Results 21 to 30 of about 673,559 (305)

A flexible ChIP-sequencing simulation toolkit

BMC Bioinformatics, 2021
Background A major challenge in evaluating quantitative ChIP-seq analyses, such as peak calling and differential binding, is a lack of reliable ground truth data.
An Zheng, Michael Lamkin, Yutong Qiu, Kevin Ren, Alon Goren, Melissa Gymrek   +5 more
doaj   +1 more source

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, Bao, Yanchun, Veronica Vinciotti, Hoen, P.A.C. 't, Vinciotti, V., Yanchun Bao, Bao, Y.C., Ernst Wit, Wit, Ernst, Vinciotti, V, Peter AC ’t Hoen, 't Hoen, Peter A C, Vinciotti, Veronica, Bao, Y, 't Hoen, PAC, Wit, E, Wit, E.   +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, Ziwei eLiang, Rafik eSalama, Rory eStark, Ines ede Santiago   +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., Marlous Hoogstraat, Dijk, A.D.J., van, Roeland C. H. J. van Ham, Ham, R.C.H.J., van, Jose M. Muiño, Aalt D. J. van Dijk, Hoogstraat, M.   +7 more
core   +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

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, Adam E Handel, Giulio Disanto, Gavin Giovannoni, Sandve, GK, Berlanga-Taylor, AJ, Geir K Sandve, Finn Drabløs, Disanto, Giulio, Drabløs, F, Giuseppe Gallone, George C Ebers, Ramagopalan, Sreeram V, Drabløs, Finn, Drablos, F, Hanwell, Heather EC, Antonio J Berlanga-Taylor, Handel, Adam E, Sandve, Geir Kjetil, Ebers, Georg C, Ramagopalan, SV, Hanwell, H, Handel, AE, Sreeram V Ramagopalan, Gallone, G, Ebers, GC, Gallone, Anna, Giovannoni, Gavin, Berlanga-Taylor, Antonio, Giovannoni, G, Disanto, G   +30 more
core   +2 more sources

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

intePareto: an R package for integrative analyses of RNA-Seq and ChIP-Seq data

BMC Genomics, 2020
Background RNA-Seq, the high-throughput sequencing (HT-Seq) of mRNAs, has become an essential tool for characterizing gene expression differences between different cell types and conditions.
Yingying Cao, Simo Kitanovski, Daniel Hoffmann   +2 more
doaj   +1 more source

An Alternative Approach to ChIP-Seq Normalization Enables Detection of Genome-Wide Changes in Histone H3 Lysine 27 Trimethylation upon EZH2 Inhibition. [PDF]

PLoS ONE, 2016
Chromatin immunoprecipitation and DNA sequencing (ChIP-seq) has been instrumental in inferring the roles of histone post-translational modifications in the regulation of transcription, chromatin compaction and other cellular processes that require ...
Brian Egan, Chih-Chi Yuan, Madeleine Lisa Craske, Paul Labhart, Gulfem D Guler, David Arnott, Tobias M Maile, Jennifer Busby, Chisato Henry, Theresa K Kelly, Charles A Tindell, Suchit Jhunjhunwala, Feng Zhao, Charlie Hatton, Barbara M Bryant, Marie Classon, Patrick Trojer   +16 more
doaj   +1 more source