4C technology: protocols and data analysis

H.J. van de Werken; P.J. de Vree; E. Splinter; S.J. Holwerda; P. Klous; E. de Wit; W. de Laat

doi:10.1016/B978-0-12-391938-0.00004-5

4C technology: protocols and data analysis

H.J. van de Werken, P.J. de Vree, E. Splinter, S.J. Holwerda, P. Klous, E. de Wit, W. de Laat

Hubrecht Institute

Onderzoeksoutput: Bijdrage aan wetenschappelijk tijdschrift/periodieke uitgave › Artikel › Wetenschappelijk › peer review

175 Citaten (Scopus)

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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.

Originele taal-2	Engels
Pagina's (van-tot)	89-112
Tijdschrift	Methods in Enzymology
Volume	513
DOI's	https://doi.org/10.1016/B978-0-12-391938-0.00004-5
Status	Gepubliceerd - 2012

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title = "4C technology: protocols and data analysis",

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.",

author = "{van de Werken}, H.J. and {de Vree}, P.J. and E. Splinter and S.J. Holwerda and P. Klous and {de Wit}, E. and {de Laat}, W.",

note = "Reporting year: 2012",

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AU - van de Werken, H.J.

AU - de Vree, P.J.

AU - Splinter, E.

AU - Holwerda, S.J.

AU - Klous, P.

AU - de Wit, E.

AU - de Laat, W.

N1 - Reporting year: 2012

PY - 2012

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N2 - 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.

AB - 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.

U2 - 10.1016/B978-0-12-391938-0.00004-5

DO - 10.1016/B978-0-12-391938-0.00004-5

M3 - Article

SN - 0076-6879

VL - 513

SP - 89

EP - 112

JO - Methods in Enzymology

JF - Methods in Enzymology

ER -

4C technology: protocols and data analysis

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