Local and global factors affecting RNA sequencing analysis
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Sendler, Edward
[1
]
Johnson, Graham D.
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Wayne State Univ, Sch Med, CS Mott Ctr Human Growth & Dev, Ctr Mol Med & Genet, Detroit, MI 48201 USAWayne State Univ, Sch Med, Dept Obstet & Gynecol, CS Mott Ctr Human Growth & Dev, Detroit, MI 48201 USA
Johnson, Graham D.
[2
]
Krawetz, Stephen A.
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Wayne State Univ, Sch Med, Dept Obstet & Gynecol, CS Mott Ctr Human Growth & Dev, Detroit, MI 48201 USA
Wayne State Univ, Sch Med, CS Mott Ctr Human Growth & Dev, Ctr Mol Med & Genet, Detroit, MI 48201 USAWayne State Univ, Sch Med, Dept Obstet & Gynecol, CS Mott Ctr Human Growth & Dev, Detroit, MI 48201 USA
Krawetz, Stephen A.
[1
,2
]
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[1] Wayne State Univ, Sch Med, Dept Obstet & Gynecol, CS Mott Ctr Human Growth & Dev, Detroit, MI 48201 USA
[2] Wayne State Univ, Sch Med, CS Mott Ctr Human Growth & Dev, Ctr Mol Med & Genet, Detroit, MI 48201 USA
High-throughput RNA sequencing (RNA-seq) continues to provide unparalleled insight into transcriptome complexity. Now the "gold standard" for assessing global transcript levels, RNA-seq is poised to revolutionize our understanding of transcription and posttranscriptional regulation of RNA. Despite significant advantages over prior experimental strategies, RNA-seq is not without pitfalls. We have identified a number of confounding factors that significantly affect sequencing coverage. These include regional CC content, preferential sites of fragmentation, and read "pile-up" due to primer affinity and transcript end effects. Independent of cell type and laboratory, when ignored, these factors can bias analyses. Understanding the underlying principles responsible for producing these artifacts is key to recognizing both their presence and how their effects may be controlled. Here we outline the causes of and strategies to avoid several previously unreported complicating factors common to RNA-seq experiments. (C) 2011 Elsevier Inc. All rights reserved.
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Univ Michigan, Dept Biol Chem, Room5301 MSRB III 1150 W Med Ctr Dr, Ann Arbor, MI 48109 USA
Univ Michigan, Dept Computat Med & Bioinformat, Room5301 MSRB III 1150 W Med Ctr Dr, Ann Arbor, MI 48109 USAUniv Michigan, Dept Biol Chem, Room5301 MSRB III 1150 W Med Ctr Dr, Ann Arbor, MI 48109 USA
Wolfe, Michael B.
Goldstrohm, Aaron C.
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Univ Minnesota, Dept Biochem Mol Biol & Biophys, Room 6-155,Jackson Hall,1214A,321 Church St SE, Minneapolis, MN 55455 USAUniv Michigan, Dept Biol Chem, Room5301 MSRB III 1150 W Med Ctr Dr, Ann Arbor, MI 48109 USA
Goldstrohm, Aaron C.
Freddolino, Peter L.
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Univ Michigan, Dept Biol Chem, Room5301 MSRB III 1150 W Med Ctr Dr, Ann Arbor, MI 48109 USA
Univ Michigan, Dept Computat Med & Bioinformat, Room5301 MSRB III 1150 W Med Ctr Dr, Ann Arbor, MI 48109 USAUniv Michigan, Dept Biol Chem, Room5301 MSRB III 1150 W Med Ctr Dr, Ann Arbor, MI 48109 USA
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British Columbia Canc Agcy, Genome Sci Ctr, Vancouver, BC V5Z 4E6, Canada
Univ British Columbia, Dept Med Genet, Vancouver, BC, CanadaBritish Columbia Canc Agcy, Genome Sci Ctr, Vancouver, BC V5Z 4E6, Canada
Griffith, Malachi
Griffith, Obi L.
