Cargando…

Chipper: discovering transcription-factor targets from chromatin immunoprecipitation microarrays using variance stabilization

Chromatin immunoprecipitation combined with microarray technology (Chip(2)) allows genome-wide determination of protein-DNA binding sites. The current standard method for analyzing Chip(2 )data requires additional control experiments that are subject to systematic error. We developed methods to asse...

Descripción completa

Detalles Bibliográficos
Autores principales:	Gibbons, Francis D, Proft, Markus, Struhl, Kevin, Roth, Frederick P
Formato:	Texto
Lenguaje:	English
Publicado:	BioMed Central 2005
Materias:	Method
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1297652/ https://www.ncbi.nlm.nih.gov/pubmed/16277751 http://dx.doi.org/10.1186/gb-2005-6-11-r96

Ejemplares similares

Extensive chromatin fragmentation improves enrichment of protein binding sites in chromatin immunoprecipitation experiments
por: Fan, Xiaochun, et al.
Publicado: (2008)

Fast chromatin immunoprecipitation assay
por: Nelson, Joel D., et al.
Publicado: (2006)

Cell-free chromatin immunoprecipitation to detect molecular pathways in heart transplantation
por: Jang, Moon Kyoo, et al.
Publicado: (2023)

A comparative analysis of genome-wide chromatin immunoprecipitation data for mammalian transcription factors
por: Ji, Hongkai, et al.
Publicado: (2006)

Model-based variance-stabilizing transformation for Illumina microarray data
por: Lin, Simon M., et al.
Publicado: (2008)

A plug and play microfluidic platform for standardized sensitive low-input chromatin immunoprecipitation
por: Dirks, René A.M., et al.
Publicado: (2021)

TAF-ChIP: an ultra-low input approach for genome-wide chromatin immunoprecipitation assay
por: Akhtar, Junaid, et al.
Publicado: (2019)

Cell‐free chromatin immunoprecipitation can determine tumor gene expression in lung cancer patients
por: Trier Maansson, Christoffer, et al.
Publicado: (2023)

Optimization of experimental design parameters for high-throughput chromatin immunoprecipitation studies
por: Ponzielli, Romina, et al.
Publicado: (2008)

The use of biotin tagging in Saccharomyces cerevisiae improves the sensitivity of chromatin immunoprecipitation
por: van Werven, Folkert J., et al.
Publicado: (2006)

Ritornello: high fidelity control-free chromatin immunoprecipitation peak calling
por: Stanton, Kelly P., et al.
Publicado: (2017)

AHT-ChIP-seq: a completely automated robotic protocol for high-throughput chromatin immunoprecipitation
por: Aldridge, Sarah, et al.
Publicado: (2013)

EGFR transcription in non‐small‐cell lung cancer tumours can be revealed in ctDNA by cell‐free chromatin immunoprecipitation (cfChIP)
por: Månsson, Christoffer Trier, et al.
Publicado: (2021)

Nanobody®-based chromatin immunoprecipitation/micro-array analysis for genome-wide identification of transcription factor DNA binding sites
por: Nguyen-Duc, Trong, et al.
Publicado: (2013)

Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA
por: Statham, Aaron L., et al.
Publicado: (2012)

Systematic evaluation of chromatin immunoprecipitation sequencing to study histone occupancy in dormancy transitions of grapevine buds
por: Hermawaty, Dina, et al.
Publicado: (2023)

Rank-statistics based enrichment-site prediction algorithm developed for chromatin immunoprecipitation on chip experiments
por: Ghosh, Srinka, et al.
Publicado: (2006)

μChIP—a rapid micro chromatin immunoprecipitation assay for small cell samples and biopsies
por: Dahl, John Arne, et al.
Publicado: (2008)

Immediate chromatin immunoprecipitation and on-bead quantitative PCR analysis: a versatile and rapid ChIP procedure
por: Harmeyer, Kayla M., et al.
Publicado: (2015)

Recovering Genetic Regulatory Networks from Chromatin Immunoprecipitation and Steady-State Microarray Data
por: Zhao, Wentao, et al.
Publicado: (2008)

Microplate-based chromatin immunoprecipitation method, Matrix ChIP: a platform to study signaling of complex genomic events
por: Flanagin, Steve, et al.
Publicado: (2008)

Binding of lac repressor-GFP fusion protein to lac operator sites inserted in the tobacco chloroplast genome examined by chromatin immunoprecipitation
por: Newell, Christine A., et al.
Publicado: (2010)

Analysis of transcription factor interactions in osteoblasts using competitive chromatin immunoprecipitation
por: Roca, Hernan, et al.
Publicado: (2008)

Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression
por: Hafemeister, Christoph, et al.
Publicado: (2019)

RNA-DNA hybrid (R-loop) immunoprecipitation mapping: an analytical workflow to evaluate inherent biases
por: Halász, László, et al.
Publicado: (2017)

Tagging of MADS domain proteins for chromatin immunoprecipitation
por: de Folter, Stefan, et al.
Publicado: (2007)

Target Gene Analysis by Microarrays and Chromatin Immunoprecipitation Identifies HEY Proteins as Highly Redundant bHLH Repressors
por: Heisig, Julia, et al.
Publicado: (2012)

Locus-Specific Biochemical Epigenetics/Chromatin Biochemistry by Insertional Chromatin Immunoprecipitation
por: Fujita, Toshitsugu, et al.
Publicado: (2013)

Quantification of global transcription patterns in prokaryotes using spotted microarrays
por: Sidders, Ben, et al.
Publicado: (2007)

Chromatin immunoprecipitation: optimization, quantitative analysis and data normalization
por: Haring, Max, et al.
Publicado: (2007)

Direct Identification of Insulator Components by Insertional Chromatin Immunoprecipitation
por: Fujita, Toshitsugu, et al.
Publicado: (2011)

Chromatin Immunoprecipitation from Human Embryonic Stem Cells
por: Bertani, Stephane, et al.
Publicado: (2008)

Chromatin Immunoprecipitation (ChIP) in Mouse T-cell Lines
por: Giaimo, Benedetto Daniele, et al.
Publicado: (2017)

Inhibition of transcription leads to rewiring of locus-specific chromatin proteomes
por: Poramba-Liyanage, Deepani W., et al.
Publicado: (2020)

MEDEA: analysis of transcription factor binding motifs in accessible chromatin
por: Mariani, Luca, et al.
Publicado: (2020)

Cross-linking, Immunoprecipitation and Proteomic Analysis to Identify Interacting Proteins in Cultured Cells
por: Wang, Hao, et al.
Publicado: (2019)

Immunoprecipitation of Reporter Nascent Chains from Active Ribosomes to Study Translation Efficiency
por: Cacioppo, Roberta, et al.
Publicado: (2023)

A Molecular Chipper technology for CRISPR sgRNA library generation and functional mapping of noncoding regions
por: Cheng, Jijun, et al.
Publicado: (2016)

Chromatin Composition Is Changed by Poly(ADP-ribosyl)ation during Chromatin Immunoprecipitation
por: Beneke, Sascha, et al.
Publicado: (2012)

Inferring transcriptional modules from ChIP-chip, motif and microarray data
por: Lemmens, Karen, et al.
Publicado: (2006)

Cannot write session to /tmp/vufind_sessions/sess_ad56v4ecladv5tpnoab5p5tndk