调整Smart-seq2方案以实现稳健的单线虫RNA测序
Adapting the Smart-seq2 Protocol for Robust Single Worm RNA-seq.
作者信息
Serra Lorrayne, Chang Dennis Z, Macchietto Marissa, Williams Katherine, Murad Rabi, Lu Dihong, Dillman Adler R, Mortazavi Ali
机构信息
Department of Developmental and Cell Biology, University of California, Irvine, California, USA.
Department of Nematology, University of California, Riverside, California, USA.
出版信息
Bio Protoc. 2018 Feb 20;8(4). doi: 10.21769/BioProtoc.2729.
Abstract
Most nematodes are small worms that lack enough RNA for regular RNA-seq protocols without pooling hundred to thousand of individuals. We have adapted the Smart-seq2 protocol in order to sequence the transcriptome of an individual worm. While developed for individual and larvae as well as embryos the protocol should be adaptable for other nematode species and small invertebrates. In addition, we describe how to analyze the RNA-seq results using the Galaxy online environment. We expect that this method will be useful for the studying gene expression variances of individual nematodes in wild type and mutant backgrounds.
摘要
大多数线虫都是小蠕虫，在不汇集成百上千个个体的情况下，其RNA量不足以用于常规RNA测序方案。我们对Smart-seq2方案进行了调整，以便对单个蠕虫的转录组进行测序。虽然该方案是为单个成虫、幼虫以及胚胎开发的，但应该也适用于其他线虫物种和小型无脊椎动物。此外，我们还描述了如何使用Galaxy在线环境分析RNA测序结果。我们预计这种方法将有助于研究野生型和突变背景下单个线虫的基因表达差异。
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