Ultra-low-input, tagmentation-based whole-genome bisulfite sequencing

被引：84

作者：

Adey, Andrew ^{[1
]}

Shendure, Jay ^{[1
]}

机构：

[1] Univ Washington, Dept Genome Sci, Seattle, WA 98195 USA

来源：

GENOME RESEARCH | 2012年 / 22卷 / 06期

关键词：

DNA METHYLATION;

D O I：

10.1101/gr.136242.111

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

We have adapted transposase-based in vitro shotgun library construction ("tagmentation") for whole-genome bisulfite sequencing. This method, Tn5mC-seq, enables a >100-fold reduction in starting material relative to conventional protocols, such that we generate highly complex bisulfite sequencing libraries from as little as 10 ng of input DNA, and ample useful sequences from 1 ng of input DNA. We demonstrate Tn5mC-seq by sequencing the methylome of a human lymphoblastoid cell line to similar to 8.6x high-quality coverage of each strand.

引用

页码：1139 / 1143

页数：5

共 16 条

[1] Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition [J].

Adey, Andrew ;

Morrison, Hilary G. ;

Asan ;

Xun, Xu ;

Kitzman, Jacob O. ;

Turner, Emily H. ;

Stackhouse, Bethany ;

MacKenzie, Alexandra P. ;

Caruccio, Nicholas C. ;

Zhang, Xiuqing ;

Shendure, Jay .

GENOME BIOLOGY, 2010, 11 (12)

[2] Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells [J].

Ball, Madeleine P. ;

Li, Jin Billy ;

Gao, Yuan ;

Lee, Je-Hyuk ;

LeProust, Emily M. ;

Park, In-Hyun ;

Xie, Bin ;

Daley, George Q. ;

Church, George M. .

NATURE BIOTECHNOLOGY, 2009, 27 (04) :361-368

[3]

CLARK SJ, 1994, NUCLEIC ACIDS RES, V22, P2990, DOI 10.1093/nar/22.15.2990

[4] Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning [J].

Cokus, Shawn J. ;

Feng, Suhua ;

Zhang, Xiaoyu ;

Chen, Zugen ;

Merriman, Barry ;

Haudenschild, Christian D. ;

Pradhan, Sriharsa ;

Nelson, Stanley F. ;

Pellegrini, Matteo ;

Jacobsen, Steven E. .

NATURE, 2008, 452 (7184) :215-219

[5] Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming [J].

Deng, Jie ;

Shoemaker, Robert ;

Xie, Bin ;

Gore, Athurva ;

LeProust, Emily M. ;

Antosiewicz-Bourget, Jessica ;

Egli, Dieter ;

Maherali, Nimet ;

Park, In-Hyun ;

Yu, Junying ;

Daley, George Q. ;

Eggan, Kevin ;

Hochedlinger, Konrad ;

Thomson, James ;

Wang, Wei ;

Gao, Yuan ;

Zhang, Kun .

NATURE BIOTECHNOLOGY, 2009, 27 (04) :353-360

[6] A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis [J].

Down, Thomas A. ;

Rakyan, Vardhman K. ;

Turner, Daniel J. ;

Flicek, Paul ;

Li, Heng ;

Kulesha, Eugene ;

Graf, Stefan ;

Johnson, Nathan ;

Herrero, Javier ;

Tomazou, Eleni M. ;

Thorne, Natalie P. ;

Backdahl, Liselotte ;

Herberth, Marlis ;

Howe, Kevin L. ;

Jackson, David K. ;

Miretti, Marcos M. ;

Marioni, John C. ;

Birney, Ewan ;

Hubbard, Tim J. P. ;

Durbin, Richard ;

Tavare, Simon ;

Beck, Stephan .

NATURE BIOTECHNOLOGY, 2008, 26 (07) :779-785

[7] Transposase mediated construction of RNA-seq libraries [J].

Gertz, Jason ;

Varley, Katherine E. ;

Davis, Nicholas S. ;

Baas, Bradley J. ;

Goryshin, Igor Y. ;

Vaidyanathan, Ramesh ;

Kuersten, Scott ;

Myers, Richard M. .

GENOME RESEARCH, 2012, 22 (01) :134-141

[8]

Grunenwald H, 2011, NEXTERA PCR FREE DNA

[9] Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling [J].

Gu, Hongcang ;

Smith, Zachary D. ;

Bock, Christoph ;

Boyle, Patrick ;

Gnirke, Andreas ;

Meissner, Alexander .

NATURE PROTOCOLS, 2011, 6 (04) :468-481

[10] Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications [J].

Harris, R. Alan ;

Wang, Ting ;

Coarfa, Cristian ;

Nagarajan, Raman P. ;

Hong, Chibo ;

Downey, Sara L. ;

Johnson, Brett E. ;

Fouse, Shaun D. ;

Delaney, Allen ;

Zhao, Yongjun ;

Olshen, Adam ;

Ballinger, Tracy ;

Zhou, Xin ;

Forsberg, Kevin J. ;

Gu, Junchen ;

Echipare, Lorigail ;

O'Geen, Henriette ;

Lister, Ryan ;

Pelizzola, Mattia ;

Xi, Yuanxin ;

Epstein, Charles B. ;

Bernstein, Bradley E. ;

Hawkins, R. David ;

Ren, Bing ;

Chung, Wen-Yu ;

Gu, Hongcang ;

Bock, Christoph ;

Gnirke, Andreas ;

Zhang, Michael Q. ;

Haussler, David ;

Ecker, Joseph R. ;

Li, Wei ;

Farnham, Peggy J. ;

Waterland, Robert A. ;

Meissner, Alexander ;

Marra, Marco A. ;

Hirst, Martin ;

Milosavljevic, Aleksandar ;

Costello, Joseph F. .

NATURE BIOTECHNOLOGY, 2010, 28 (10) :1097-U194

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