High-resolution transcriptome analysis with long-read RNA sequencing.

RNA sequencing (RNA-seq) enables characterization and quantification of individual transcriptomes as well as detection of patterns of allelic expression and alternative splicing. Current RNA-seq protocols depend on high-throughput short-read sequencing of cDNA. However, as ongoing advances are rapid...

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Autores principales:	Hyunghoon Cho, Joe Davis, Xin Li, Kevin S Smith, Alexis Battle, Stephen B Montgomery
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/d4b54e189ae8400da95c277d2d2aa905
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spelling	oai:doaj.org-article:d4b54e189ae8400da95c277d2d2aa9052021-11-25T05:59:24ZHigh-resolution transcriptome analysis with long-read RNA sequencing.1932-620310.1371/journal.pone.0108095https://doaj.org/article/d4b54e189ae8400da95c277d2d2aa9052014-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0108095https://doaj.org/toc/1932-6203RNA sequencing (RNA-seq) enables characterization and quantification of individual transcriptomes as well as detection of patterns of allelic expression and alternative splicing. Current RNA-seq protocols depend on high-throughput short-read sequencing of cDNA. However, as ongoing advances are rapidly yielding increasing read lengths, a technical hurdle remains in identifying the degree to which differences in read length influence various transcriptome analyses. In this study, we generated two paired-end RNA-seq datasets of differing read lengths (2×75 bp and 2×262 bp) for lymphoblastoid cell line GM12878 and compared the effect of read length on transcriptome analyses, including read-mapping performance, gene and transcript quantification, and detection of allele-specific expression (ASE) and allele-specific alternative splicing (ASAS) patterns. Our results indicate that, while the current long-read protocol is considerably more expensive than short-read sequencing, there are important benefits that can only be achieved with longer read length, including lower mapping bias and reduced ambiguity in assigning reads to genomic elements, such as mRNA transcript. We show that these benefits ultimately lead to improved detection of cis-acting regulatory and splicing variation effects within individuals.Hyunghoon ChoJoe DavisXin LiKevin S SmithAlexis BattleStephen B MontgomeryPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 9, p e108095 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Hyunghoon Cho Joe Davis Xin Li Kevin S Smith Alexis Battle Stephen B Montgomery High-resolution transcriptome analysis with long-read RNA sequencing.
description	RNA sequencing (RNA-seq) enables characterization and quantification of individual transcriptomes as well as detection of patterns of allelic expression and alternative splicing. Current RNA-seq protocols depend on high-throughput short-read sequencing of cDNA. However, as ongoing advances are rapidly yielding increasing read lengths, a technical hurdle remains in identifying the degree to which differences in read length influence various transcriptome analyses. In this study, we generated two paired-end RNA-seq datasets of differing read lengths (2×75 bp and 2×262 bp) for lymphoblastoid cell line GM12878 and compared the effect of read length on transcriptome analyses, including read-mapping performance, gene and transcript quantification, and detection of allele-specific expression (ASE) and allele-specific alternative splicing (ASAS) patterns. Our results indicate that, while the current long-read protocol is considerably more expensive than short-read sequencing, there are important benefits that can only be achieved with longer read length, including lower mapping bias and reduced ambiguity in assigning reads to genomic elements, such as mRNA transcript. We show that these benefits ultimately lead to improved detection of cis-acting regulatory and splicing variation effects within individuals.
format	article
author	Hyunghoon Cho Joe Davis Xin Li Kevin S Smith Alexis Battle Stephen B Montgomery
author_facet	Hyunghoon Cho Joe Davis Xin Li Kevin S Smith Alexis Battle Stephen B Montgomery
author_sort	Hyunghoon Cho
title	High-resolution transcriptome analysis with long-read RNA sequencing.
title_short	High-resolution transcriptome analysis with long-read RNA sequencing.
title_full	High-resolution transcriptome analysis with long-read RNA sequencing.
title_fullStr	High-resolution transcriptome analysis with long-read RNA sequencing.
title_full_unstemmed	High-resolution transcriptome analysis with long-read RNA sequencing.
title_sort	high-resolution transcriptome analysis with long-read rna sequencing.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/d4b54e189ae8400da95c277d2d2aa905
work_keys_str_mv	AT hyunghooncho highresolutiontranscriptomeanalysiswithlongreadrnasequencing AT joedavis highresolutiontranscriptomeanalysiswithlongreadrnasequencing AT xinli highresolutiontranscriptomeanalysiswithlongreadrnasequencing AT kevinssmith highresolutiontranscriptomeanalysiswithlongreadrnasequencing AT alexisbattle highresolutiontranscriptomeanalysiswithlongreadrnasequencing AT stephenbmontgomery highresolutiontranscriptomeanalysiswithlongreadrnasequencing
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High-resolution transcriptome analysis with long-read RNA sequencing.

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