A dual platform approach to transcript discovery for the planarian Schmidtea mediterranea to establish RNAseq for stem cell and regeneration biology.
A dual platform approach to transcript discovery for the planarian Schmidtea mediterranea to establish RNAseq for stem cell and regeneration biology.
复制标题
DOI：
10.1371/journal.pone.0015617
复制
发表时间：
2010-12-14
期刊：
影响因子：
3.7
通讯作者：
Aboobaker AA
中科院分区：
文献类型：
--
作者：
Blythe MJ;Kao D;Malla S;Rowsell J;Wilson R;Evans D;Jowett J;Hall A;Lemay V;Lam S;Aboobaker AA
作为一个模式系统的使用正在扩大，控制涡虫再生的机制正在阐明。尤其是扁虫Schmidtea medialacea已经成为一种选择。目前，Planarian研究社区已经获得了这个全基因组测序项目和超过70，000个表达序列标签。然而，大规模并行测序技术的建立提供了前所未有的详细定义遗传内容，特别是转录组的机会。在这里，我们将这种方法应用于涡虫模型系统。我们已经测序，绘制和组装了来自前7天的完整和混合阶段的RNA的581，365个长和507，719，814个短读段。我们使用迭代作图方法来识别和定义具有短读段的从头剪接位点，并增加我们的转录预测的置信度。我们将目前由公开可用的EST定义的转录本数量增加了一倍多，从而收集了25，053个通过组合平台描述的转录本。我们还证明了该集合的实用性，用于RNAseq方法，通过比较辐照和完整的真涡虫之间的转录组全表达水平来鉴定在新生干细胞及其后代中富集的潜在转录物。我们的实验已经定义了一个广泛的真涡虫转录组，可以用作RNAseq的模板，也可以帮助注释S。mediterranea genome.我们预计，其他组学方法的套件也将通过建立在这个全面的数据集，包括RNAseq在许多涡虫再生阶段，场景，组织和RNAi产生的表型。
The use of planarians as a model system is expanding and the mechanisms that control planarian regeneration are being elucidated. The planarian Schmidtea mediterranea in particular has become a species of choice. Currently the planarian research community has access to this whole genome sequencing project and over 70,000 expressed sequence tags. However, the establishment of massively parallel sequencing technologies has provided the opportunity to define genetic content, and in particular transcriptomes, in unprecedented detail. Here we apply this approach to the planarian model system. We have sequenced, mapped and assembled 581,365 long and 507,719,814 short reads from RNA of intact and mixed stages of the first 7 days of planarian regeneration. We used an iterative mapping approach to identify and define de novo splice sites with short reads and increase confidence in our transcript predictions. We more than double the number of transcripts currently defined by publicly available ESTs, resulting in a collection of 25,053 transcripts described by combining platforms. We also demonstrate the utility of this collection for an RNAseq approach to identify potential transcripts that are enriched in neoblast stem cells and their progeny by comparing transcriptome wide expression levels between irradiated and intact planarians. Our experiments have defined an extensive planarian transcriptome that can be used as a template for RNAseq and can also help to annotate the S. mediterranea genome. We anticipate that suites of other 'omic approaches will also be facilitated by building on this comprehensive data set including RNAseq across many planarian regenerative stages, scenarios, tissues and phenotypes generated by RNAi.
登录
查看更多内容
影响因子：
7.2
作者：
Adell, Teresa;Cebria, Francesc;Salo, Emili
通讯作者：
Salo, Emili
影响因子：
14.9
作者：
Finn RD;Mistry J;Tate J;Coggill P;Heger A;Pollington JE;Gavin OL;Gunasekaran P;Ceric G;Forslund K;Holm L;Sonnhammer EL;Eddy SR;Bateman A
通讯作者：
Bateman A
影响因子：
11.8
作者：
Guo, Tingxia;Peters, Antoine H. F. M.;Newmark, Phillip A.
通讯作者：
Newmark, Phillip A.
影响因子：
56.9
作者：
Gurley, Kyle A.;Rink, Jochen C.;Alvarado, Alejandro Sanchez
通讯作者：
Alvarado, Alejandro Sanchez
影响因子：
4.6
作者：
Iglesias, Marta;Luis Gomez-Skarmeta, Jose;Adell, Teresa
通讯作者：
Adell, Teresa