The CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, 100029 Beijing, China.
Genomics. 2010 Nov;96(5):259-65. doi: 10.1016/j.ygeno.2010.07.010. Epub 2010 Aug 3.
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.
为了比较两种 RNA 测序方案，核糖体减去 RNA 测序（rmRNA-seq）和 polyA 选择的 RNA 测序（mRNA-seq），我们分别从老鼠大脑中获得了转录组数据-52 和 3200 万个 35 个碱基长的可比对读取。我们发现，与 mRNA-seq 数据集相比，rmRNA-seq 唯一可比对的读取分别有 44%和 25%位于基因间区和内含子区，而分别有 23%和 15%。进一步的分析还发现了 rmRNA-seq 数据集中的蛋白质编码基因（如 Histone、Heg1 和 Dux）、ncRNA、snoRNA、snRNA 和新的 ncRNA 以及重复元件的转录本。这一结果表明，rmRNA-seq 方法应该能够检测到更多的 polyA 或双形态转录本。最后，通过对多个数据集的基因表达谱进行比较分析，我们证明了不同的 RNA 样本制备方法可能导致基因表达谱的显著差异。
