GEO DataSets

(Submitter supplied) Human embryonic stem cells share identical genomic sequences with other lineage-committed cells yet possess the remarkable properties of self-renewal and pluripotency. It has been proposed that epigenetic regulatory mechanisms, involving DNA methylation and various chromatin modifications, are at least partly responsible for the distinct cellular properties between different cell types. Previous studies focusing largely on gene promoters and CpG islands have identified close association between several chromatin modifications and DNA methylation, but revealed a relatively small degree of differences between pluripotent and lineage-committed cells. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL9115 GPL9052

7 Samples

Download data: BED, TXT

(Submitter supplied) Transcriptional enhancers play critical roles in regulation of gene expression, but their identification has remained a challenge. Recently, it was shown that enhancers in the mammalian genome are associated with characteristic histone modification patterns, which have been increasingly exploited for enhancer identification. However, only a limited number of histone modifications have previously been investigated for this purpose, leaving the questions answered whether there exist an optimal set of histone modifications that could improve the enhancer prediction. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL9115 GPL11154

3 Samples

Download data: BED

(Submitter supplied) Human embryonic stem cells (hESCs) are offering a new therapeutic approach because of their unique ability to proliferate indefinitely in vitro and differentiate into multiple cell types. However, our understanding of the molecular mechanisms of pluripotency and self-renewal remain incomplete. To elucidate the key regulatory sequences and genes responsible for these cellular properties, we have determined potential enhancers and insulators in the genome of human ES cells and examined the dynamics of four key chromatin modifications (H3K4me1, H3K4me3, H3K27ac and H3K27me3) at both promoters and enhancers during the differentiation of these cells. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9115

3 Samples

Download data: BED, TXT

(Submitter supplied) The human embryonic stem cells (hESCs) are a unique model system for investigating the mechanisms of human development due to their ability to replicate indefinitely while retaining the capacity to differentiate into a host of functionally distinct cell types. In addition, these cells could be potentially used as therapeutic agents in regenerative medicine. Differentiation of hESCs involves selective activation or silencing of genes, a process controlled in part by the epigenetic state of the cell. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

6 related Platforms

878 Samples

Download data: BAM, BED, WIG

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

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platform:

GPL13304

15 Samples

Download data: WIG

(Submitter supplied) In this study, we further characterized the hkCP and dCP enhancers, which were identified by STARR-seq, and shown to have an intrinsic capacity to interact with a specific type of core promoter depending on the presence of a DRE motif [9]. hkCP enhancers are marked by H3K4me3, associated with TAD borders, and mediate large TSS-clustered interactions to promote robust transcription. Furthermore, they contain the architectural proteins CAP-H2, Chromator, DREF and Z4. more...

Organism:

Drosophila melanogaster

Type:

Other

Platform:

GPL13304

6 Samples

Download data: HIC, TXT

(Submitter supplied) In this study, we further characterized the hkCP and dCP enhancers, which were identified by STARR-seq, and shown to have an intrinsic capacity to interact with a specific type of core promoter depending on the presence of a DRE motif [9]. hkCP enhancers are marked by H3K4me3, associated with TAD borders, and mediate large TSS-clustered interactions to promote robust transcription. Furthermore, they contain the architectural proteins CAP-H2, Chromator, DREF and Z4. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13304

9 Samples

Download data: WIG

(Submitter supplied) Cell fate transitions involve integration of genomic information encoded by regulatory elements, such as enhancers, with the cellular environment. However, identification of the genomic sequences that control the earliest steps of human embryonic development represents a formidable challenge. Here we show that in human embryonic stem cells (hESCs) unique chromatin signatures identify two distinct classes of genomic elements, both of which are marked by the presence of chromatin regulators p300 and BRG1, and monomethylation of histone H3 at lysine 4 (H3K4me1). more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL9052

16 Samples

Download data: BED, TXT

(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:

GPL4559 GPL1454

124 Samples

Download data: GPR, PAIR

(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

Download data

(Submitter supplied) We report the chromatin modification dynamics at p53 binding sites upon treatment with DMSO or nutlin3-a (5uM) in IMR90 human lung fibroblasts using ChIP-seq and RNA-seq analyses. We assessed the genomewide changes in H3, H3K4me3, H3K4me2, H3K4me1, H3K27ac, H4K16ac, RNA polymerase II, and p53 in response to p53 activation.

Organism:

Homo sapiens

Type:

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

Platforms:

GPL11154 GPL18573

22 Samples

Download data: BED, BEDGRAPH, BIGWIG, TXT

(Submitter supplied) Paired-end sequencing of MNase digested H1 and H9 hESCs.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

2 Samples

Download data: BED, WIG

(Submitter supplied) Cytosine methylation of DNA is an evolutionarily conserved mechanism from plants to animals with crucial roles in gene regulation. However, the variation between methylomes of normal tissues is largely unexplored. To better understand the epigenetic variation of a normal individual, we profiled DNA methylation using whole genome bisulfite sequencing in 17 tissues isolated from an individual mouse. We observed a unique distribution of CpG methylation for each tissue, which cluster based on cell lineage. more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL13112

17 Samples

Download data: TXT

(Submitter supplied) Epigenetic mechanisms are known to regulate gene expression during chondrogenesis. In this study, we have characterised the epigenome during in vitro differentiation of human mesenchymal stem cells (hMSCs) into chondrocytes. Chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) was used to assess a range of N-terminal post-transcriptional modifications (marks) to histone H3 lysines (H3K4me3, H3K4me1, H3K27ac, H3K27me3 and H3K36me3) in both hMSCs and differentiated chondrocytes. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL18573 GPL16791

24 Samples

Download data: BIGWIG

(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) Here we show how chromatin structure is involved in glucocorticoid receptor (GR) binding in a mouse mammary cell line. We show that GR binds to accessible chromatin sites that are either nucleosome-free or contain a nucleosome.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

12 Samples

Download data: TDF

(Submitter supplied) Glucocorticoid hormone plays a major role in metabolism and many related diseases. The hormone-bound glucocorticoid receptor (GR) binds to a specific set of enhancers in different cell types, resulting in unique patterns of gene expression. GR-responsive enhancers have an accessible chromatin structure prior to hormone treatment (“pre-programmed”), whereas unresponsive enhancers specific to other cell types are inaccessible and inactive. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

4 Samples

Download data: TDF

(Submitter supplied) The regulatory elements that direct tissue-specific gene expression in the developing mammalian embryo remain largely unknown. Although chromatin profiling has proven to be a powerful method for mapping regulatory sequences in cultured cells, chromatin states characteristic of active developmental enhancers have not been directly identified in embryonic tissues. Here we use whole transcriptome analysis coupled with genome-wide profiling of H3K27ac and H3K27me3 to map chromatin states and enhancers in mouse embryonic forelimb and hindlimb. more...

Organism:

Mus musculus

Type:

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

Platforms:

GPL13112 GPL11002

24 Samples

Download data: BED, BW, SAM