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

Department of Molecular Medicine

Resultado de la investigación: Article › revisión exhaustiva

38 Citas (Scopus)

Resumen

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).

Idioma original	English (US)
Páginas (desde-hasta)	126-134
Número de páginas	9
Publicación	Methods
Volumen	63
N.º	2
DOI	https://doi.org/10.1016/j.ymeth.2013.03.023
Estado	Published - sept 15 2013

ASJC Scopus subject areas

Molecular Biology
Biochemistry, Genetics and Molecular Biology(all)

Acceder al documento

10.1016/j.ymeth.2013.03.023

Otros archivos y enlaces

Citar esto

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, n.º 2, pp. 126-134. https://doi.org/10.1016/j.ymeth.2013.03.023

@article{d1510299bde94c67834c759767f7040d,

title = "A new method for stranded whole transcriptome RNA-seq",

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).",

keywords = "Duplex-specific nuclease, Gene expression, RNA-seq, Transcriptome",

author = "Miller, {David F.B.} and Yan, {Pearlly S.} and Aaron Buechlein and Rodriguez, {Benjamin A.} and Yilmaz, {Ayse S.} and Shokhi Goel and Hai Lin and Bridgette Collins-Burow and Rhodes, {Lyndsay V.} and Chris Braun and Sunila Pradeep and Rajesha Rupaimoole and Mehmet Dalkilic and Sood, {Anil K.} and Burow, {Matthew E.} and Haixu Tang and Huang, {Tim H.} and Yunlong Liu and Rusch, {Douglas B.} and Nephew, {Kenneth P.}",

year = "2013",

month = sep,

day = "15",

doi = "10.1016/j.ymeth.2013.03.023",

language = "English (US)",

volume = "63",

pages = "126--134",

journal = "Methods",

issn = "1046-2023",

publisher = "Academic Press Inc.",

number = "2",

}

TY - JOUR

T1 - A new method for stranded whole transcriptome RNA-seq

AU - Miller, David F.B.

AU - Yan, Pearlly S.

AU - Buechlein, Aaron

AU - Rodriguez, Benjamin A.

AU - Yilmaz, Ayse S.

AU - Goel, Shokhi

AU - Lin, Hai

AU - Collins-Burow, Bridgette

AU - Rhodes, Lyndsay V.

AU - Braun, Chris

AU - Pradeep, Sunila

AU - Rupaimoole, Rajesha

AU - Dalkilic, Mehmet

AU - Sood, Anil K.

AU - Burow, Matthew E.

AU - Tang, Haixu

AU - Huang, Tim H.

AU - Liu, Yunlong

AU - Rusch, Douglas B.

AU - Nephew, Kenneth P.

PY - 2013/9/15

Y1 - 2013/9/15

N2 - 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).

AB - 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).

KW - Duplex-specific nuclease

KW - Gene expression

KW - RNA-seq

KW - Transcriptome

UR - http://www.scopus.com/inward/record.url?scp=84885171004&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84885171004&partnerID=8YFLogxK

U2 - 10.1016/j.ymeth.2013.03.023

DO - 10.1016/j.ymeth.2013.03.023

M3 - Article

C2 - 23557989

AN - SCOPUS:84885171004

SN - 1046-2023

VL - 63

SP - 126

EP - 134

JO - Methods

JF - Methods

IS - 2

ER -

A new method for stranded whole transcriptome RNA-seq

Resumen

ASJC Scopus subject areas

Acceder al documento

Otros archivos y enlaces

Huella

Citar esto