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Genome-wide identification of PAR domain protein 1 (PDP1) targets through ChIP-seq reveals the regulation of diapause-specific characteristics in Culex pipiens. [PDF]

Insect Mol Biol
Dhungana P, Wei X, Meuti ME, Sim C.
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Analysis of Controls in ChIP-seq

Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics, 2017
The chromatin immunoprecipitation followed by high throughput sequencing (ChIP-seq) method, initially introduced a decade ago, is widely used by the scientific community to detect protein/DNA binding and histone modifications across the genome in various cell lines. Every experiment is prone to noise and bias, and ChIP-seq experiments are no exception.
Aseel Awdeh, Theodore J. Perkins
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The Analysis of ChIP-Seq Data

2011
Chromatin immunoprecipitation coupled with ultra-high-throug put parallel DNA sequencing (ChIP-seq) is an effective technology for the investigation of genome-wide protein-DNA interactions. Examples of applications include the studies of RNA polymerases transcription, transcriptional regulation, and histone modifications.
Wenxiu, Ma, Wing Hung, Wong
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Sequential ChIP-Seq

ChIP-Seq has been used extensively to profile genome-wide transcription factor binding and post-translational histone modifications. A sequential ChIP assay determines the in vivo co-localization of two proteins to the same genomic locus. In this chapter, we combine the two protocols in Sequential ChIP-Seq, a method for identifying genome-wide sites of
Joseph D, Schinderle, Irina M, Bochkis
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ChIP-Seq Analysis in Neurospora crassa

2018
Chromatin immunoprecipitation paired with next-generation sequencing (ChIP-seq) can be used to determine genome-wide distribution of transcriptions factors, transcriptional machinery, or histone modifications. DNA-protein interactions are covalently cross-linked with the addition of formaldehyde.
Aileen R, Ferraro, Zachary A, Lewis
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Summary of ChIP-Seq Methods and Description of an Optimized ChIP-Seq Protocol

Chromatin immunoprecipitation (ChIP) is an invaluable method to characterize interactions between proteins and genomic DNA, such as the genomic localization of transcription factors and post-translational modification of histones. DNA and proteins are reversibly and covalently crosslinked using formaldehyde.
Maria Theresa M, Fadri, Jessica B, Lee, Albert J, Keung   +2 more
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ChIP-Seq: Library Preparation and Sequencing

2016
Chromatin immunoprecipitation with massively parallel DNA sequencing (ChIP-Seq) has been used extensively to determine the genome-wide location of DNA-binding factors, such as transcription factors, posttranscriptionally modified histones, and members of the transcription complex, to assess regulatory input, epigenetic modifications, and ...
Karyn L, Sheaffer, Jonathan, Schug
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Chromatin Immunoprecipitation for ChIP-chip and ChIP-seq

2014
Bacterial adaptation to given environmental conditions is largely achieved by complex gene regulatory processes. To address the question how and to what extend single transcriptional regulators modulate gene expression, chromatin immunoprecipitation (ChIP) coupled to DNA microarrays (ChIP-chip) or to next-generation sequencing (ChIP-seq) is one of the ...
Sebastian Schulz, Susanne Häussler
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Epigenetic Analysis: ChIP-chip and ChIP-seq

2011
The access of transcription factors and the replication machinery to DNA is regulated by the epigenetic state of chromatin. In eukaryotes, this complex layer of regulatory processes includes the direct methylation of DNA, as well as covalent modifications to histones. Using next-generation sequencers, it is now possible to obtain profiles of epigenetic
Pellegrini M, Ferrari R
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