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ChIP-seq

Cold Spring Harbor Protocols, 2018
Owing to its digital nature, ChIP-seq has become the standard method for genome-wide ChIP analysis. Using next-generation sequencing platforms (notably the Illumina Genome Analyzer), millions of short sequence reads can be obtained. The densities of recovered ChIP sequence reads along the genome are used to determine the binding sites of the protein ...
Kim, Tae Hoon, Dekker, Job
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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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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 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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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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