A new method for stranded whole transcriptome RNA-seq. Methods 2013 Sep 15;63(2):126-34
Date
04/06/2013Pubmed ID
23557989Pubmed Central ID
PMC3739992DOI
10.1016/j.ymeth.2013.03.023Scopus ID
2-s2.0-84885171004 (requires institutional sign-in at Scopus site) 40 CitationsAbstract
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).
Author List
Miller DF, Yan PS, Buechlein A, Rodriguez BA, Yilmaz AS, Goel S, Lin H, Collins-Burow B, Rhodes LV, Braun C, Pradeep S, Rupaimoole R, Dalkilic M, Sood AK, Burow ME, Tang H, Huang TH, Liu Y, Rusch DB, Nephew KPAuthor
Sunila Pradeep PhD Associate Professor in the Obstetrics and Gynecology department at Medical College of WisconsinMESH terms used to index this publication - Major topics in bold
Cell Line, TumorGene Expression Profiling
Gene Library
High-Throughput Nucleotide Sequencing
Humans
Molecular Sequence Annotation
Polymorphism, Single Nucleotide
Protein Isoforms
RNA, Messenger
RNA, Ribosomal
Real-Time Polymerase Chain Reaction
Reverse Transcriptase Polymerase Chain Reaction
Ribonucleases
Sequence Analysis, RNA
