title: Application of RNA-Seq Technology in Cancer Chemoprevention.
abstract: RNA-sequencing is a revolutionary tool to follow differential expression after treatment with cancer chemopreventive agents. It allows a real genome-wide screening independent of prior assumptions and is well suited for analyzing coding but also long noncoding RNAs. It still consents the discovery of new genes and isoforms and increased our knowledge of antisense and other noncoding RNAs in a tremendous manner. Moreover, it permits to detect low-abundance and biologically critical isoforms and reveals genetic variants and gene fusions in one single assay. Here, we provide a detailed protocol for stranded RNA-sequencing.
authors.affiliation: Translational Oncogenomics Unit, Italian National Cancer Institute "Regina Elena", Via Elio Chianesi, 53, 00144, Rome, Italy. goeman@ifo.it.
authors.forename: Frauke
authors.initials: F
authors.lastname: Goeman
authors.affiliation: Laboratory of Epigenetic, Molecular Medicine Area, Italian National Cancer Institute "Regina Elena", 00144, Rome, Italy.
authors.forename: Maurizio
authors.initials: M
authors.lastname: Fanciulli
mesh_terms: D018890:Chemoprevention; D006801:Humans; D009369:Neoplasms / Q000235:genetics* / Q000517:prevention & control*; D016133:Polymerase Chain Reaction; D011786:Quality Control; D012313:RNA / Q000737:chemistry / Q000235:genetics* / Q000302:isolation & purification; D015203:Reproducibility of Results; D048348:Reverse Transcription; D012270:Ribosomes / Q000235:genetics; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D012313:RNA
keywords: Chemoprevention; Deep-sequencing; Long noncoding RNA; Novel transcript and isoform discovery; RNA-Seq; Stranded RNA-Seq; Transcriptional signature; Transcriptome profiling