title: Targeted LncRNA Sequencing with the SeqCap RNA Enrichment System.
abstract: Sequencing-based whole-transcriptome analysis (i.e., RNA-Seq) can be a powerful tool when used to measure gene expression, detect novel transcripts, characterize transcript isoforms, and identify sequence polymorphisms. However, this method can be inefficient when the goal is to study only one component of the transcriptome, such as long noncoding RNAs (lncRNAs), which constitute only a small fraction of transcripts in a total RNA sample. Here, we describe a target enrichment method where a total RNA sample is converted to a sequencing-ready cDNA library and hybridized to a complex pool of lncRNA-specific biotinylated long oligonucleotide capture probes prior to sequencing. The resulting sequence data are highly enriched for the targets of interest, dramatically increasing the efficiency of next-generation sequencing approaches for the analysis of lncRNAs.
authors.affiliation: Roche NimbleGen, Inc, 500 S. Rosa Road, Madison, WI, USA. john.tan.jt1@roche.com.
authors.forename: John C
authors.initials: JC
authors.lastname: Tan
authors.affiliation: Roche NimbleGen, Inc, 500 S. Rosa Road, Madison, WI, USA.
authors.forename: Venera D
authors.initials: VD
authors.lastname: Bouriakov
authors.affiliation: Roche NimbleGen, Inc, 500 S. Rosa Road, Madison, WI, USA.
authors.forename: Liang
authors.initials: L
authors.lastname: Feng
authors.affiliation: Roche NimbleGen, Inc, 500 S. Rosa Road, Madison, WI, USA.
authors.forename: Todd A
authors.initials: TA
authors.lastname: Richmond
authors.affiliation: Roche NimbleGen, Inc, 500 S. Rosa Road, Madison, WI, USA. daniel.burgess@roche.com.
authors.forename: Daniel
authors.initials: D
authors.lastname: Burgess
mesh_terms: D000818:Animals; D020869:Gene Expression Profiling / Q000379:methods; D015723:Gene Library; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D016133:Polymerase Chain Reaction / Q000379:methods; D015347:RNA Probes / Q000235:genetics; D062085:RNA, Long Noncoding / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods*; D059467:Transcriptome
chemical_list: D015347:RNA Probes; D062085:RNA, Long Noncoding
keywords: RNA-Seq; Rare transcript detection; SeqCap RNA; Target enrichment; lncRNA sequencing