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Targeted LncRNA Sequencing with the SeqCap RNA Enrichment System

  • John C. Tan
  • Venera D. Bouriakov
  • Liang Feng
  • Todd A. Richmond
  • Daniel Burgess
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1402)

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.

Key words

Target enrichment SeqCap RNA lncRNA sequencing RNA-Seq Rare transcript detection 

Notes

Acknowledgement

NIMBLEGEN and SEQCAP are trademarks of Roche.

All other product names and trademarks are the property of their respective owners.

For life science research only. Not for use in diagnostic procedures.

© 2015 Roche NimbleGen, Inc.

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Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  1. 1.Roche NimbleGen, IncMadisonUSA

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