Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization.

Details

Ressource 1Download: 1157.pdf (1734.42 [Ko])
State: Public
Version: Final published version
License: Not specified
Serval ID
serval:BIB_4F25C7234592
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization.
Journal
Genome Research
Author(s)
Bonhoure N., Bounova G., Bernasconi D., Praz V., Lammers F., Canella D., Willis I.M., Herr W., Hernandez N., Delorenzi M.
Working group(s)
CycliX Consortium
Contributor(s)
Hernandez N., Delorenzi M., Deplancke B., Desvergne B., Guex N., Herr W., Naef F., Rougemont J., Schibler U., Andersin T., Cousin P., Gilardi F., Gos P., Lammers F., Raghav S., Villeneuve D., Fabbretti R., Vlegel V., Xenarios I., Migliavacca E., Praz V., David F., Jarosz Y., Kuznetsov D., Liechti R., Martin O., Delafontaine J., Cajan J., Gustafson K., Krier I., Leleu M., Molina N., Naldi A., Rib L., Symul L., Bounova G.
ISSN
1549-5469 (Electronic)
ISSN-L
1088-9051
Publication state
Published
Issued date
2014
Peer-reviewed
Oui
Volume
24
Number
7
Pages
1157-1168
Language
english
Abstract
Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) experiments are widely used to determine, within entire genomes, the occupancy sites of any protein of interest, including, for example, transcription factors, RNA polymerases, or histones with or without various modifications. In addition to allowing the determination of occupancy sites within one cell type and under one condition, this method allows, in principle, the establishment and comparison of occupancy maps in various cell types, tissues, and conditions. Such comparisons require, however, that samples be normalized. Widely used normalization methods that include a quantile normalization step perform well when factor occupancy varies at a subset of sites, but may miss uniform genome-wide increases or decreases in site occupancy. We describe a spike adjustment procedure (SAP) that, unlike commonly used normalization methods intervening at the analysis stage, entails an experimental step prior to immunoprecipitation. A constant, low amount from a single batch of chromatin of a foreign genome is added to the experimental chromatin. This "spike" chromatin then serves as an internal control to which the experimental signals can be adjusted. We show that the method improves similarity between replicates and reveals biological differences including global and largely uniform changes.
Pubmed
Web of science
Open Access
Yes
Create date
05/08/2014 18:45
Last modification date
18/02/2020 7:20
Usage data