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RNA sequencing (RNAseq) samples the majority of expressed genes infrequently, owing to the large size, complex splicing and wide dynamic range of eukaryotic transcriptomes. This results in sparse sequencing coverage that can hinder robust isoform assembly and quantification. RNA capture sequencing (CaptureSeq) addresses this challenge by using oligonucleotide probes to capture selected genes or regions of interest for targeted sequencing. Targeted RNAseq provides enhanced coverage for sensitive gene discovery, robust transcript assembly and accurate gene quantification. Here we describe a detailed protocol for all stages of RNA CaptureSeq, from initial probe design considerations and capture of targeted genes to final assembly and quantification of captured transcripts. Initial probe design and final analysis can take less than 1 d, whereas the central experimental capture stage requires ∼7 d.

Original publication

DOI

10.1038/nprot.2014.058

Type

Journal article

Journal

Nat Protoc

Publication Date

05/2014

Volume

9

Pages

989 - 1009

Keywords

Exons, Genetic Association Studies, Nucleic Acid Amplification Techniques, Oligonucleotide Probes, Sequence Analysis, RNA, Software