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 P. Nephew

doi:10.1016/j.ymeth.2013.03.023

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 P. Nephew

Gynecological Oncology & Reproductive Medicine

Research output: Contribution to journal › Article › peer-review

40 Scopus citations

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 language	English (US)
Pages (from-to)	126-134
Number of pages	9
Journal	Methods
Volume	63
Issue number	2
DOIs	https://doi.org/10.1016/j.ymeth.2013.03.023
State	Published - Sep 15 2013

Keywords

Duplex-specific nuclease
Gene expression
RNA-seq
Transcriptome

ASJC Scopus subject areas

Molecular Biology
General Biochemistry, Genetics and Molecular Biology

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10.1016/j.ymeth.2013.03.023

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Miller, D. F. B., Yan, P. S., Buechlein, A., Rodriguez, B. A., Yilmaz, A. S., Goel, S., Lin, H., Collins-Burow, B., Rhodes, L. V., Braun, C., Pradeep, S., Rupaimoole, R., Dalkilic, M., Sood, A. K., Burow, M. E., Tang, H., Huang, T. H., Liu, Y., Rusch, D. B., & Nephew, K. P. (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

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, KP 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

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AU - Rhodes, Lyndsay V.

AU - Braun, Chris

AU - Pradeep, Sunila

AU - Rupaimoole, Rajesha

AU - Dalkilic, Mehmet

AU - Sood, Anil K.

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AU - Tang, Haixu

AU - Huang, Tim H.

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AU - Rusch, Douglas B.

AU - Nephew, Kenneth P.

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A new method for stranded whole transcriptome RNA-seq

Abstract

Keywords

ASJC Scopus subject areas

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