Impact of artefact removal on ChIP quality metrics in ChIP-seq and ChIP-exo data.
Frontiers in Genetics, 2014 With the advent of ChIP-seq multiplexing technologies and the subsequent increase in ChIP-seq throughput, the development of working standards for the quality assessment of ChIP-seq studies has received significant attention.
Thomas Samuel Carroll +4 more
doaj +1 more source
Evaluation of experimental design and computational parameter choices affecting analyses of ChIP-seq and RNA-seq data in undomesticated poplar trees. [PDF]
, 2014 BackgroundOne of the great advantages of next generation sequencing is the ability to generate large genomic datasets for virtually all species, including non-model organisms.
Filkov, Vladimir +4 more
core +2 more sources
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
Genome Research, 2012 Chromatin immunoprecipitation (ChIP) followed by high-throughput DNA sequencing (ChIP-seq) has become a valuable and widely used approach for mapping the genomic location of transcription-factor binding and histone modifications in living cells.
S. Landt +47 more
semanticscholar +1 more source
Protocol to apply spike-in ChIP-seq to capture massive histone acetylation in human cells
STAR Protocols, 2021 Summary Inhibition of histone deacetylases causes rapid and robust acetylation of histones. In this case, histone acetylation is likely increased on nearly every nucleosome, and the per-cell DNA/chromatin yield in chromatin immunoprecipitation (ChIP ...
Di Wu, Liguo Wang, Haojie Huang
semanticscholar +1 more source
Joint modeling of ChIP-seq data via a Markov random field model [PDF]
, 2013 Chromatin ImmunoPrecipitation-sequencing (ChIP-seq) experiments have now become routine in biology for the detection of protein-binding sites. In this paper, we present a Markov random field model for the joint analysis of multiple ChIP-seq experiments ...
Dhavala +9 more
core +2 more sources
Methods for ChIP-seq analysis: A practical workflow and advanced applications.
Methods, 2020 Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a central method in epigenomic research. Genome-wide analysis of histone modifications, such as enhancer analysis and genome-wide chromatin state annotation, enables systematic analysis ...
Ryuichiro Nakato, Toyonori Sakata
semanticscholar +1 more source
A simple method for generating high-resolution maps of genome-wide protein binding
eLife, 2015 Chromatin immunoprecipitation (ChIP) and its derivatives are the main techniques used to determine transcription factor binding sites. However, conventional ChIP with sequencing (ChIP-seq) has problems with poor resolution, and newer techniques require ...
Peter J Skene, Steven Henikoff
doaj +1 more source
The DAXX co-repressor is directly recruited to active regulatory elements genome-wide to regulate autophagy programs in a model of human prostate cancer. [PDF]
, 2015 While carcinoma of the prostate is the second most common cause of cancer death in the US, current methods and markers used to predict prostate cancer (PCa) outcome are inadequate.
Benner, Christopher +2 more
core +2 more sources
ChIP‐Atlas: a data‐mining suite powered by full integration of public ChIP‐seq data
EMBO Reports, 2018 We have fully integrated public chromatin chromatin immunoprecipitation sequencing (ChIP‐seq) and DNase‐seq data (n > 70,000) derived from six representative model organisms (human, mouse, rat, fruit fly, nematode, and budding yeast), and have devised a ...
Shinya Oki +9 more
semanticscholar +1 more source
Systematic comparison of monoclonal versus polyclonal antibodies for mapping histone modifications by ChIP-seq. [PDF]
, 2016 BackgroundThe robustness of ChIP-seq datasets is highly dependent upon the antibodies used. Currently, polyclonal antibodies are the standard despite several limitations: They are non-renewable, vary in performance between lots and need to be validated ...
Busby, Michele +11 more
core +1 more source