Tissue-specific transcriptome sequencing analysis expands the non-human primate reference transcriptome resource (NHPRTR).
Tissue-specific transcriptome sequencing analysis expands the non-human primate reference transcriptome resource (NHPRTR).
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DOI：
10.1093/nar/gku1110
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发表时间：
2015-01
影响因子：
14.9
通讯作者：
Mason CE
中科院分区：
文献类型：
--
作者：
Peng X;Thierry-Mieg J;Thierry-Mieg D;Nishida A;Pipes L;Bozinoski M;Thomas MJ;Kelly S;Weiss JM;Raveendran M;Muzny D;Gibbs RA;Rogers J;Schroth GP;Katze MG;Mason CE
非人灵长类动物参考转录组资源（NHPRTR，可在http：//nhprtr.org/在线获得）旨在从各种各样的非人灵长类动物（NHP）（从狐猴到人科动物）生成全面的RNA-seq数据。在NHPRTR项目的2012年第一阶段，从15个物种和亚种的1020个组织中收集了190亿个片段或3.8个转录组序列。在这里，我们通过添加101亿个组织特异性RNA-seq数据片段来描述NHPRTR的主要扩展。为此，我们从最初的15种NHP物种和亚种中选择了11种，并为每种中相同的15种组织构建了总RNA文库。序列质量是这样的，88%的读数与人类参考序列对齐，使我们能够使用映射到人类基因的读数计算每个物种所有组织的表达丰度的完整列表。本次更新还包括来自恒河猴和食蟹猴RNA-seq数据的改进的转录本注释，这是两种最常用的NHP模型，以及从相关项目中编译的其他RNA-seq数据。总之，这些来自多个灵长类动物的综合参考转录组作为基因组注释，基因动态和比较功能分析的宝贵社区资源。
The non-human primate reference transcriptome resource (NHPRTR, available online at http://nhprtr.org/) aims to generate comprehensive RNA-seq data from a wide variety of non-human primates (NHPs), from lemurs to hominids. In the 2012 Phase I of the NHPRTR project, 19 billion fragments or 3.8 terabases of transcriptome sequences were collected from pools of ∼20 tissues in 15 species and subspecies. Here we describe a major expansion of NHPRTR by adding 10.1 billion fragments of tissue-specific RNA-seq data. For this effort, we selected 11 of the original 15 NHP species and subspecies and constructed total RNA libraries for the same ∼15 tissues in each. The sequence quality is such that 88% of the reads align to human reference sequences, allowing us to compute the full list of expression abundance across all tissues for each species, using the reads mapped to human genes. This update also includes improved transcript annotations derived from RNA-seq data for rhesus and cynomolgus macaques, two of the most commonly used NHP models and additional RNA-seq data compiled from related projects. Together, these comprehensive reference transcriptomes from multiple primates serve as a valuable community resource for genome annotation, gene dynamics and comparative functional analysis.
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使用深层转录组测序数据的评估和改善印度 - 原始猕猴和毛丽丽 - 毛裂囊肿基因组注释。
影响因子：
0.7
作者：
Peng X;Pipes L;Xiong H;Green RR;Jones DC;Ruzzo WL;Schroth GP;Mason CE;Palermo RE;Katze MG
通讯作者：
Katze MG
影响因子：
14.9
作者：
Flicek P;Amode MR;Barrell D;Beal K;Billis K;Brent S;Carvalho-Silva D;Clapham P;Coates G;Fitzgerald S;Gil L;Girón CG;Gordon L;Hourlier T;Hunt S;Johnson N;Juettemann T;Kähäri AK;Keenan S;Kulesha E;Martin FJ;Maurel T;McLaren WM;Murphy DN;Nag R;Overduin B;Pignatelli M;Pritchard B;Pritchard E;Riat HS;Ruffier M;Sheppard D;Taylor K;Thormann A;Trevanion SJ;Vullo A;Wilder SP;Wilson M;Zadissa A;Aken BL;Birney E;Cunningham F;Harrow J;Herrero J;Hubbard TJ;Kinsella R;Muffato M;Parker A;Spudich G;Yates A;Zerbino DR;Searle SM
通讯作者：
Searle SM
影响因子：
46.9
作者：
Wang, Charles;Gong, Binsheng;Bushel, Pierre R.;Thierry-Mieg, Jean;Thierry-Mieg, Danielle;Xu, Joshua;Fang, Hong;Hong, Huixiao;Shen, Jie;Su, Zhenqiang;Meehan, Joe;Li, Xiaojin;Yang, Lu;Li, Haiqing;Labaj, Pawel P.;Kreil, David P.;Megherbi, Dalila;Gaj, Stan;Caiment, Florian;van Delft, Joost;Kleinjans, Jos;Scherer, Andreas;Devanarayan, Viswanath;Wang, Jian;Yang, Yong;Qian, Hui-Rong;Lancashire, Lee J.;Bessarabova, Marina;Nikolsky, Yuri;Furlanello, Cesare;Chierici, Marco;Albanese, Davide;Jurman, Giuseppe;Riccadonna, Samantha;Filosi, Michele;Visintainer, Roberto;Zhang, Ke K.;Li, Jainying;Hsieh, Jui-Hua;Svoboda, Daniel L.;Fuscoe, James C.;Deng, Youping;Shi, Leming;Paules, Richard S.;Auerbach, Scott S.;Tong, Weida
通讯作者：
Tong, Weida
影响因子：
46.9
作者：
Li, Sheng;Tighe, Scull W.;Nicolet, Charles M.;Grove, Deborah;Levy, Shawn;Farmerie, William;Viale, Agnes;Wright, Chris;Schweitzer, Peter A.;Gao, Yuan;Kim, Dewey;Boland, Joe;Hicks, Belynda;Kim, Ryan;Chhangawala, Sagar;Jafari, Nadereh;Raghavachari, Nalini;Gandara, Jorge;Garcia-Reyero, Natalia;Hendrickson, Cynthia;Roberson, David;Rosenfeldr, Jeffrey;Smith, Todd;Underwood, Jason G.;Wang, May;Zumbo, Paul;Baldwin, Don A.;Grills, George S.;Mason, Christopher E.
通讯作者：
Mason, Christopher E.
影响因子：
56.9
作者：
Gibbs, Richard A.;Rogers, Jeffrey;Zwieg, Ann S.
通讯作者：
Zwieg, Ann S.