title: RNA-seq in the tetraploid Xenopus laevis enables genome-wide insight in a classic developmental biology model organism.
abstract: Advances in sequencing technology have significantly advanced the landscape of developmental biology research. The dissection of genetic networks in model and non-model 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.
authors.affiliation: University of North Carolina, McAllister Heart Institute, UNC-Chapel Hill, Chapel Hill, NC 27599-3280, USA; Department of Genetics, UNC-Chapel Hill, Chapel Hill, NC 27599-3280, USA.
authors.forename: Nirav M
authors.initials: NM
authors.lastname: Amin
authors.affiliation: University of North Carolina, McAllister Heart Institute, UNC-Chapel Hill, Chapel Hill, NC 27599-3280, USA; Department of Genetics, UNC-Chapel Hill, Chapel Hill, NC 27599-3280, USA.
authors.forename: Panna
authors.initials: P
authors.lastname: Tandon
authors.affiliation: Department of Biology, UNC-Chapel Hill, Chapel Hill, NC 27599-3280, USA.
authors.forename: Erin
authors.initials: E
authors.lastname: Osborne Nishimura
authors.affiliation: University of North Carolina, McAllister Heart Institute, UNC-Chapel Hill, Chapel Hill, NC 27599-3280, USA; Department of Biology, UNC-Chapel Hill, Chapel Hill, NC 27599-3280, USA; Department of Genetics, UNC-Chapel Hill, Chapel Hill, NC 27599-3280, USA. Electronic address: frank_conlon@med.unc.edu.
authors.forename: Frank L
authors.initials: FL
authors.lastname: Conlon
mesh_terms: D000818:Animals; D015509:Developmental Biology / Q000379:methods; D016678:Genome; D023421:Models, Animal; D017423:Sequence Analysis, RNA / Q000379:methods*; D014982:Xenopus laevis / Q000235:genetics* / Q000254:growth & development
keywords: Differential expression; RNA-seq; Xenopus