Adapting the Smart-seq2 Protocol for Robust Single Worm RNA-seq

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 <i>Steinernema carpocapsae</i> and <i>Caenorhabditis elegans</i> larvae as well as embryos<i>,</i> 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.