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

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• 作者：Peng Cui ; Qiang Lin ; Feng Ding ; Chengqi Xin ; Wei Gong ; Lingfang Zhang ; Jianing Geng ; Bing Zhang ; Xiaomin Yu ; Jin Yang ; Songnian Hu ; Jun Yu
• 关键词：Ribominus ; RNA-seq ; mRNA-seq
• 刊名：Genomics
• 出版年：2010
• 出版时间：November 2010
• 年：2010
• 卷：96
• 期：5
• 页码：259-265
• 全文大小：1010 K

文摘

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.