Results 261 to 270 of about 570,629 (303)

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
openaire   +2 more sources

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
openaire   +2 more sources

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
openaire   +2 more sources

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
openaire   +2 more sources

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
openaire   +2 more sources

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
openaire   +2 more sources

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
openaire   +4 more sources

Computational Analysis of ChIP-seq Data

2010
Chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-seq) is a new technology to map protein-DNA interactions in a genome. The genome-wide transcription factor binding site and chromatin modification data produced by ChIP-seq provide invaluable information for studying gene regulation. This chapter reviews basic characteristics
openaire   +2 more sources

Modelling ChIP-seq Data Using HMMs

2017
Chromatin ImmunoPrecipitation-sequencing (ChIP-seq) experiments have now become routine in biology for the detection of protein binding sites. In this chapter, we show how hidden Markov models can be used for the analysis of data generated by ChIP-seq experiments.
openaire   +2 more sources

Statistical Analysis of ChIP-seq Data with MOSAiCS

2013
Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) is invaluable for identifying genome-wide binding of transcription factors and mapping of epigenomic profiles. We present a statistical protocol for analyzing ChIP-seq data.
Guannan, Sun, Dongjun, Chung, Kun, Liang, Sündüz, Keleş   +3 more
openaire   +2 more sources