| Literature DB >> 23557989 |
David F B Miller1, Pearlly S Yan, Aaron Buechlein, Benjamin A Rodriguez, Ayse S Yilmaz, Shokhi Goel, Hai Lin, Bridgette Collins-Burow, Lyndsay V Rhodes, Chris Braun, Sunila Pradeep, Rajesha Rupaimoole, Mehmet Dalkilic, Anil K Sood, Matthew E Burow, Haixu Tang, Tim H Huang, Yunlong Liu, Douglas B Rusch, Kenneth P Nephew.
Abstract
This report describes an improved protocol to generate stranded, barcoded RNA-seq libraries to capture the whole transcriptome. By optimizing the use of duplex specific nuclease (DSN) to remove ribosomal RNA reads from stranded barcoded libraries, we demonstrate improved efficiency of multiplexed next generation sequencing (NGS). This approach detects expression profiles of all RNA types, including miRNA (microRNA), piRNA (Piwi-interacting RNA), snoRNA (small nucleolar RNA), lincRNA (long non-coding RNA), mtRNA (mitochondrial RNA) and mRNA (messenger RNA) without the use of gel electrophoresis. The improved protocol generates high quality data that can be used to identify differential expression in known and novel coding and non-coding transcripts, splice variants, mitochondrial genes and SNPs (single nucleotide polymorphisms).Entities:
Keywords: DSN; Duplex-specific nuclease; FLgRNA; Gene expression; LgRNA; RNA-seq; Transcriptome; duplex-specific nuclease; fragmented LgRNA; large total RNA >200 nt; smRNA; small total RNA <200 nt
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Year: 2013 PMID： 23557989 PMCID： PMC3739992 DOI： 10.1016/j.ymeth.2013.03.023
Source DB: PubMed Journal: Methods ISSN： 1046-2023 Impact factor: 3.608