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

Research output: Contribution to journalArticlepeer-review

138 Scopus citations


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 languageEnglish (US)
Pages (from-to)259-265
Number of pages7
Issue number5
StatePublished - 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.


  • MRNA-seq
  • RNA-seq
  • Ribominus

ASJC Scopus subject areas

  • Genetics


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