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British Columbia Canc Agcy, Genome Sci Ctr, Vancouver, BC V5Z 4E6, Canada
Univ British Columbia, Dept Med Genet, Vancouver, BC, CanadaBritish Columbia Canc Agcy, Genome Sci Ctr, Vancouver, BC V5Z 4E6, Canada
Griffith, Obi L.
Mwenifumbo, Jill
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British Columbia Canc Agcy, Genome Sci Ctr, Vancouver, BC V5Z 4E6, CanadaBritish Columbia Canc Agcy, Genome Sci Ctr, Vancouver, BC V5Z 4E6, Canada
Mwenifumbo, Jill
Goya, Rodrigo
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British Columbia Canc Agcy, Genome Sci Ctr, Vancouver, BC V5Z 4E6, CanadaBritish Columbia Canc Agcy, Genome Sci Ctr, Vancouver, BC V5Z 4E6, Canada
Goya, Rodrigo
Morrissy, A. Sorana
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British Columbia Canc Agcy, Genome Sci Ctr, Vancouver, BC V5Z 4E6, Canada
Univ British Columbia, Dept Med Genet, Vancouver, BC, CanadaBritish Columbia Canc Agcy, Genome Sci Ctr, Vancouver, BC V5Z 4E6, Canada
Morrissy, A. Sorana
Morin, Ryan D.
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British Columbia Canc Agcy, Genome Sci Ctr, Vancouver, BC V5Z 4E6, CanadaBritish Columbia Canc Agcy, Genome Sci Ctr, Vancouver, BC V5Z 4E6, Canada
Morin, Ryan D.
Corbett, Richard
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British Columbia Canc Agcy, Genome Sci Ctr, Vancouver, BC V5Z 4E6, CanadaBritish Columbia Canc Agcy, Genome Sci Ctr, Vancouver, BC V5Z 4E6, Canada
Corbett, Richard
Tang, Michelle J.
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British Columbia Canc Agcy, Genome Sci Ctr, Vancouver, BC V5Z 4E6, CanadaBritish Columbia Canc Agcy, Genome Sci Ctr, Vancouver, BC V5Z 4E6, Canada
Tang, Michelle J.
Hou, Ying-Chen
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British Columbia Canc Agcy, Genome Sci Ctr, Vancouver, BC V5Z 4E6, CanadaBritish Columbia Canc Agcy, Genome Sci Ctr, Vancouver, BC V5Z 4E6, Canada
Hou, Ying-Chen
Pugh, Trevor J.
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British Columbia Canc Agcy, Genome Sci Ctr, Vancouver, BC V5Z 4E6, Canada
Univ British Columbia, Dept Med Genet, Vancouver, BC, CanadaBritish Columbia Canc Agcy, Genome Sci Ctr, Vancouver, BC V5Z 4E6, Canada
Pugh, Trevor J.
Robertson, Gordon
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British Columbia Canc Agcy, Genome Sci Ctr, Vancouver, BC V5Z 4E6, CanadaBritish Columbia Canc Agcy, Genome Sci Ctr, Vancouver, BC V5Z 4E6, Canada
Robertson, Gordon
Chittaranjan, Suganthi
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British Columbia Canc Agcy, Genome Sci Ctr, Vancouver, BC V5Z 4E6, CanadaBritish Columbia Canc Agcy, Genome Sci Ctr, Vancouver, BC V5Z 4E6, Canada
Chittaranjan, Suganthi
Ally, Adrian
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British Columbia Canc Agcy, Genome Sci Ctr, Vancouver, BC V5Z 4E6, CanadaBritish Columbia Canc Agcy, Genome Sci Ctr, Vancouver, BC V5Z 4E6, Canada
Ally, Adrian
Asano, Jennifer K.
