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Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27me3

ABSTRACT: Chromatin immunoprecipitation was performed using monoclonal antibodiesd. DNA was amplified, fluorescently labeled and hybridized to a series of 38 arrays containing a total of 14.6 million 50-mer oligonucleotides Keywords: ChIP-chip hES whole genome

ORGANISM(S): Homo sapiens

PROVIDER: GSE8463 | GEO | 2007/09/14

SECONDARY ACCESSION(S): PRJNA101545

REPOSITORIES: GEO

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Whole genome ChIP/chip tiling of human ES cells for H3K4me3 and H3K27me3

Project description:Chromatin immunoprecipitation was performed using monoclonal antibodiesd. DNA was amplified, fluorescently labeled and hybridized to a series of 38 arrays containing a total of 14.6 million 50-mer oligonucleotides Keywords: ChIP-chip hES whole genome Chromatin immunoprecipitated DNA from H3K4me

2007-09-14 | E-GEOD-8463 | biostudies-arrayexpress

Differential roles of promoters, enhancers, and insulators in cell-type specific gene expression

Project description:Chromatin immunoprecipitation was performed using antibodies against CTCF and formaldehyde crosslinked chromatin from K562 Chromatin cells. The immunoprecipitated DNA was amplified, fluorescently labeled and hybridized to a 391K element tiling array based on NCBI35 build of the human genome (hg17) that contains overlapping 50-mer oligonucleotides, positioned at every 38 basepairs (bp) throughout the ENCODE regions. Keywords: ChIP-chip

2008-11-01 | GSE8098 | GEO

Differential roles of promoters, enhancers, and insulators in cell-type specific gene expression

2010-05-17 | E-GEOD-8098 | biostudies-arrayexpress

ChIP-seq profiling of H3K4me3 and H3K27me3 in an invasive insect, <i>Bactrocera</i> <i>dorsalis</i>.

Project description:Introduction: While it has been suggested that histone modifications can facilitate animal responses to rapidly changing environments, few studies have profiled whole-genome histone modification patterns in invasive species, leaving the regulatory landscape of histone modifications in invasive species unclear. Methods: Here, we screen genome-wide patterns of two important histone modifications, trimethylated Histone H3 Lysine 4 (H3K4me3) and trimethylated Histone H3 Lysine 27 (H3K27me3), in adult thorax muscles of a notorious invasive pest, the Oriental fruit fly Bactrocera dorsalis (Hendel) (Diptera: Tephritidae), using Chromatin Immunoprecipitation with high-throughput sequencing (ChIP-seq). Results: We identified promoters featured by the occupancy of H3K4me3, H3K27me3 or bivalent histone modifications that were respectively annotated with unique genes key to muscle development and structure maintenance. In addition, we found H3K27me3 occupied the entire body of genes, where the average enrichment was almost constant. Transcriptomic analysis indicated that H3K4me3 is associated with active gene transcription, and H3K27me3 is mostly associated with transcriptional repression. Importantly, we identified genes and putative motifs modified by distinct histone modification patterns that may possibly regulate flight activity. Discussion: These findings provide the first evidence of histone modification signature in B. dorsalis, and will be useful for future studies of epigenetic signature in other invasive insect species.

| S-EPMC9996634 | biostudies-literature

Escherichia coli Tiling Array for In vivo Protein Occupancy Display

Project description:Using a high-density tiling array containing 25-mer oligonucleotides at the resolution of one every four base pairs across the entire genome, we developed In vivo Protein Occupancy Display (IPOD), a technology that reveals protein occupancy across an entire bacterial chromosome at the resolution of individual binding sites. Application to Escherichia coli reveals thousands of protein occupancy peaks, highly enriched within and in close proximity to non-coding regulatory regions.

