Results 1 to 10 of about 459,773 (306)

CSSQ: a ChIP-seq signal quantifier pipeline [PDF]

Frontiers in Cell and Developmental Biology, 2023
Chromatin immunoprecipitation followed by sequencing (ChIP-seq) has revolutionized the studies of epigenomes and the massive increase in ChIP-seq datasets calls for robust and user-friendly computational tools for quantitative ChIP-seq. Quantitative ChIP-
Ashwath Kumar, Michael Y. Hu, Yajun Mei, Yajun Mei, Yuhong Fan, Yuhong Fan   +5 more
doaj   +4 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 Data Processing and Relative and Quantitative Signal Normalization for Saccharomyces cerevisiae [PDF]

Bio-Protocol
Chromatin immunoprecipitation with high-throughput sequencing (ChIP-seq) is a widely used technique for genome-wide analyses of protein–DNA interactions. This protocol provides a guide to ChIP-seq data processing in Saccharomyces cerevisiae, with a focus
Kris Alavattam, Bradley Dickson, Rina Hirano, Rachel Dell, Toshio Tsukiyama   +4 more
doaj   +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, Sridhar Hannenhalli, Rahul Siddharthan   +2 more
doaj   +4 more sources

In silico pooling of ChIP-seq control experiments.

PLoS ONE, 2014
As next generation sequencing technologies are becoming more economical, large-scale ChIP-seq studies are enabling the investigation of the roles of transcription factor binding and epigenome on phenotypic variation.
Guannan Sun, Rajini Srinivasan, Camila Lopez-Anido, Holly A Hung, John Svaren, Sündüz Keleş   +5 more
doaj   +4 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, Xu Shi, Andrew F. Neuwald, Leena Hilakivi-Clarke, Robert Clarke, Jianhua Xuan   +5 more
doaj   +1 more source

SeqAcademy: an educational pipeline for RNA-Seq and ChIP-Seq analysis [version 4; peer review: 2 approved, 1 not approved]

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, Olaitan Igbagbo Awe, Thomas J. Butler, Tamiru Denka, Stephen Andrew Semick, Wanhu Tang, Ben Busby   +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, Marcel Turcotte, Theodore J. Perkins   +2 more
doaj   +1 more source

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, Alexander Q Wixom, Elisabeth F Heuston, Belinda Giardine, Chris C -S Hsiung, Maria R Long, Amber Miller, Stacie M Anderson, April Cockburn, Gerd A Blobel, David M Bodine, Ross C Hardison   +11 more
doaj   +1 more source

MER41 repeat sequences contain inducible STAT1 binding sites. [PDF]

PLoS ONE, 2010
Chromatin immunoprecipitation combined with massively parallel sequencing methods (ChIP-seq) is becoming the standard approach to study interactions of transcription factors (TF) with genomic sequences.
Christoph D Schmid, Philipp Bucher
doaj   +1 more source