RNA-Seq: Genome Wide Full-Length Transcript Analysis Using 5' and 3' Paired-End-Tag N

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Genome Wide Full-Length Transcript Analysis Using 5' and 3' Paired-End-Tag Next Generation Sequencing (RNA-PET).

Methods Mol Biol. 2012;809:535-62

Authors: Ruan X, Ruan Y

Abstract
RNA-PET is a paired end tag (PET) sequencing method for full-length mRNA transcripts analysis using the next generation sequencer platforms such as Illumina GA and SOLiD. Unlike RNA-Seq method that sequences randomly sheared shotgun RNA short fragments, RNA-PET captures and sequences the 5' and 3' end tags of full-length cDNA fragments of all expressed genes in a biological sample. When mapped to reference genome, RNA-PET sequences can demarcate the boundaries of transcription units genome-wide, in addition to its ability to quantify the transcription level of each expression genes. Furthermore, the unique feature of RNA-PET is to identify fusion transcripts. Therefore, RNA-PET has been regarded as the best PET for genome annotation (1). Here in this chapter, we describe the details of the RNA-PET protocol and discuss the critical issues.


PMID: 22113299 [PubMed - in process]



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[rulerwoods]

It's a detailed protocol of RNA-PET. Very nice. Im thinking of using this strategy to detect some novel fusion.