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.
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Acknowledgments
The authors would like to thank GOH, Yufen; Ho, Andrea; QUEK, Kelly, KHNG, Alexis, CHOY, Yeen Hui, Atif, Shahab; ONG, WaiLoon; POH, WanTing; Lavanya Veeravalli; Thoreau, Herve; Ong, ChinThing; Dawn, Sum; Leong, SeeTing and all other members of the GTB research and sequence group. This work was supported by NIH ENCODE grant and A-STAR, Singapore.
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Ruan, X., Ruan, Y. (2012). Genome Wide Full-Length Transcript Analysis Using 5′ and 3′ Paired-End-Tag Next Generation Sequencing (RNA-PET). In: Vancura, A. (eds) Transcriptional Regulation. Methods in Molecular Biology, vol 809. Springer, New York, NY. https://doi.org/10.1007/978-1-61779-376-9_35
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DOI: https://doi.org/10.1007/978-1-61779-376-9_35
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