期刊
NATURE PROTOCOLS
卷 8, 期 3, 页码 539-554出版社
NATURE PUBLISHING GROUP
DOI: 10.1038/nprot.2013.023
关键词
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资金
- Weizmann institute
- Human Frontiers Science Program, Career Development Award
- Israel Science Foundation (ISF) Bikura Institutional Research Grant Program
- ERC [309788]
- Center for Excellence in Genome Science from the National Human Genome Research Institute (NHGRI) [1P50HG006193]
- European Research Council (ERC) [309788] Funding Source: European Research Council (ERC)
Dynamic protein binding to DNA elements regulates genome function and cell fate. Although methods for mapping in vivo protein-DNA interactions are becoming crucial for every aspect of genomic research, they are laborious and costly, thereby limiting progress. Here we present a protocol for mapping in vivo protein-DNA interactions using a high-throughput chromatin immunoprecipitation (HT-ChIP) approach. By using paramagnetic beads, we streamline the entire ChIP and indexed library construction process: sample transfer and loss is minimized and the need for manually labor-intensive procedures such as washes, gel extraction and DNA precipitation is eliminated. All of this allows for fully automated, cost effective and highly sensitive 96-well ChIP sequencing (ChIP-seq). Sample preparation takes 3 d from cultured cells to pooled libraries. Compared with previous methods, HT-ChIP is more suitable for large-scale in vivo studies, specifically those measuring the dynamics of a large number of different chromatin modifications/transcription factors or multiple perturbations.
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