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Methods Mol Biol. 2017;1528:211-227.

A Spiking Strategy for ChIP-chip Data Normalization in S. cerevisiae.

Author information

1
Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC, Canada, H2W 1R7.
2
Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC, Canada, H2W 1R7. francois.robert@ircm.qc.ca.
3
Département de médecine, Faculté de médecine, Université de Montréal, 2900 Boulevard Edouard-Montpetit, Montréal, QC, Canada, H3T 1J4. francois.robert@ircm.qc.ca.

Abstract

Chromatin immunoprecipitation coupled to DNA microarrays (ChIP-chip) is widely used in the chromatin field, notably to map the position of histone variants or histone modifications along the genome. Often, the position and the occupancy of these epigenetic marks are to be compared between different experiments. It is now increasingly recognized that such cross-sample comparison is better done using externally added exogenous controls for normalization but no such method has been described for ChIP-chip. Here we describe a spiking normalization strategy that makes use of phiX174 phage DNA as a spiked control for normalization of ChIP-chip signals across different experiments.

KEYWORDS:

ChIP-chip; Chromatin; Chromatin immunoprecipitation; DNA tiling microarrays; Histone modifications; Histone variant; Microarray normalization; S. cerevisiae; Spike-in control

PMID:
27854024
DOI:
10.1007/978-1-4939-6630-1_13
[Indexed for MEDLINE]

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