MOROKOSHI: transcriptome database in Sorghum bicolor.
MOROKOSHI: transcriptome database in Sorghum bicolor.
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DOI：
10.1093/pcp/pcu187
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发表时间：
2015-01
影响因子：
4.9
通讯作者：
Matsui M
中科院分区：
文献类型：
--
作者：
Makita Y;Shimada S;Kawashima M;Kondou-Kuriyama T;Toyoda T;Matsui M
在转录组分析中，每个转录单位及其表达谱的准确注释是必不可少的。全长cDNA（FL-cDNA）的收集有助于转录注释的完善，准确的转录起始位点有助于解开转录调控。我们构建了一个标准化的FL-cDNA文库，从8个生长阶段的气生组织中分离出37，607个克隆。从5′和/或3′末端对这些克隆进行桑格测序，共获得38，981个高质量的表达序列标签（EST）。大约三分之一的已知基因的转录本被捕获作为FL-cDNA克隆资源。除此之外，我们还注释了272个新基因，323个反义转录本和1，672个候选亚型。这些克隆可从RIKEN Bioresource Center获得。在获得转录单位的准确注释后，我们进行了表达谱分析。我们进行了小穗，种子和茎特异性RNA测序（RNA-Seq）分析，并确认了70.6%的新鉴定基因的表达。我们还下载了23个公开的高粱RNA-Seq样本，这些样本与我们原始的FL-cDNA和RNA-Seq数据一起显示在基因组浏览器上。利用我们的原始和公开数据，我们制作了每个基因的表达谱，并确定了表达最相似的前20个基因。此外，我们可视化了它们在基因共表达网络中的关系。用户可以在http://sorghum.riken.jp上访问和比较来自S，bicolor的各种转录组数据。
In transcriptome analysis, accurate annotation of each transcriptional unit and its expression profile is essential. A full-length cDNA (FL-cDNA) collection facilitates the refinement of transcriptional annotation, and accurate transcription start sites help to unravel transcriptional regulation. We constructed a normalized FL-cDNA library from eight growth stages of aerial tissues in Sorghum bicolor and isolated 37,607 clones. These clones were Sanger sequenced from the 5′ and/or 3′ ends and in total 38,981 high-quality expressed sequence tags (ESTs) were obtained. About one-third of the transcripts of known genes were captured as FL-cDNA clone resources. In addition to these, we also annotated 272 novel genes, 323 antisense transcripts and 1,672 candidate isoforms. These clones are available from the RIKEN Bioresource Center. After obtaining accurate annotation of transcriptional units, we performed expression profile analysis. We carried out spikelet-, seed- and stem-specific RNA sequencing (RNA-Seq) analysis and confirmed the expression of 70.6% of the newly identified genes. We also downloaded 23 sorghum RNA-Seq samples that are publicly available and these are shown on a genome browser together with our original FL-cDNA and RNA-Seq data. Using our original and publicly available data, we made an expression profile of each gene and identified the top 20 genes with the most similar expression. In addition, we visualized their relationships in gene co-expression networks. Users can access and compare various transcriptome data from S, bicolor at http://sorghum.riken.jp.
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影响因子：
14.9
作者：
Monaco MK;Stein J;Naithani S;Wei S;Dharmawardhana P;Kumari S;Amarasinghe V;Youens-Clark K;Thomason J;Preece J;Pasternak S;Olson A;Jiao Y;Lu Z;Bolser D;Kerhornou A;Staines D;Walts B;Wu G;D'Eustachio P;Haw R;Croft D;Kersey PJ;Stein L;Jaiswal P;Ware D
通讯作者：
Ware D
影响因子：
14.9
作者：
Hunter S;Jones P;Mitchell A;Apweiler R;Attwood TK;Bateman A;Bernard T;Binns D;Bork P;Burge S;de Castro E;Coggill P;Corbett M;Das U;Daugherty L;Duquenne L;Finn RD;Fraser M;Gough J;Haft D;Hulo N;Kahn D;Kelly E;Letunic I;Lonsdale D;Lopez R;Madera M;Maslen J;McAnulla C;McDowall J;McMenamin C;Mi H;Mutowo-Muellenet P;Mulder N;Natale D;Orengo C;Pesseat S;Punta M;Quinn AF;Rivoire C;Sangrador-Vegas A;Selengut JD;Sigrist CJ;Scheremetjew M;Tate J;Thimmajanarthanan M;Thomas PD;Wu CH;Yeats C;Yong SY
通讯作者：
Yong SY
影响因子：
1.1
作者：
Ogihara, Y;Mochida, K;Yamazaki, Y
通讯作者：
Yamazaki, Y
影响因子：
4.4
作者：
Kawaura K;Mochida K;Enju A;Totoki Y;Toyoda A;Sakaki Y;Kai C;Kawai J;Hayashizaki Y;Seki M;Shinozaki K;Ogihara Y
通讯作者：
Ogihara Y
影响因子：
4.4
作者：
Gelli M;Duo Y;Konda AR;Zhang C;Holding D;Dweikat I
通讯作者：
Dweikat I