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Global ChIP-seq Normalization Reveals Epigenome Modulations

ABSTRACT: Epigenomic profiling by ChIP-seq is a prevailing methodology used to investigate chromatin-based regulation in biological systems, such as human disease, yet the lack of an empirical methodology to normalize amongst experiments has limited the usefulness of this technique. Here we describe a “spike-in” normalization method that allows the quantitative comparison of histone modification status across cell populations using defined quantities of a reference epigenome. We demonstrate the utility of this method in measuring epigenomic changes following chemical perturbations and show how control normalization of ChIP-seq experiments enables discovery of disease-relevant changes in histone modification occupancy.

ORGANISM(S): Homo sapiens Drosophila melanogaster

PROVIDER: GSE60104 | GEO | 2014/10/30

SECONDARY ACCESSION(S): PRJNA257491

REPOSITORIES: GEO

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Global ChIP-seq Normalization Reveals Epigenome Modulations

Project description:Epigenomic profiling by ChIP-seq is a prevailing methodology used to investigate chromatin-based regulation in biological systems, such as human disease, yet the lack of an empirical methodology to normalize amongst experiments has limited the usefulness of this technique. Here we describe a “spike-in” normalization method that allows the quantitative comparison of histone modification status across cell populations using defined quantities of a reference epigenome. We demonstrate the utility of this method in measuring epigenomic changes following chemical perturbations and show how control normalization of ChIP-seq experiments enables discovery of disease-relevant changes in histone modification occupancy. ChIP-Seq of histone modifications H3K79me2 and H3K4me3 in human samples treated with EPZ-5676 with/without reference epigenome spike-in.

2014-10-30 | E-GEOD-60104 | biostudies-arrayexpress

Global ChIP-seq Normalization Reveals Epigenome Modulations

Project description:Global ChIP-seq Normalization Reveals Epigenome Modulations

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proteiNorm – A user-friendly tool for normalization and analysis of TMT and label-free protein quantification

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2021-09-09 | PXD018152 | Pride

"The Wild West of Spike-in Normalization": Benchmarking the ChIP-seq spike-in normalization method

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"The Wild West of Spike-in Normalization": Benchmarking the ChIP-seq spike-in normalization method

Project description:"The Wild West of Spike-in Normalization": Benchmarking the ChIP-seq spike-in normalization method

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Osmolality-based normalization enhances statistical discrimination of untargeted metabolomic urine analysis: results from a comparative study

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