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HiChIP: Efficient and sensitive analysis of protein-directed genome architecture

Maxwell R. Mumbach, Adam J. Rubin, Ryan A. Flynn, Chao Dai, Paul A. Khavari, William J. Greenleaf, Howard Y. Chang
doi: https://doi.org/10.1101/073619
Maxwell R. Mumbach
1Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305.
2Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305.
3Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305.
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Adam J. Rubin
2Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305.
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Ryan A. Flynn
1Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305.
2Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305.
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Chao Dai
1Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305.
2Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305.
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Paul A. Khavari
2Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305.
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William J. Greenleaf
1Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305.
3Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305.
4Department of Applied Physics, Stanford University, Stanford, CA 94025.
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Howard Y. Chang
1Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305.
2Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305.
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Abstract

Genome conformation is central to gene control but challenging to interrogate. Here we present HiChIP, a protein-centric chromatin conformation method. HiChIP improves the yield of conformation-informative reads by over 10-fold and lowers input requirement over 100-fold relative to ChIA-PET. HiChIP of cohesin reveals multi-scale genome architecture with greater signal to background than in situ Hi-C. Thus, HiChIP adds to the toolbox of 3D genome structure and regulation for diverse biomedical applications.

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Posted September 08, 2016.
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HiChIP: Efficient and sensitive analysis of protein-directed genome architecture
Maxwell R. Mumbach, Adam J. Rubin, Ryan A. Flynn, Chao Dai, Paul A. Khavari, William J. Greenleaf, Howard Y. Chang
bioRxiv 073619; doi: https://doi.org/10.1101/073619
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HiChIP: Efficient and sensitive analysis of protein-directed genome architecture
Maxwell R. Mumbach, Adam J. Rubin, Ryan A. Flynn, Chao Dai, Paul A. Khavari, William J. Greenleaf, Howard Y. Chang
bioRxiv 073619; doi: https://doi.org/10.1101/073619

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