GEO DataSets

(Submitter supplied) Eukaryotic gene regulatory information is contained within the DNA sequences of cis-regulatory elements and the epigenetic features of the chromatin surrounding these elements. Recent investigations in yeast, fly, and mammalian systems have made significant contributions toward our understanding of the relationship between gene activation and chromatin architecture at transcriptional promoters, but much work remains to improve our knowledge of this relationship at human promoters and other transcriptional regulatory elements, such as enhancers. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL4558 GPL4559 GPL1454

64 Samples

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(Submitter supplied) The readout of genome information is controlled by transcriptional regulatory elements, but a comprehensive view of the combinatorial control by these DNA sequences, which bind regulatory protein and/or the modified histones in regulating gene transcription, is clearly preliminary. We have developed an experimental strategy for comprehensive determination of such functional elements in human DNA. This strategy involves the application of genome-wide location analysis, also known as ChIP-chip, to a panel of well-characterized regulatory proteins and histones with specific modifications, known to generally associate with transcriptional regulatory elements in vivo. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL1454 GPL4559

124 Samples

Download data: GPR, PAIR

(Submitter supplied) CD34+ positively isolated from healthy donors (stimulated by G-CSF) with magnetic beads (after blood leukapheresis) CD34- obtained from 10dd cytokine cultured CD34+ Keywords: differentiation

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

5 Samples

Download data: CEL

(Submitter supplied) The simultaneous genotyping of tens of thousands of SNP using SNP microarrays is a very important tool that is revolutionizing genetics and molecular biology. In this work, we present a new application of this technique by using it to assess chromatin immunoprecipitation (CHIP) as a means to assess the multiple genomic locations bound by a protein complex recognized by an antibody. We illustrate the use of this technique with an analysis of the change in histone H4 acetylation, a marker of open chromatin and transcriptionally active genomic regions, which occur during the differentiation of human myoblasts into myotubes. more...

Organism:

Homo sapiens

Type:

Expression profiling by array; Genome binding/occupancy profiling by SNP array; SNP genotyping by SNP array

Platforms:

GPL97 GPL3400 GPL96

21 Samples

Download data: CEL, EXP

(Submitter supplied) We assessed the genomic distribution of H4-acetylated chromatin by ChIP using SNP chips and an antibody specific to four acetylated lysine residues of H4. Keywords: Comparative genomic hybridization

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by SNP array; SNP genotyping by SNP array

Platform:

GPL3400

9 Samples

Download data: CEL, EXP

(Submitter supplied) Gene expression was determined for both myotubes and myoblasts using Affymetrix HG-U133 A/B arrays. Keywords: Comparative expression

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL97 GPL96

12 Samples

Download data: CEL, EXP

(Submitter supplied) DNaseI sensitivity/hypersensitivity using DNase-array method (Sabo et al Nature Methods 3:511-18, 2006) on Affymetrix whole-genome tiling DNA microarrays. Background: Focal alteration in chromatin structure in vivo, detectable through hypersensitivity to DNaseI and other nucleases, is the sine qua non of diverse transcriptional regulatory elements including enhancers, promoters, insulators, and locus control regions. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

7 related Platforms

76 Samples

Download data: CEL

(Submitter supplied) To understand the molecular basis that supports the dynamic gene expression programs unique to T cells, we investigated the genomic landscape of activating histone modifications, including histone H3 K9/K14 diacetylation (H3K9acK14ac), H3 K4 trimethylation (H3K4me3), and the repressive histone modification H3 K27 trimethylation (H3K27me3) in primary human T cells. We show that H3K9acK14ac and H3K4me3 are associated with active genes required for T cell function and development, whereas H3K27me3 is associated with silent genes that are involved in development in other cell types. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL4812

2 Samples

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(Submitter supplied) The goal of this study was to map DNaseI sensitivity and DNaseI hypersensitive sites over the ENCODE regions in multiple human cell types (GM06990, CACO2, HepG2). Keywords: DNase/Array

