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Free keywords:
Chromatin Immunoprecipitation
Computational Biology/*methods/standards
Databases, Genetic
Epigenesis, Genetic
Epigenomics/methods
Genomics/*methods/standards
*High-Throughput Nucleotide Sequencing
Humans
Molecular Sequence Annotation
Sequence Alignment
*Sequence Analysis, DNA/methods
*Software
Bioconductor
ChIP-seq
Computational biology
DNA enrichment
DNA methylation
Epigenetics
MeDIP-seq
Quality control
Sequencing
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".
