.contributor.authorAri Hong-
dc.contributor.authorPark, Chan-Woo-
dc.contributor.authorReska, Tim-
dc.contributor.authorGagneur, Julien-
dc.contributor.authorHyeshik Chang-
dc.contributor.authorSpletter, Maria L.-
dc.contributor.authorYoon, Ki-Jun-
dc.contributor.authorMing, Guo-li-
dc.contributor.authorSong, Hongjun-
dc.contributor.authorCanzar, Stefan-
dc.date.accessioned2022-05-25T04:39:32Z-
dc.date.available2022-05-25T04:39:32Z-
dc.date.created2022-01-25-
dc.date.issued2022-05-
dc.identifier.issn1087-0156-
dc.identifier.urihttps://pr.ibs.re.kr/handle/8788114/11540-
dc.description.abstract© 2022, The Author(s), under exclusive licence to Springer Nature America, Inc.The accuracy of methods for assembling transcripts from short-read RNA sequencing data is limited by the lack of long-range information. Here we introduce Ladder-seq, an approach that separates transcripts according to their lengths before sequencing and uses the additional information to improve the quantification and assembly of transcripts. Using simulated data, we show that a kallisto algorithm extended to process Ladder-seq data quantifies transcripts of complex genes with substantially higher accuracy than conventional kallisto. For reference-based assembly, a tailored scheme based on the StringTie2 algorithm reconstructs a single transcript with 30.8% higher precision than its conventional counterpart and is more than 30% more sensitive for complex genes. For de novo assembly, a similar scheme based on the Trinity algorithm correctly assembles 78% more transcripts than conventional Trinity while improving precision by 78%. In experimental data, Ladder-seq reveals 40% more genes harboring isoform switches compared to conventional RNA sequencing and unveils widespread changes in isoform usage upon m6A depletion by Mettl14 knockout.-
dc.language영어-
dc.publisherNature Research-
dc.titlePartitioning RNAs by length improves transcriptome reconstruction from short-read RNA-seq data-
dc.typeArticle-
dc.type.rimsART-
dc.identifier.wosid000741591700001-
dc.identifier.scopusid2-s2.0-85122675318-
dc.identifier.rimsid77140-
dc.contributor.affiliatedAuthorAri Hong-
dc.contributor.affiliatedAuthorHyeshik Chang-
dc.identifier.doi10.1038/s41587-021-01136-7-
dc.identifier.bibliographicCitationNature Biotechnology, v.40, no.5, pp.741 - 750-
dc.relation.isPartOfNature Biotechnology-
dc.citation.titleNature Biotechnology-
dc.citation.volume40-
dc.citation.number5-
dc.citation.startPage741-
dc.citation.endPage750-
dc.type.docTypeArticle-
dc.description.journalClass1-
dc.description.journalClass1-
dc.description.isOpenAccessN-
dc.description.journalRegisteredClassscie-
dc.description.journalRegisteredClassscopus-
dc.relation.journalResearchAreaBiotechnology & Applied Microbiology-
dc.relation.journalWebOfScienceCategoryBiotechnology & Applied Microbiology-
dc.subject.keywordPlusINTRON RETENTION-
dc.subject.keywordPlusGENE-
dc.subject.keywordPlusISOFORM-
dc.subject.keywordPlusLANDSCAPE-
dc.subject.keywordPlusSTRINGTIE-
Appears in Collections:
Center for RNA Research(RNA 연구단) > 1. Journal Papers (저널논문)
Files in This Item:
There are no files associated with this item.

qrcode

  • facebook

    twitter

  • Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.
해당 아이템을 이메일로 공유하기 원하시면 인증을 거치시기 바랍니다.

Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.

Browse