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.
authors.affiliation: The CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, 100029 Beijing, China.
authors.forename: Peng
authors.initials: P
authors.lastname: Cui
authors.forename: Qiang
authors.initials: Q
authors.lastname: Lin
authors.forename: Feng
authors.initials: F
authors.lastname: Ding
authors.forename: Chengqi
authors.initials: C
authors.lastname: Xin
authors.forename: Wei
authors.initials: W
authors.lastname: Gong
authors.forename: Lingfang
authors.initials: L
authors.lastname: Zhang
authors.forename: Jianing
authors.initials: J
authors.lastname: Geng
authors.forename: Bing
authors.initials: B
authors.lastname: Zhang
authors.forename: Xiaomin
authors.initials: X
authors.lastname: Yu
authors.forename: Jin
authors.initials: J
authors.lastname: Yang
authors.forename: Songnian
authors.initials: S
authors.lastname: Hu
authors.forename: Jun
authors.initials: J
authors.lastname: Yu
mesh_terms: D000818:Animals; D054022:Cerebrum / Q000737:chemistry / Q000378:metabolism; D020869:Gene Expression Profiling; D016678:Genome / Q000235:genetics; D051379:Mice; D011061:Poly A / Q000235:genetics*; D011506:Proteins / Q000235:genetics / Q000378:metabolism; D012313:RNA / Q000145:classification / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D012335:RNA, Ribosomal / Q000235:genetics*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D011506:Proteins; D012333:RNA, Messenger; D012335:RNA, Ribosomal; D011061:Poly A; D012313:RNA