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Methods Enzymol. 2012;513:89-112. doi: 10.1016/B978-0-12-391938-0.00004-5.

4C technology: protocols and data analysis.

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1
Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, The Netherlands.

Abstract

Chromosome conformation capture (3C) technology and its genome-wide derivatives have revolutionized our knowledge on chromatin folding and nuclear organization. 4C-seq Technology combines 3C principles with high-throughput sequencing (4C-seq) to enable for unbiased genome-wide screens for DNA contacts made by single genomic sites of interest. Here, we discuss in detail the design, application, and data analysis of 4C-seq experiments. Based on many hundreds of different 4C-seq experiments, we define criteria to assess data quality and show how different restriction enzymes and cross-linking conditions affect results. We describe in detail the mapping strategy of 4C-seq reads and show advanced strategies for data analysis.

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