A new method for stranded whole transcriptome RNA-seq

David F B Miller, 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 Nephew

Research output: Contribution to journalArticle

32 Citations (Scopus)

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).

Original languageEnglish
Pages (from-to)126-134
Number of pages9
JournalMethods
Volume63
Issue number2
DOIs
StatePublished - Sep 15 2013

Fingerprint

Long Noncoding RNA
Transcriptome
Libraries
Small Nucleolar RNA
RNA
Ribosomal RNA
Mitochondrial Genes
Electrophoresis
Polymorphism
MicroRNAs
Small Interfering RNA
Single Nucleotide Polymorphism
Nucleotides
Genes
Gels
Messenger RNA
Data Accuracy
mitochondrial RNA

Keywords

  • Duplex-specific nuclease
  • Gene expression
  • RNA-seq
  • Transcriptome

ASJC Scopus subject areas

  • Molecular Biology
  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

Miller, D. F. B., Yan, P. S., Buechlein, A., Rodriguez, B. A., Yilmaz, A. S., Goel, S., ... Nephew, K. (2013). A new method for stranded whole transcriptome RNA-seq. Methods, 63(2), 126-134. https://doi.org/10.1016/j.ymeth.2013.03.023

A new method for stranded whole transcriptome RNA-seq. / Miller, David F B; Yan, Pearlly S.; Buechlein, Aaron; Rodriguez, Benjamin A.; Yilmaz, Ayse S.; Goel, Shokhi; Lin, Hai; Collins-Burow, Bridgette; Rhodes, Lyndsay V.; Braun, Chris; Pradeep, Sunila; Rupaimoole, Rajesha; Dalkilic, Mehmet; Sood, Anil K.; Burow, Matthew E.; Tang, Haixu; Huang, Tim H.; Liu, Yunlong; Rusch, Douglas B.; Nephew, Kenneth.

In: Methods, Vol. 63, No. 2, 15.09.2013, p. 126-134.

Research output: Contribution to journalArticle

Miller, DFB, 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, K 2013, 'A new method for stranded whole transcriptome RNA-seq', Methods, vol. 63, no. 2, pp. 126-134. https://doi.org/10.1016/j.ymeth.2013.03.023
Miller DFB, Yan PS, Buechlein A, Rodriguez BA, Yilmaz AS, Goel S et al. A new method for stranded whole transcriptome RNA-seq. Methods. 2013 Sep 15;63(2):126-134. https://doi.org/10.1016/j.ymeth.2013.03.023
Miller, David F B ; Yan, Pearlly S. ; Buechlein, Aaron ; Rodriguez, Benjamin A. ; Yilmaz, Ayse S. ; Goel, Shokhi ; Lin, Hai ; Collins-Burow, Bridgette ; Rhodes, Lyndsay V. ; Braun, Chris ; Pradeep, Sunila ; Rupaimoole, Rajesha ; Dalkilic, Mehmet ; Sood, Anil K. ; Burow, Matthew E. ; Tang, Haixu ; Huang, Tim H. ; Liu, Yunlong ; Rusch, Douglas B. ; Nephew, Kenneth. / A new method for stranded whole transcriptome RNA-seq. In: Methods. 2013 ; Vol. 63, No. 2. pp. 126-134.
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