Accounting for immunoprecipitation efficiencies in the statistical analysis of ChIP-seq data [PDF]
, 2013 Background: ImmunoPrecipitation (IP) efficiencies may vary largely between different antibodies and between repeated experiments with the same antibody.
’t Hoen, Peter AC +16 more
core +1 more source
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
Comprehensive assessment of differential ChIP-seq tools guides optimal algorithm selection
Genome Biology, 2022 Background The analysis of chromatin binding patterns of proteins in different biological states is a main application of chromatin immunoprecipitation followed by sequencing (ChIP-seq).
Thomas Eder, Florian Grebien
doaj +1 more source
PRI-CAT: a web-tool for the analysis, storage and visualization of plant ChIP-seq experiments. [PDF]
, 2011 Although several tools for the analysis of ChIP-seq data have been published recently, there is a growing demand, in particular in the plant research community, for computational resources with which such data can be processed, analyzed, stored ...
Muino, J.M. +7 more
core +1 more source
Vitamin D receptor ChIP-seq in primary CD4+ cells: relationship to serum 25-hydroxyvitamin D levels and autoimmune disease. [PDF]
, 2013 BACKGROUND: Vitamin D insufficiency has been implicated in autoimmunity. ChIP-seq experiments using immune cell lines have shown that vitamin D receptor (VDR) binding sites are enriched near regions of the genome associated with autoimmune diseases.
Heather Hanwell +30 more
core +2 more sources
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
ILM-MLOlab/ChIP-seq-GATA1: v.1.0.0
, 2022 Here is the depository for the code and source data for ChIP-seq GATA1 ...
mattiasmoller, ILM-MLOlab
core +1 more source
CMT: a constrained multi-level thresholding approach for ChIP-Seq data analysis. [PDF]
PLoS ONE, 2014 Genome-wide profiling of DNA-binding proteins using ChIP-Seq has emerged as an alternative to ChIP-chip methods. ChIP-Seq technology offers many advantages over ChIP-chip arrays, including but not limited to less noise, higher resolution, and more ...
Iman Rezaeian, Luis Rueda
doaj +1 more source
Results of ChIP-Seq and DNase-Seq
, 2023 Results of ChIP-Seq and DNase-Seq for Cavendish banana ...
Xiuxiu Li (13880603)
core +1 more source
Low-Cell-Number Epigenome Profiling Aids the Study of Lens Aging and Hematopoiesis
Cell Reports, 2015 Understanding how chromatin modification regulates development and disease can be limited by available material. Despite recent progress, balancing high-quality and reliable mapping using chromatin-immunoprecipitation-based deep sequencing (ChIP-seq ...
Xiaobin Zheng +5 more
doaj +1 more source