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Methods. 2015 Jan 15;72:65-75. doi: 10.1016/j.ymeth.2014.10.031. Epub 2014 Nov 6.

The Hitchhiker's guide to Hi-C analysis: practical guidelines.

Author information

1
Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605-0103, USA. Electronic address: Bryan.lajoie@umassmed.edu.
2
Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605-0103, USA. Electronic address: Job.dekker@umassmed.edu.
3
Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605-0103, USA. Electronic address: noam.kaplan2@gmail.com.

Abstract

Over the last decade, development and application of a set of molecular genomic approaches based on the chromosome conformation capture method (3C), combined with increasingly powerful imaging approaches, have enabled high resolution and genome-wide analysis of the spatial organization of chromosomes. The aim of this paper is to provide guidelines for analyzing and interpreting data obtained with genome-wide 3C methods such as Hi-C and 3C-seq that rely on deep sequencing to detect and quantify pairwise chromatin interactions.

KEYWORDS:

Bioinformatics; Chromatin structure; Chromosome conformation capture; Deep sequencing; Hi-C

PMID:
25448293
PMCID:
PMC4347522
DOI:
10.1016/j.ymeth.2014.10.031
[Indexed for MEDLINE]
Free PMC Article

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