A new method for stranded whole transcriptome RNA-seq.
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).
['Miller|David F B|DF|', 'Yan|Pearlly S|PS|', 'Buechlein|Aaron|A|', 'Rodriguez|Benjamin A|BA|', 'Yilmaz|Ayse S|AS|', 'Goel|Shokhi|S|', 'Lin|Hai|H|', 'Collins-Burow|Bridgette|B|', 'Rhodes|Lyndsay V|LV|', 'Braun|Chris|C|', 'Pradeep|Sunila|S|', 'Rupaimoole|Rajesha|R|', 'Dalkilic|Mehmet|M|', 'Sood|Anil K|AK|', 'Burow|Matthew E|ME|', 'Tang|Haixu|H|', 'Huang|Tim H|TH|', 'Liu|Yunlong|Y|', 'Rusch|Douglas B|DB|', 'Nephew|Kenneth P|KP|']
D045744:Cell Line, Tumor D020869:Gene Expression Profiling D015723:Gene Library D059014:High-Throughput Nucleotide Sequencing D006801:Humans D058977:Molecular Sequence Annotation D020641:Polymorphism, Single Nucleotide D020033:Protein Isoforms D012333:RNA, Messenger D012335:RNA, Ribosomal D060888:Real-Time Polymerase Chain Reaction D020133:Reverse Transcriptase Polymerase Chain Reaction D012260:Ribonucleases D017423:Sequence Analysis, RNA
Transcriptome RNA-seq DSN Duplex-specific nuclease FLgRNA Gene expression LgRNA duplex-specific nuclease fragmented LgRNA large total RNA >200 nt smRNA small total RNA <200 nt