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British Columbia Canc Agcy, Genome Sci Ctr, Vancouver, BC V5Z 4E6, CanadaBritish Columbia Canc Agcy, Genome Sci Ctr, Vancouver, BC V5Z 4E6, Canada
Asano, Jennifer K.
Chan, Susanna Y.
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British Columbia Canc Agcy, Genome Sci Ctr, Vancouver, BC V5Z 4E6, CanadaBritish Columbia Canc Agcy, Genome Sci Ctr, Vancouver, BC V5Z 4E6, Canada
Chan, Susanna Y.
Li, Haiyan I.
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British Columbia Canc Agcy, Genome Sci Ctr, Vancouver, BC V5Z 4E6, CanadaBritish Columbia Canc Agcy, Genome Sci Ctr, Vancouver, BC V5Z 4E6, Canada
Li, Haiyan I.
McDonald, Helen
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British Columbia Canc Agcy, Genome Sci Ctr, Vancouver, BC V5Z 4E6, CanadaBritish Columbia Canc Agcy, Genome Sci Ctr, Vancouver, BC V5Z 4E6, Canada
McDonald, Helen
Teague, Kevin
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British Columbia Canc Agcy, Genome Sci Ctr, Vancouver, BC V5Z 4E6, CanadaBritish Columbia Canc Agcy, Genome Sci Ctr, Vancouver, BC V5Z 4E6, Canada
Teague, Kevin
Zhao, Yongjun
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British Columbia Canc Agcy, Genome Sci Ctr, Vancouver, BC V5Z 4E6, CanadaBritish Columbia Canc Agcy, Genome Sci Ctr, Vancouver, BC V5Z 4E6, Canada
Zhao, Yongjun
Zeng, Thomas
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British Columbia Canc Agcy, Genome Sci Ctr, Vancouver, BC V5Z 4E6, CanadaBritish Columbia Canc Agcy, Genome Sci Ctr, Vancouver, BC V5Z 4E6, Canada
Zeng, Thomas
Delaney, Allen
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British Columbia Canc Agcy, Genome Sci Ctr, Vancouver, BC V5Z 4E6, CanadaBritish Columbia Canc Agcy, Genome Sci Ctr, Vancouver, BC V5Z 4E6, Canada
Delaney, Allen
Hirst, Martin
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British Columbia Canc Agcy, Genome Sci Ctr, Vancouver, BC V5Z 4E6, CanadaBritish Columbia Canc Agcy, Genome Sci Ctr, Vancouver, BC V5Z 4E6, Canada
Hirst, Martin
Morin, Gregg B.
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British Columbia Canc Agcy, Genome Sci Ctr, Vancouver, BC V5Z 4E6, Canada
Univ British Columbia, Dept Med Genet, Vancouver, BC, CanadaBritish Columbia Canc Agcy, Genome Sci Ctr, Vancouver, BC V5Z 4E6, Canada
Morin, Gregg B.
Jones, Steven J. M.
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British Columbia Canc Agcy, Genome Sci Ctr, Vancouver, BC V5Z 4E6, Canada
Univ British Columbia, Dept Med Genet, Vancouver, BC, CanadaBritish Columbia Canc Agcy, Genome Sci Ctr, Vancouver, BC V5Z 4E6, Canada
Jones, Steven J. M.
Tai, Isabella T.
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British Columbia Canc Agcy, Genome Sci Ctr, Vancouver, BC V5Z 4E6, Canada
Univ British Columbia, Dept Med, Vancouver, BC, CanadaBritish Columbia Canc Agcy, Genome Sci Ctr, Vancouver, BC V5Z 4E6, Canada
Tai, Isabella T.
Marra, Marco A.
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British Columbia Canc Agcy, Genome Sci Ctr, Vancouver, BC V5Z 4E6, Canada
Univ British Columbia, Dept Med Genet, Vancouver, BC, CanadaBritish Columbia Canc Agcy, Genome Sci Ctr, Vancouver, BC V5Z 4E6, Canada