Tandonnet Sophie, Torres Tatiana Teixeira
Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil.
Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, SP, Brazil; Research Center on Biodiversity and Computing (BioComp-USP), Universidade de São Paulo (USP), São Paulo, SP, Brazil.
Genom Data. 2016 Nov 18;11:9-16. doi: 10.1016/j.gdata.2016.11.002. eCollection 2017 Mar.
One limitation of the widely used RNA-seq method is that long transcripts are represented by more reads than shorter transcripts, resulting in a biased estimation of expression levels. The 3' RNA-seq method, which yields only one sequence per transcript, bypasses this limitation. Here, RNA was extracted from two samples, in which we expected to find differentially expressed genes. Each was processed by both traditional and 3' RNA-seq protocols. Both methods yielded similar differentially expressed genes and estimated expression levels in a comparable way, confirming they both represent valid tools for RNA-seq analysis. Notably, however, we identified more differentially expressed transcripts with the 3' RNA-seq method, suggesting a greater power to detect expression variation using this method. Hence, when little genomic information is available for the species studied, the standard RNA-seq presents a better cost-benefit compromise, whereas for model species, the 3' RNA-seq method might more accurately detect differential expression.
广泛使用的RNA测序方法的一个局限性是，长转录本比短转录本有更多的读数来代表，导致表达水平的估计有偏差。3' RNA测序方法，每个转录本只产生一个序列，绕过了这个局限性。在这里，从两个样本中提取了RNA，我们预期在其中找到差异表达的基因。每个样本都通过传统和3' RNA测序方案进行处理。两种方法都产生了相似的差异表达基因，并以可比的方式估计了表达水平，证实它们都是RNA测序分析的有效工具。然而，值得注意的是，我们用3' RNA测序方法鉴定出了更多差异表达的转录本，表明使用这种方法检测表达变异的能力更强。因此，当所研究的物种可用的基因组信息很少时，标准RNA测序提供了更好的成本效益折衷方案，而对于模式物种，3' RNA测序方法可能更准确地检测差异表达。
