Trinity : reconstructing a full-length transcriptome without a genome from RNA-Seq data-猫眼课题宝

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2016

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M. Grabherr;B. Haas;M. Yassour;J. Levin;Dawn A Thompson;I. Amit;Xian Adiconis;Lin Fan;R. Raychowdhu

大规模平行测序为深入有效地探测转录本开辟了道路。目前根据这些数据重建转录本的方法通常依赖于将读数与参考基因组进行比对，因此不适合具有部分或缺失参考基因组的样本。在这里，我们提出了从新开始全长转录组重建的三位一体方法，并在来自分裂酵母、小鼠和烟粉虱的样本上进行了评估-一种尚未测序的昆虫。利邦完全重建了数据中存在的一大部分抄本，还报告了替代剪接异构体和用户的抄本可以查看、打印、复制、下载和文本以及数据挖掘此类文件中的内容，用于学术研究，但始终受全部使用条件的限制：http://www.nature.com/authors/editorial_policies/license.html#terms的通信和材料请求应发送至nir@cs.huji.ac.il(NF)，aregev@Broad.mit.edu(AR)。*这些作者对这部作品的贡献是一样的，并按字母顺序排列。这些作者对这部作品的作者贡献是一样的。MGG、MY、BJH、KLT、NF和AR构思和设计了这项研究。BJH、MGG和MY分别开发了InchWorm、Chysalis和蝴蝶组件。NR、FDP、BB、CN、KLT为本研究的构思和实施做出了贡献。JZL、DAT、XA、LF、RR、IA、NH、AR和AG设计并执行所有实验。QZ、ZC和EM提供了计算分析。MGG、BJH和我设计、实现并评估了所有方法。AR、NF、MGG、BJH和MY撰写了这份手稿，所有作者都提供了意见。作者声明没有相互竞争的经济利益。数据可用性。数据可在基因表达总表或SRA中获得(裂变酵母数据为SRP005611 15，小鼠为GSEXXX)。HHS公共访问作者手稿Nat Biotechnol。作者手稿；可在PMC 2013年2月13日获得。最终编辑形式出版为：NAT Biotechnol。；29(7)：644-652。DOI：10.1038/nbt.1883.Uhor M成绩单

Massively-parallel cDNA sequencing has opened the way to deep and efficient probing of transcriptomes. Current approaches for transcript reconstruction from such data often rely on aligning reads to a reference genome, and are thus unsuitable for samples with a partial or missing reference genome. Here, we present the Trinity methodology for de novo full-length transcriptome reconstruction, and evaluate it on samples from fission yeast, mouse, and whitefly – an insect whose genome has not yet been sequenced. Trinity fully reconstructs a large fraction of the transcripts present in the data, also reporting alternative splice isoforms and transcripts from Users may view, print, copy, download and text and datamine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use: http://www.nature.com/authors/editorial_policies/license.html#terms Correspondence and requests for materials should be addressed to nir@cs.huji.ac.il (NF), aregev@broad.mit.edu (AR). *These authors contributed equally to this work and appear in alphabetical order ‡These authors contributed equally to this work Author Contributions. MGG, MY, BJH, KLT, NF and AR conceived and designed the study. BJH, MGG and MY developed the Inchworm, Chrysalis, and Butterfly components, respectively. NR, FDP, BB, CN, KLT contributed to the study’s conception and execution. JZL, DAT, XA, LF, RR, IA, NH, AR and AG designed and performed all experiments. QZ, ZC and EM contributed computational analyses. MGG, BJH and MY designed, implemented, and evaluated all methods. AR, NF, MGG, BJH and MY wrote the manuscript, with input from all authors. The authors declare no competing financial interest. Data Availability. Data is available in the gene expression omnibus or SRA (Fission yeast data is SRP005611 15, mouse is GSEXXX). HHS Public Access Author manuscript Nat Biotechnol. Author manuscript; available in PMC 2013 February 13. Published in final edited form as: Nat Biotechnol. ; 29(7): 644–652. doi:10.1038/nbt.1883. A uhor M anscript

Trinity : reconstructing a full-length transcriptome without a genome from RNA-Seq data

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