Comprehensive comparative analysis of 5'-end RNA-sequencing methods.
Comprehensive comparative analysis of 5'-end RNA-sequencing methods.
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DOI：
10.1038/s41592-018-0014-2
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发表时间：
2018-07
期刊：
影响因子：
48
通讯作者：
Levin JZ
中科院分区：
文献类型：
--
作者：
Adiconis X;Haber AL;Simmons SK;Levy Moonshine A;Ji Z;Busby MA;Shi X;Jacques J;Lancaster MA;Pan JQ;Regev A;Levin JZ
RNA-Seq是研究转录组的有效方法，但需要专门的方法来鉴定转录物的5'端。有几种已发表的战略存在这一特定目的，但他们的相对优点还没有得到系统的分析。在这里，我们直接比较了六种这样的方法的性能-用细胞RNA测试五种方法，以及一种新型的加标RNA检测方法，该方法有助于解决注释或RNA处理中的不确定性所带来的解释挑战。使用单个人类RNA样品，我们用这些方法构建并测序了18个文库和一个标准对照RNA-Seq文库。我们发现CAGE方法对mRNA的表现最好，并且其大多数未注释的峰得到了其他基因组方法证据的支持。然后，我们将CAGE应用于8个脑相关样本，并揭示了样本特异性转录起始位点（TSS）的使用以及胎儿和成人大脑之间TSS使用的转录组范围内的变化。
RNA-Seq is an effective method to study the transcriptome, but specialized methods are required to identify 5’ ends of transcripts. Several published strategies exist for this specific purpose, but their relative merits have not been systematically analyzed. Here, we directly compare the performance of six such methods – testing five with cellular RNA as well as a novel spike-in RNA assay that helps address interpretation challenges that arise from uncertainties in annotation or RNA processing. Using a single human RNA sample, we constructed and sequenced 18 libraries with these methods and one standard, control RNA-Seq library. We find that the CAGE method performed best for mRNA and that most of its unannotated peaks are supported by evidence from other genomic methods. We then applied CAGE to eight brain-related samples and revealed sample-specific transcription start site (TSS) usage as well as a transcriptome-wide shift in TSS usage between fetal and adult brain.
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DOI：
10.1126/science.1244392
发表时间：
2014-02-14
期刊：
Science (New York, N.Y.)
影响因子：
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DOI：
10.1126/science.1259418
发表时间：
2015-02-27
期刊：
Science (New York, N.Y.)
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Hayashizaki Y
DOI：
10.1002/ajmg.b.32148
发表时间：
2013-06-01
影响因子：
2.8
作者：
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通讯作者：
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影响因子：
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作者：
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