A comparison between ribo-minus RNA-sequencing and polyA-selected RNA-sequencing

Peng Cui; Qiang Lin; Feng Ding; Chengqi Xin; Wei Gong; Lingfang Zhang; Jianing Geng; Bing Zhang; Xiaomin Yu; Jin Yang; Songnian Hu; Jun Yu

doi:10.1016/j.ygeno.2010.07.010

A comparison between ribo-minus RNA-sequencing and polyA-selected RNA-sequencing

Peng Cui, Qiang Lin, Feng Ding, Chengqi Xin, Wei Gong, Lingfang Zhang, Jianing Geng, Bing Zhang, Xiaomin Yu, Jin Yang, Songnian Hu^*, Jun Yu

^*Corresponding author for this work

Biological, Environmental Sciences and Engineering

Research output: Contribution to journal › Article › peer-review

146 Scopus citations

Abstract

To compare the two RNA-sequencing protocols, ribo-minus RNA-sequencing (rmRNA-seq) and polyA-selected RNA-sequencing (mRNA-seq), we acquired transcriptomic data-52 and 32 million alignable reads of 35 bases in length-from the mouse cerebrum, respectively. We found that a higher proportion, 44% and 25%, of the uniquely alignable rmRNA-seq reads, is in intergenic and intronic regions, respectively, as compared to 23% and 15% from the mRNA-seq dataset. Further analysis made an additional discovery of transcripts of protein-coding genes (such as Histone, Heg1, and Dux), ncRNAs, snoRNAs, snRNAs, and novel ncRNAs as well as repeat elements in rmRNA-seq dataset. This result suggests that rmRNA-seq method should detect more polyA- or bimorphic transcripts. Finally, through comparative analyses of gene expression profiles among multiple datasets, we demonstrated that different RNA sample preparations may result in significant variations in gene expression profiles.

Original language	English (US)
Pages (from-to)	259-265
Number of pages	7
Journal	Genomics
Volume	96
Issue number	5
DOIs	https://doi.org/10.1016/j.ygeno.2010.07.010
State	Published - Nov 2010

Bibliographical note

Funding Information:
This study is supported by a grant ( 2006CB910401 , 2006CB910403 , 2006CB910404 ) from the National Basic Research Program (973 Program), the Ministry of Science and Technology of the People's Republic of China. The authors especially thank the LT's experts Hongying Yin, Xin Li, Jiandong Sun, Yangzhou Wang, Bob Nutter, Max Ingman for supporting on the technique and reagents of the experiments.

Keywords

MRNA-seq
RNA-seq
Ribominus

ASJC Scopus subject areas

Genetics

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10.1016/j.ygeno.2010.07.010

Cite this

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title = "A comparison between ribo-minus RNA-sequencing and polyA-selected RNA-sequencing",

abstract = "To compare the two RNA-sequencing protocols, ribo-minus RNA-sequencing (rmRNA-seq) and polyA-selected RNA-sequencing (mRNA-seq), we acquired transcriptomic data-52 and 32 million alignable reads of 35 bases in length-from the mouse cerebrum, respectively. We found that a higher proportion, 44% and 25%, of the uniquely alignable rmRNA-seq reads, is in intergenic and intronic regions, respectively, as compared to 23% and 15% from the mRNA-seq dataset. Further analysis made an additional discovery of transcripts of protein-coding genes (such as Histone, Heg1, and Dux), ncRNAs, snoRNAs, snRNAs, and novel ncRNAs as well as repeat elements in rmRNA-seq dataset. This result suggests that rmRNA-seq method should detect more polyA- or bimorphic transcripts. Finally, through comparative analyses of gene expression profiles among multiple datasets, we demonstrated that different RNA sample preparations may result in significant variations in gene expression profiles.",

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author = "Peng Cui and Qiang Lin and Feng Ding and Chengqi Xin and Wei Gong and Lingfang Zhang and Jianing Geng and Bing Zhang and Xiaomin Yu and Jin Yang and Songnian Hu and Jun Yu",

note = "Funding Information: This study is supported by a grant ( 2006CB910401 , 2006CB910403 , 2006CB910404 ) from the National Basic Research Program (973 Program), the Ministry of Science and Technology of the People's Republic of China. The authors especially thank the LT's experts Hongying Yin, Xin Li, Jiandong Sun, Yangzhou Wang, Bob Nutter, Max Ingman for supporting on the technique and reagents of the experiments.",

year = "2010",

month = nov,

doi = "10.1016/j.ygeno.2010.07.010",

language = "English (US)",

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pages = "259--265",

journal = "Genomics",

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AU - Cui, Peng

AU - Lin, Qiang

AU - Ding, Feng

AU - Xin, Chengqi

AU - Gong, Wei

AU - Zhang, Lingfang

AU - Geng, Jianing

AU - Zhang, Bing

AU - Yu, Xiaomin

AU - Yang, Jin

AU - Hu, Songnian

AU - Yu, Jun

N1 - Funding Information: This study is supported by a grant ( 2006CB910401 , 2006CB910403 , 2006CB910404 ) from the National Basic Research Program (973 Program), the Ministry of Science and Technology of the People's Republic of China. The authors especially thank the LT's experts Hongying Yin, Xin Li, Jiandong Sun, Yangzhou Wang, Bob Nutter, Max Ingman for supporting on the technique and reagents of the experiments.

PY - 2010/11

Y1 - 2010/11

N2 - To compare the two RNA-sequencing protocols, ribo-minus RNA-sequencing (rmRNA-seq) and polyA-selected RNA-sequencing (mRNA-seq), we acquired transcriptomic data-52 and 32 million alignable reads of 35 bases in length-from the mouse cerebrum, respectively. We found that a higher proportion, 44% and 25%, of the uniquely alignable rmRNA-seq reads, is in intergenic and intronic regions, respectively, as compared to 23% and 15% from the mRNA-seq dataset. Further analysis made an additional discovery of transcripts of protein-coding genes (such as Histone, Heg1, and Dux), ncRNAs, snoRNAs, snRNAs, and novel ncRNAs as well as repeat elements in rmRNA-seq dataset. This result suggests that rmRNA-seq method should detect more polyA- or bimorphic transcripts. Finally, through comparative analyses of gene expression profiles among multiple datasets, we demonstrated that different RNA sample preparations may result in significant variations in gene expression profiles.

AB - To compare the two RNA-sequencing protocols, ribo-minus RNA-sequencing (rmRNA-seq) and polyA-selected RNA-sequencing (mRNA-seq), we acquired transcriptomic data-52 and 32 million alignable reads of 35 bases in length-from the mouse cerebrum, respectively. We found that a higher proportion, 44% and 25%, of the uniquely alignable rmRNA-seq reads, is in intergenic and intronic regions, respectively, as compared to 23% and 15% from the mRNA-seq dataset. Further analysis made an additional discovery of transcripts of protein-coding genes (such as Histone, Heg1, and Dux), ncRNAs, snoRNAs, snRNAs, and novel ncRNAs as well as repeat elements in rmRNA-seq dataset. This result suggests that rmRNA-seq method should detect more polyA- or bimorphic transcripts. Finally, through comparative analyses of gene expression profiles among multiple datasets, we demonstrated that different RNA sample preparations may result in significant variations in gene expression profiles.

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A comparison between ribo-minus RNA-sequencing and polyA-selected RNA-sequencing

Abstract

Bibliographical note

Keywords

ASJC Scopus subject areas

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