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Nat Protoc. 2014 May;9(5):989-1009. doi: 10.1038/nprot.2014.058. Epub 2014 Apr 3.

Targeted sequencing for gene discovery and quantification using RNA CaptureSeq.

Author information

1
1] Garvan Institute of Medical Research, Sydney, New South Wales, Australia. [2].
2
1] Garvan Institute of Medical Research, Sydney, New South Wales, Australia. [2] Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia. [3].
3
1] Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia. [2].
4
Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, Australia.
5
Mater Research Institute-The University of Queensland, Translational Research Institute, Woolloongabba, Queensland, Australia.
6
Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia.
7
Garvan Institute of Medical Research, Sydney, New South Wales, Australia.

Abstract

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.

PMID:
24705597
DOI:
10.1038/nprot.2014.058
[Indexed for MEDLINE]
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