Low-cost, Low-bias and Low-input RNA-seq with High Experimental Verifiability based on Semiconductor Sequencing

Abstract Low-input RNA-seq is powerful to represent the gene expression profiles with limited number of cells, especially when single-cell variations are not the aim. However, pre-amplification-based and molecule index-based library construction methods boost bias or require higher throughput. Here...

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Autores principales:	Zhibiao Mai, Chuanle Xiao, Jingjie Jin, Gong Zhang
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/6658cb2a6d154f31904cc68f248dfdad
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spelling	oai:doaj.org-article:6658cb2a6d154f31904cc68f248dfdad2021-12-02T15:05:14ZLow-cost, Low-bias and Low-input RNA-seq with High Experimental Verifiability based on Semiconductor Sequencing10.1038/s41598-017-01165-w2045-2322https://doaj.org/article/6658cb2a6d154f31904cc68f248dfdad2017-04-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-01165-whttps://doaj.org/toc/2045-2322Abstract Low-input RNA-seq is powerful to represent the gene expression profiles with limited number of cells, especially when single-cell variations are not the aim. However, pre-amplification-based and molecule index-based library construction methods boost bias or require higher throughput. Here we demonstrate a simple, low-cost, low-bias and low-input RNA-seq with ion torrent semiconductor sequencing (LIEA RNA-seq). We also developed highly accurate and error-tolerant spliced mapping algorithm FANSe2splice to accurately map the single-ended reads to the reference genome with better experimental verifiability than the previous spliced mappers. Combining the experimental and computational advancements, our solution is comparable with the bulk mRNA-seq in quantification, reliably detects splice junctions and minimizes the bias with much less mappable reads.Zhibiao MaiChuanle XiaoJingjie JinGong ZhangNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-10 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Zhibiao Mai Chuanle Xiao Jingjie Jin Gong Zhang Low-cost, Low-bias and Low-input RNA-seq with High Experimental Verifiability based on Semiconductor Sequencing
description	Abstract Low-input RNA-seq is powerful to represent the gene expression profiles with limited number of cells, especially when single-cell variations are not the aim. However, pre-amplification-based and molecule index-based library construction methods boost bias or require higher throughput. Here we demonstrate a simple, low-cost, low-bias and low-input RNA-seq with ion torrent semiconductor sequencing (LIEA RNA-seq). We also developed highly accurate and error-tolerant spliced mapping algorithm FANSe2splice to accurately map the single-ended reads to the reference genome with better experimental verifiability than the previous spliced mappers. Combining the experimental and computational advancements, our solution is comparable with the bulk mRNA-seq in quantification, reliably detects splice junctions and minimizes the bias with much less mappable reads.
format	article
author	Zhibiao Mai Chuanle Xiao Jingjie Jin Gong Zhang
author_facet	Zhibiao Mai Chuanle Xiao Jingjie Jin Gong Zhang
author_sort	Zhibiao Mai
title	Low-cost, Low-bias and Low-input RNA-seq with High Experimental Verifiability based on Semiconductor Sequencing
title_short	Low-cost, Low-bias and Low-input RNA-seq with High Experimental Verifiability based on Semiconductor Sequencing
title_full	Low-cost, Low-bias and Low-input RNA-seq with High Experimental Verifiability based on Semiconductor Sequencing
title_fullStr	Low-cost, Low-bias and Low-input RNA-seq with High Experimental Verifiability based on Semiconductor Sequencing
title_full_unstemmed	Low-cost, Low-bias and Low-input RNA-seq with High Experimental Verifiability based on Semiconductor Sequencing
title_sort	low-cost, low-bias and low-input rna-seq with high experimental verifiability based on semiconductor sequencing
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/6658cb2a6d154f31904cc68f248dfdad
work_keys_str_mv	AT zhibiaomai lowcostlowbiasandlowinputrnaseqwithhighexperimentalverifiabilitybasedonsemiconductorsequencing AT chuanlexiao lowcostlowbiasandlowinputrnaseqwithhighexperimentalverifiabilitybasedonsemiconductorsequencing AT jingjiejin lowcostlowbiasandlowinputrnaseqwithhighexperimentalverifiabilitybasedonsemiconductorsequencing AT gongzhang lowcostlowbiasandlowinputrnaseqwithhighexperimentalverifiabilitybasedonsemiconductorsequencing
_version_	1718388894024597504

Low-cost, Low-bias and Low-input RNA-seq with High Experimental Verifiability based on Semiconductor Sequencing

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