A comparative study of ChIP-seq sequencing library preparation methods

被引:15
|
作者
Sundaram, Arvind Y. M. [1 ,2 ]
Hughes, Timothy [1 ,2 ]
Biondi, Shea [3 ]
Bolduc, Nathalie [4 ]
Bowman, Sarah K. [5 ,11 ]
Camilli, Andrew [6 ,7 ]
Chew, Yap C. [3 ]
Couture, Catherine [8 ]
Farmer, Andrew [4 ]
Jerome, John P. [9 ]
Lazinski, David W. [6 ,7 ]
McUsic, Andrew [8 ]
Peng, Xu [10 ]
Shazand, Kamran [9 ]
Xu, Feng [10 ]
Lyle, Robert [1 ,2 ]
Gilfillan, Gregor D. [1 ,2 ]
机构
[1] Oslo Univ Hosp, Dept Med Genet, Oslo, Norway
[2] Univ Oslo, Oslo, Norway
[3] Zymo Res Corp, 7062 Murphy Ave, Irvine, CA 92614 USA
[4] Takara Bio USA Inc, 1290 Terra Bella Ave, Mountain View, CA 94043 USA
[5] Harvard Med Sch, Mass Gen Hosp, Mol Biol, 185 Cambridge St,CPZN 7250, Boston, MA 02114 USA
[6] Tufts Univ, Dept Mol Biol & Microbiol, 136 Harrison Ave, Boston, MA 02111 USA
[7] Tufts Univ, Howard Hughes Med Inst, 136 Harrison Ave, Boston, MA 02111 USA
[8] Swift Biosci Inc, Suite 100,58 Parkland Plaza, Ann Arbor, MI 48103 USA
[9] Rubicon Genom Inc, 4743 Venture Dr, Ann Arbor, MI 48108 USA
[10] ASTAR, Singapore Inst Clin Sci, Singapore 117609, Singapore
[11] Directed Genom, 240 Cty Rd, Ipswich, MA 01938 USA
来源
BMC GENOMICS | 2016年 / 17卷
关键词
HTS; NGS; Low-input; Micro-ChIP; Chromatin immunoprecipitation; CHROMATIN IMMUNOPRECIPITATION ASSAY; MU-CHIP; EPIGENETIC CHARACTERIZATION; LIMITED NUMBERS; AMPLIFICATION; CELLS; PLURIPOTENT; PROFILES; DYNAMICS; PROTOCOL;
D O I
10.1186/s12864-016-3135-y
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
摘要
Background: ChIP-seq is the primary technique used to investigate genome-wide protein-DNA interactions. As part of this procedure, immunoprecipitated DNA must undergo "library preparation" to enable subsequent high-throughput sequencing. To facilitate the analysis of biopsy samples and rare cell populations, there has been a recent proliferation of methods allowing sequencing library preparation from low-input DNA amounts. However, little information exists on the relative merits, performance, comparability and biases inherent to these procedures. Notably, recently developed single-cell ChIP procedures employing microfluidics must also employ library preparation reagents to allow downstream sequencing. Results: In this study, seven methods designed for low-input DNA/ChIP-seq sample preparation (Accel-NGS (R) 2S, Bowman-method, HTML-PCR, SeqPlex (TM) , DNA SMART (TM), TELP and ThruPLEX (R)) were performed on five replicates of 1 ng and 0.1 ng input H3K4me3 ChIP material, and compared to a "gold standard" reference PCR-free dataset. The performance of each method was examined for the prevalence of unmappable reads, amplification-derived duplicate reads, reproducibility, and for the sensitivity and specificity of peak calling. Conclusions: We identified consistent high performance in a subset of the tested reagents, which should aid researchers in choosing the most appropriate reagents for their studies. Furthermore, we expect this work to drive future advances by identifying and encouraging use of the most promising methods and reagents. The results may also aid judgements on how comparable are existing datasets that have been prepared with different sample library preparation reagents.
引用
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页数:12
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