Results 11 to 20 of about 928,240 (334)
ChIPmentation: fast, robust, low-input ChIP-seq for histones and transcription factors
Nature Methods, 2015 Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is widely used to map histone marks and transcription factor binding throughout the genome.
Christian Schmidl +2 more
exaly +2 more sources
Normalization of ChIP-seq data with control [PDF]
BMC Bioinformatics, 2012 Background ChIP-seq has become an important tool for identifying genome-wide protein-DNA interactions, including transcription factor binding and histone modifications. In ChIP-seq experiments, ChIP samples are usually coupled with their matching control
Liang Kun, Keleş Sündüz
doaj +3 more sources
ChIP–seq: advantages and challenges of a maturing technology
Nature Reviews Genetics, 2009 Peter J Park
exaly +2 more sources
ChIPulate: A comprehensive ChIP-seq simulation pipeline.
PLoS Computational Biology, 2019 ChIP-seq (Chromatin Immunoprecipitation followed by sequencing) is a high-throughput technique to identify genomic regions that are bound in vivo by a particular protein, e.g., a transcription factor (TF).
Vishaka Datta +2 more
doaj +4 more sources
Identifying ChIP-seq enrichment using MACS [PDF]
Nature Protocols, 2012 Model-based analysis of ChIP-seq (MACS) is a computational algorithm that identifies genome-wide locations of transcription/chromatin factor binding or histone modification from ChIP-seq data. MACS consists of four steps: removing redundant reads, adjusting read position, calculating peak enrichment and estimating the empirical false discovery rate ...
Jianxing Feng +4 more
semanticscholar +3 more sources
ChIP-BIT2: a software tool to detect weak binding events using a Bayesian integration approach
BMC Bioinformatics, 2021 Background ChIP-seq combines chromatin immunoprecipitation assays with sequencing and identifies genome-wide binding sites for DNA binding proteins. While many binding sites have strong ChIP-seq ‘peak’ observations and are well captured, there are still ...
Xi Chen +5 more
doaj +1 more source
F1000Research, 2020 Quantification of gene expression and characterization of gene transcript structures are central problems in molecular biology. RNA sequencing (RNA-Seq) and chromatin immunoprecipitation sequencing (ChIP-Seq) are important methods, but can be cumbersome ...
Syed Hussain Ather +6 more
doaj +1 more source
WACS: improving ChIP-seq peak calling by optimally weighting controls
BMC Bioinformatics, 2021 Background Chromatin immunoprecipitation followed by high throughput sequencing (ChIP-seq), initially introduced more than a decade ago, is widely used by the scientific community to detect protein/DNA binding and histone modifications across the genome.
Aseel Awdeh +2 more
doaj +1 more source
De novo ChIP-seq analysis [PDF]
Genome Biology, 2015 Methods for the analysis of chromatin immunoprecipitation sequencing (ChIP-seq) data start by aligning the short reads to a reference genome. While often successful, they are not appropriate for cases where a reference genome is not available. Here we develop methods for de novo analysis of ChIP-seq data.
He, Xin +5 more
openaire +5 more sources
Effects of sheared chromatin length on ChIP-seq quality and sensitivity
G3: Genes, Genomes, Genetics, 2021 Chromatin immunoprecipitation followed by massively parallel, high throughput sequencing (ChIP-seq) is the method of choice for genome-wide identification of DNA segments bound by specific transcription factors or in chromatin with particular histone ...
Cheryl A Keller +11 more
doaj +1 more source