2009-09-01 | GSE16414 | GEO

BCL6 ChIP on chip using a Nimblegen custom tiling array

Project description:To determine whether BCL6 binds to the certain locus we performed genomic localization studies by chromatin immunoprecipitations (ChIP) using a densely tiled custom oligonucleotide microarray covering the genomic loci of different genes. Keywords: ChIP-chip, Transcription Factor localization The experiment was performed in Ramos cell. Triplicate ChIP with BCL6 or actin (negative control) antibodies were cohybridized to the arrays versus the respective input chromatin.The fold enrichment for each oligonucleotide was calculated as the ratio of Cy5 vs. Cy3. Any peaks involving >5 oligonucleotides and with > 2.5 fold enrichment were considered potentially positive hits.

2010-06-10 | E-GEOD-7673 | biostudies-arrayexpress

LINE1 and PRC2 control nucleolar organization and repression of the 8C-state in human ESCs [H3K27me3 ChIP-seq,RSeT+DT_L1KD]

Project description:In this study, we performed H3K27me3 ChIP-seq to compare LINE1 knockdown naive hES cells with the control.

2024-09-09 | GSE263290 | GEO

Starr: Simple Tiling ARRay analysis of Affymetrix ChIP-chip data.

Project description:BackgroundChromatin immunoprecipitation combined with DNA microarrays (ChIP-chip) is an assay used for investigating DNA-protein-binding or post-translational chromatin/histone modifications. As with all high-throughput technologies, it requires thorough bioinformatic processing of the data for which there is no standard yet. The primary goal is to reliably identify and localize genomic regions that bind a specific protein. Further investigation compares binding profiles of functionally related proteins, or binding profiles of the same proteins in different genetic backgrounds or experimental conditions. Ultimately, the goal is to gain a mechanistic understanding of the effects of DNA binding events on gene expression.ResultsWe present a free, open-source R/Bioconductor package Starr that facilitates comparative analysis of ChIP-chip data across experiments and across different microarray platforms. The package provides functions for data import, quality assessment, data visualization and exploration. Starr includes high-level analysis tools such as the alignment of ChIP signals along annotated features, correlation analysis of ChIP signals with complementary genomic data, peak-finding and comparative display of multiple clusters of binding profiles. It uses standard Bioconductor classes for maximum compatibility with other software. Moreover, Starr automatically updates microarray probe annotation files by a highly efficient remapping of microarray probe sequences to an arbitrary genome.ConclusionStarr is an R package that covers the complete ChIP-chip workflow from data processing to binding pattern detection. It focuses on the high-level data analysis, e.g., it provides methods for the integration and combined statistical analysis of binding profiles and complementary functional genomics data. Starr enables systematic assessment of binding behaviour for groups of genes that are alingned along arbitrary genomic features.

| S-EPMC2868012 | biostudies-literature

ChIP-Seq of human embryonic stem cells of a differentiation time course with antibody against H3K4me3

Project description:H3K4me3 ChIP-Seq profiling of a directed differentiation time course converting human embryonic stem cells (hES) into immature pancreatic beta cell precursors. CyT49, a Viacyte proprietary male hESC line with normal karyotype was used.

2012-10-13 | E-MTAB-821 | biostudies-arrayexpress

ChIP-on-chip from multiple donors of BM-MSCs with H3K4me3 and H3K27me3

Project description:Bone marrow-derived multipotent stromal cells (BM-MSCs) exhibit therapuetically valuable properties, including the capacity to differentiate into skeletal tissues and modulate immune system activity. These properties depend on proper regulation of dynamic gene expression in response to environmental and developmental stimuli. This study used chromatin immunoprecipitation (ChIP) coupled with human promoter tiling microarray analysis (ChIP-on-chip) to profile histones H3K4me3 and H3K27me3 at promoters genome-wide. The goal of the study was to identify gene promoters marked by H3K27me3 and H3K4me3 in BM-MSCs. ChIP-on-chip performed with antibodies to H3K4me3 and H3K27me3 on BM-MSCs from 3 different donors (labeled 1632, 167696, and 8F3560) and with technical replicates.

2015-02-09 | E-GEOD-64172 | biostudies-arrayexpress

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