GEO DataSets

(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) Whole-genome single-base resolution methylcytosine and hydroxymethylcytosine maps reveal profound changes that occur during frontal cortex development in humans and mice.

Organism:

Homo sapiens; Mus musculus

Type:

Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL13112 GPL11154

65 Samples

Download data: BAM, 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:

GPL11154 GPL9115

3 Samples

Download data: BED

(Submitter supplied) Characterization of the reference epigenome in humans in a diverse panel of ES cells, tissue stem cells, reprogrammed stem cells, primary cells and tissues **************** For data usage terms and conditions, please refer to: http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies ****************

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL10999 GPL9115

55 Samples

Download data: WIG

(Submitter supplied) Characterization of the reference epigenome in humans in a diverse panel of ES cells, tissue stem cells, reprogrammed stem cells, primary cells and tissues. **************** For data usage terms and conditions, please refer to: http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies ****************

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL10999 GPL9115

10 Samples

Download data: WIG

(Submitter supplied) The NIH Roadmap Epigenomics Mapping Consortium aims to produce a public resource of epigenomic maps for stem cells and primary ex vivo tissues selected to represent the normal counterparts of tissues and organ systems frequently involved in human disease. Characterization of chromatin modification by ChIP-Seq in human subject. **************** For data usage terms and conditions, please refer to: http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies ****************

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL10999 GPL9115

358 Samples

Download data: BED, WIG

(Submitter supplied) The NIH Roadmap Epigenomics Mapping Consortium aims to produce a public resource of epigenomic maps for stem cells and primary ex vivo tissues selected to represent the normal counterparts of tissues and organ systems frequently involved in human disease. Study of chromatin accessibility and expression using exon arrays. **************** For data usage terms and conditions, please refer to: http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies ****************

Organism:

Homo sapiens

Type:

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

5 related Platforms

758 Samples

Download data: BAM, BED, CEL, TXT, WIG

(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) 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:

GPL9052 GPL9115

7 Samples

Download data: BED, TXT

(Submitter supplied) The NIH Roadmap Epigenomics Mapping Consortium aims to produce a public resource of epigenomic maps for stem cells and primary ex vivo tissues selected to represent the normal counterparts of tissues and organ systems frequently involved in human disease. Characterization of the reference epigenome in humans by use of ChIP-Seq in a diverse panel of ES cells, tissue stem cells, reprogrammed stem cells, primary cells and tissues **************** For data usage terms and conditions, please refer to: http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies ****************

Organism:

Homo sapiens

Type:

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

4 related Platforms

633 Samples

Download data: BAM, BED, CEL, WIG

(Submitter supplied) The epigenome is the dynamic interface between our changing environment and the static genome, and understanding it is a goal of immense importance to human health. We will map reference cell epigenomes of the brain, breast, blood and approved embryonic stem cells, inclusive of males and females and different racial groups. This cooperative work will transform our understanding of the short and long-lasting consequences of environment impact on human health and disease. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL9115 GPL11154 GPL10999

529 Samples

Download data: BAM, BED, TAB, WIG

(Submitter supplied) We examined the locations of Cbx3 by chromatin immunoprecipitation in ESCs and pre-iPSCs

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

4 Samples

Download data: WIG

(Submitter supplied) Transition from a partially reprogrammed pre-iPSC state to iPSC state can be achieved by modulating levels of histone modifying enzymes or proteins that can bind to histone modifications We used microarrays to determine the gene expression profile of pre-iPSCs depleted for either 3 histone methyltransferases together or the HP1gamma protein

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

8 Samples

Download data: CEL

(Submitter supplied) A dramatic difference in global DNA methylation between male and female cells characterizes mouse embryonic stem cells (ESCs), unlike somatic cells. We analyzed DNA methylation changes during reprogramming of male and female somatic cells and in resulting induced pluripotent stem cells (iPSCs). At an intermediate reprogramming stage, somatic and pluripotency enhancers are targeted for partial methylation and demethylation. more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL13112

13 Samples

Download data: TXT

(Submitter supplied) Mammalian somatic cells can be directly reprogrammed into induced pluripotent stem cells (iPSCs) by introducing defined sets of transcription factors. Somatic cell reprogramming involves epigenomic reconfiguration, conferring iPSCs with characteristics similar to embryonic stem (ES) cells. Human ES cells contain 5-hydroxymethylcytosine (5hmC), which is generated though the oxidation of 5-methylcytosine (5mC) by the TET family of enzymes. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL11154

19 Samples

Download data: BED

(Submitter supplied) In this work, we characterized the epigenomic integrity of 17 hiPSC lines derived from six different cell types with varied reprogramming efficiencies. We demonstrate that epigenetic aberrations are a general feature of the hiPSC state and are independent of the somatic cell source. Additionally, we determine that both shared and line-specific epigenetic aberrations in hiPSCs can directly translate into changes in gene expression in both the pluripotent and differentiated states.

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platforms:

GPL10999 GPL11154

65 Samples

Download data: BED

(Submitter supplied) We cultured hESC and hiPSC lines and compared the transcriptome of untreated cells with cells treated with Activin or BMP4 during 5 days

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6244

18 Samples

Download data: CEL

(Submitter supplied) We examined genome-wide gene expression with human iPSC lines derived from different cell types, and human ESC lines using Agilent Whole Human Genome Microarray chips G4112F.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6480

16 Samples

Download data: TXT

(Submitter supplied) We examined genome-wide DNA methylation with 22 human iPSC lines derived from different cell types and human ESC lines using Illumina’s Infinium HumanMethylation27 and focused on aberrant methylation sites in iPSCs for up to 42-week continuous cultivation. The iPSCs exhibited distinct epigenetic distances from ESCs at early passage. Continuous passaging of the iPSCs diminishes these differences between iPSCs and ESCs.

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL8490

47 Samples

Download data: TXT

(Submitter supplied) The reprogramming of human fibroblasts to generate induced pluripotent stem cells (hiPSCs) has been achieved through the expression of only a few exotic factors1-8, which is morphologically and molecularly verified in outer cellular states by characteristic markers, due to the remodeling of the somatic cell transcription programs in inner cellular states to the ES-like condition. Transcription factor-induced reprogramming to self-renewal and pluripotency raises the question as to how the exotic factors act to bring about these changes in the two cellular states9-11. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS3842

Platform:

GPL4133

51 Samples

Download data: TXT