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL2131

3 Samples

Download data: PDF, TXT

(Submitter supplied) The goal of this study was to map DNaseI sensitivity and DNaseI hypersensitive sites over the ENCODE regions in human lymphoblastoid cells (GM06990, Coriell). Keywords: DNase/Array

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL2131

1 Sample

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(Submitter supplied) Identifying the chromosomal targets of transcription factors is important for reconstructing the transcriptional regulatory networks underlying global gene expression programs. We have developed an unbiased genomic method called sequence tag analysis of genomic enrichment (STAGE) to identify the direct binding targets of transcription factors in vivo. STAGE is based on high-throughput sequencing of concatemerized tags derived from target DNA enriched by chromatin immunoprecipitation. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL1485

2 Samples

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(Submitter supplied) 2091 mock vs. 2091 E2F4 IP - Human 13K promoter microarray 2091 cells were serum starved for 72hours and fixed with formaldehyde. Keywords: repeat sample

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL1525

2 Samples

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(Submitter supplied) To gain insights into the function of DNA methylation at cis-regulatory regions and its impact on gene expression, we measured methylation, RNA polymerase II and histone modifications at 24.000 promoters in primary human soma and germline cells. Keywords: DNA methylation, MeDIP

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array; Methylation profiling by genome tiling array

Platform:

GPL3497

11 Samples

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(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

30 Samples

Download data: BROADPEAK, BW, NARROWPEAK, TXT

(Submitter supplied) The activity of enhancers and promoters fine-tunes the transcriptional program of mammalian cells through the recruitment and interplay between cell type-specific and ubiquitous transcription factors. Despite their key role in modulating transcription, the identification of enhancers is challenged by their limited sequence conservation and highly variable distance from target genes. Although enhancers are characterised by the strong enrichment of mono-methylation at lysine 4 of histone H3, mirrored by low tri-methylation at the same residue, a comprehensive list of enhancers-associated histone post-translational modifications (PTMs) is still lacking. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

1 Sample

Download data: TXT

(Submitter supplied) The activity of enhancers and promoters fine-tunes the transcriptional program of mammalian cells through the recruitment and interplay between cell type-specific and ubiquitous transcription factors. Despite their key role in modulating transcription, the identification of enhancers is challenged by their limited sequence conservation and highly variable distance from target genes. Although enhancers are characterised by the strong enrichment of mono-methylation at lysine 4 of histone H3, mirrored by low tri-methylation at the same residue, a comprehensive list of enhancers-associated histone post-translational modifications (PTMs) is still lacking. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

29 Samples

Download data: BED, BROADPEAK, BW, NARROWPEAK

(Submitter supplied) Histones of higher eukaryotes are assembled into chromatin primarily during DNA replication, but at other times the histone H3.3 variant replaces canonical H3. We introduce a novel strategy for profiling epigenetic patterns based on H3.3 replacement, using microarrays covering about one third of the Drosophila melanogaster genome at 100-bp resolution. Striking patterns of H3.3 replacement were found over active genes and transposons. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by array; Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL2678 GPL1908

11 Samples

Download data: BEDGRAPH

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Expression profiling by array; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL6887 GPL9250 GPL9185

42 Samples

Download data: WIG

(Submitter supplied) The limited number of in vivo germ cells poses an impediment to genome-wide studies. Here, we applied a small-scale ChIP-Seq method on purified mouse fetal germ cells to generate genome-wide maps of four histone modifications (H3K4me3, H3K27me3, H3K27ac and H2BK20ac), facilitating the identification of active and repressed cis-regulatory elements in germ cells in vivo. Comparison of active chromatin state between somatic, embryonic stem cells (ESC) and germ cells revealed promoters and enhancers needed for stem cell maintenance and germ cell development. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL9250 GPL9185

31 Samples

Download data: WIG

(Submitter supplied) We used microarrays to profile global gene expression changes of Pou5f1-GFP-positive germ cells between E11.5 to E15.5.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6887

11 Samples

Download data: TXT