RNA-seq in the tetraploid Xenopus laevis enables genome-wide insight in a classic developmental biology model organism.
RNA-seq in the tetraploid Xenopus laevis enables genome-wide insight in a classic developmental biology model organism.
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DOI：
10.1016/j.ymeth.2013.06.009
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发表时间：
2014-04-01
期刊：
影响因子：
4.8
通讯作者：
Conlon, Frank L.
中科院分区：
文献类型：
--
作者：
Amin, Nirav M.;Tandon, Panna;Nishimura, Erin Osborne;Conlon, Frank L.
测序技术的进步极大地推动了发育生物学研究的发展。高通量测序技术极大地增强了模型和非模型生物体中遗传网络的解剖。RNA-seq已经彻底改变了在没有公布基因组序列的生物体中进行发育生物学研究的能力。在这里，我们描述了发育生物学家对解剖组织或整个胚胎进行RNA-seq的协议。我们从RNA的分离和测序文库的产生开始。我们进一步展示了如何解释和分析RNA-seq中生成的大量测序数据。我们探讨的能力，检查差异表达，基因复制，转录组装，选择性剪接和SNP的发现。出于本文的目的，我们使用非洲爪蟾作为模式生物来讨论RNA-seq在没有完全注释的基因组序列的生物中的用途。
Advances in sequencing technology have significantly advanced the landscape of developmental biology research. The dissection of genetic networks in model and nonmodel organisms has been greatly enhanced with high-throughput sequencing technologies. RNA-seq has revolutionized the ability to perform developmental biology research in organisms without a published genome sequence. Here, we describe a protocol for developmental biologists to perform RNA-seq on dissected tissue or whole embryos. We start with the isolation of RNA and generation of sequencing libraries. We further show how to interpret and analyze the large amount of sequencing data that is generated in RNA-seq. We explore the abilities to examine differential expression, gene duplication, transcript assembly, alternative splicing and SNP discovery. For the purposes of this article, we use Xenopus laevis as the model organism to discuss uses of RNA-seq in an organism without a fully annotated genome sequence.
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DOI：
10.1002/bdra.20793
发表时间：
2011-06
影响因子：
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作者：
Kaltenbrun, Erin;Tandon, Panna;Amin, Nirav M.;Waldron, Lauren;Showell, Chris;Conlon, Frank L.
通讯作者：
Conlon, Frank L.