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

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...

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Autores principales: Bonhoure, Nicolas, Bounova, Gergana, Bernasconi, David, Praz, Viviane, Lammers, Fabienne, Canella, Donatella, Willis, Ian M., Herr, Winship, Hernandez, Nouria, Delorenzi, Mauro, Deplancke, Bart, Desvergne, Béatrice, Guex, Nicolas, Naef, Felix, Rougemont, Jacques, Schibler, Ueli, Andersin, Teemu, Cousin, Pascal, Gilardi, Federica, Gos, Pascal, Raghav, Sunil, Villeneuve, Dominic, Fabbretti, Roberto, Vlegel, Volker, Xenarios, Ioannis, Migliavacca, Eugenia, David, Fabrice, Jarosz, Yohan, Kuznetsov, Dmitry, Liechti, Robin, Martin, Olivier, Delafontaine, Julien, Cajan, Julia, Gustafson, Kyle, Krier, Irina, Leleu, Marion, Molina, Nacho, Naldi, Aurélien, Rib, Leonor, Symul, Laura
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory Press 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4079971/
https://www.ncbi.nlm.nih.gov/pubmed/24709819
http://dx.doi.org/10.1101/gr.168260.113
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author Bonhoure, Nicolas
Bounova, Gergana
Bernasconi, David
Praz, Viviane
Lammers, Fabienne
Canella, Donatella
Willis, Ian M.
Herr, Winship
Hernandez, Nouria
Delorenzi, Mauro
Hernandez, Nouria
Delorenzi, Mauro
Deplancke, Bart
Desvergne, Béatrice
Guex, Nicolas
Herr, Winship
Naef, Felix
Rougemont, Jacques
Schibler, Ueli
Andersin, Teemu
Cousin, Pascal
Gilardi, Federica
Gos, Pascal
Lammers, Fabienne
Raghav, Sunil
Villeneuve, Dominic
Fabbretti, Roberto
Vlegel, Volker
Xenarios, Ioannis
Migliavacca, Eugenia
Praz, Viviane
David, Fabrice
Jarosz, Yohan
Kuznetsov, Dmitry
Liechti, Robin
Martin, Olivier
Delafontaine, Julien
Cajan, Julia
Gustafson, Kyle
Krier, Irina
Leleu, Marion
Molina, Nacho
Naldi, Aurélien
Rib, Leonor
Symul, Laura
Bounova, Gergana
author_facet Bonhoure, Nicolas
Bounova, Gergana
Bernasconi, David
Praz, Viviane
Lammers, Fabienne
Canella, Donatella
Willis, Ian M.
Herr, Winship
Hernandez, Nouria
Delorenzi, Mauro
Hernandez, Nouria
Delorenzi, Mauro
Deplancke, Bart
Desvergne, Béatrice
Guex, Nicolas
Herr, Winship
Naef, Felix
Rougemont, Jacques
Schibler, Ueli
Andersin, Teemu
Cousin, Pascal
Gilardi, Federica
Gos, Pascal
Lammers, Fabienne
Raghav, Sunil
Villeneuve, Dominic
Fabbretti, Roberto
Vlegel, Volker
Xenarios, Ioannis
Migliavacca, Eugenia
Praz, Viviane
David, Fabrice
Jarosz, Yohan
Kuznetsov, Dmitry
Liechti, Robin
Martin, Olivier
Delafontaine, Julien
Cajan, Julia
Gustafson, Kyle
Krier, Irina
Leleu, Marion
Molina, Nacho
Naldi, Aurélien
Rib, Leonor
Symul, Laura
Bounova, Gergana
author_sort Bonhoure, Nicolas
collection PubMed
description 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.
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spelling pubmed-40799712014-07-17 Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization Bonhoure, Nicolas Bounova, Gergana Bernasconi, David Praz, Viviane Lammers, Fabienne Canella, Donatella Willis, Ian M. Herr, Winship Hernandez, Nouria Delorenzi, Mauro Hernandez, Nouria Delorenzi, Mauro Deplancke, Bart Desvergne, Béatrice Guex, Nicolas Herr, Winship Naef, Felix Rougemont, Jacques Schibler, Ueli Andersin, Teemu Cousin, Pascal Gilardi, Federica Gos, Pascal Lammers, Fabienne Raghav, Sunil Villeneuve, Dominic Fabbretti, Roberto Vlegel, Volker Xenarios, Ioannis Migliavacca, Eugenia Praz, Viviane David, Fabrice Jarosz, Yohan Kuznetsov, Dmitry Liechti, Robin Martin, Olivier Delafontaine, Julien Cajan, Julia Gustafson, Kyle Krier, Irina Leleu, Marion Molina, Nacho Naldi, Aurélien Rib, Leonor Symul, Laura Bounova, Gergana Genome Res Method 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. Cold Spring Harbor Laboratory Press 2014-07 /pmc/articles/PMC4079971/ /pubmed/24709819 http://dx.doi.org/10.1101/gr.168260.113 Text en © 2014 Bonhoure et al.; Published by Cold Spring Harbor Laboratory Press http://creativecommons.org/licenses/by-nc/4.0/ This article, published in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
spellingShingle Method
Bonhoure, Nicolas
Bounova, Gergana
Bernasconi, David
Praz, Viviane
Lammers, Fabienne
Canella, Donatella
Willis, Ian M.
Herr, Winship
Hernandez, Nouria
Delorenzi, Mauro
Hernandez, Nouria
Delorenzi, Mauro
Deplancke, Bart
Desvergne, Béatrice
Guex, Nicolas
Herr, Winship
Naef, Felix
Rougemont, Jacques
Schibler, Ueli
Andersin, Teemu
Cousin, Pascal
Gilardi, Federica
Gos, Pascal
Lammers, Fabienne
Raghav, Sunil
Villeneuve, Dominic
Fabbretti, Roberto
Vlegel, Volker
Xenarios, Ioannis
Migliavacca, Eugenia
Praz, Viviane
David, Fabrice
Jarosz, Yohan
Kuznetsov, Dmitry
Liechti, Robin
Martin, Olivier
Delafontaine, Julien
Cajan, Julia
Gustafson, Kyle
Krier, Irina
Leleu, Marion
Molina, Nacho
Naldi, Aurélien
Rib, Leonor
Symul, Laura
Bounova, Gergana
Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization
title Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization
title_full Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization
title_fullStr Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization
title_full_unstemmed Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization
title_short Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization
title_sort quantifying chip-seq data: a spiking method providing an internal reference for sample-to-sample normalization
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4079971/
https://www.ncbi.nlm.nih.gov/pubmed/24709819
http://dx.doi.org/10.1101/gr.168260.113
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