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Methods Mol Biol. 2016;1418:191-208. doi: 10.1007/978-1-4939-3578-9_10.

Quantitative Comparison of Large-Scale DNA Enrichment Sequencing Data.

Author information

1
Max Planck Institute for Molecular Genetics, Ihnestr. 63 - 73, 14195, Berlin, Germany.
2
German Cancer Research Center, In Neuenheimer Feld 580, 69120, Heidelberg, Germany. l.chavez@dkfz.de.

Abstract

DNA enrichment followed by sequencing (DNA-IP seq) is a versatile tool in molecular biology with a wide variety of applications. Computational analysis of differential DNA enrichment between conditions is important for identifying epigenetic alterations in disease compared to healthy controls and for revealing dynamic epigenetic modifications throughout normal and distorted cell differentiation and development. We present a protocol for genome-wide comparative analysis of DNA-IP sequencing data to identify statistically significant differential sequencing coverage between two conditions by considering variation across replicates. The protocol provides a detailed description for the comparative analysis of DNA-IP sequencing data including basic data processing, quality controls, and identification of differential enrichment using the Bioconductor package "MEDIPS".

KEYWORDS:

Bioconductor; ChIP-seq; Computational biology; DNA enrichment; DNA methylation; Epigenetics; MeDIP-seq; Quality control; Sequencing

PMID:
27008016
DOI:
10.1007/978-1-4939-3578-9_10
[Indexed for MEDLINE]

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