Mapping and quantifying mammalian transcriptomes by RNA-Seq
Mapping and quantifying mammalian transcriptomes by RNA-Seq
复制标题
DOI：
10.1038/nmeth.1226
复制
发表时间：
2008-07-01
期刊：
影响因子：
48
通讯作者：
Wold, Barbara
中科院分区：
文献类型：
--
作者：
Mortazavi, Ali;Williams, Brian A.;Wold, Barbara
我们通过对小鼠转录组进行深度测序并记录每个基因在序列样本中的出现频率（RNA-Seq），绘制并量化了小鼠转录组。这提供了一个数字测量的存在和流行的转录本从已知的和以前未知的基因。我们报告的参考测量组成的41-52万映射的25个碱基对读取聚（A）选择RNA从成年小鼠脑，肝和骨骼肌组织。我们使用RNA标准品来量化转录本流行率，并测试转录本检测的线性范围，其跨越五个数量级。尽管> 90%的独特定位的读段落在已知的外显子内，但剩余的数据表明新的和修订的基因模型，包括改变的或额外的启动子、外显子和3'非转录区，以及新的候选microRNA前体。RNA剪接事件，这是不容易测量的标准基因表达微阵列或基因表达方法的系列分析，直接通过映射剪接交叉序列读取检测。我们观察到1.45 × 10（5）个不同的剪接，并且选择性剪接是突出的，有3，500个不同的基因表达一个或多个交替的内部剪接。
We have mapped and quantified mouse transcriptomes by deeply sequencing them and recording how frequently each gene is represented in the sequence sample (RNA-Seq). This provides a digital measure of the presence and prevalence of transcripts from known and previously unknown genes. We report reference measurements composed of 41-52 million mapped 25-base-pair reads for poly(A)-selected RNA from adult mouse brain, liver and skeletal muscle tissues. We used RNA standards to quantify transcript prevalence and to test the linear range of transcript detection, which spanned five orders of magnitude. Although > 90% of uniquely mapped reads fell within known exons, the remaining data suggest new and revised gene models, including changed or additional promoters, exons and 3' untranscribed regions, as well as new candidate microRNA precursors. RNA splice events, which are not readily measured by standard gene expression microarray or serial analysis of gene expression methods, were detected directly by mapping splice-crossing sequence reads. We observed 1.45 x 10(5) distinct splices, and alternative splices were prominent, with 3,500 different genes expressing one or more alternate internal splices.