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Links from GEO DataSets

Items: 20

1.

UCSD Human Reference Epigenome Mapping Project

(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
2.

Global epigenomic reconfiguration during mammalian brain development

(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:
GPL11154 GPL13112
65 Samples
Download data: BAM, TXT
Series
Accession:
GSE47966
ID:
200047966
3.

BI Human Reference Epigenome Mapping Project: Characterization of DNA methylation by RRBS in human subject

(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
4.

BI Human Reference Epigenome Mapping Project: Characterization of DNA methylation by RRBS

(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
5.

BI Human Reference Epigenome Mapping Project: ChIP-Seq in human subject

(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
6.

University of Washington Human Reference Epigenome Mapping Project

(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
7.

Chromatin States in Human ES Cells Reveal Key Regulatory Sequences and Genes Involved in Pluripotency and Self-renewal

(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
Series
Accession:
GSE18292
ID:
200018292
8.

Distinct epigenomic landscapes of pluripotent and lineage-committed human cells

(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
Series
Accession:
GSE17917
ID:
200017917
9.

BI Human Reference Epigenome Mapping Project

(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
10.

UCSF-UBC Human Reference Epigenome Mapping Project

(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:
GPL10999 GPL9115 GPL11154
529 Samples
Download data: BAM, BED, TAB, WIG
11.

Genome-wide maps of Cbx3 in pluripotent mESC and pre-iPSCs

(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
Series
Accession:
GSE44242
ID:
200044242
12.

Expression data from pre-iPSCs with a control, histone methyltransferase or Cbx3 (HP1g) knockdown

(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
Series
Accession:
GSE44084
ID:
200044084
13.

5-hydroxymethylcytosine-mediated epigenetic modifications between iPSCs and hESCs

(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
Series
Accession:
GSE37050
ID:
200037050
14.

Identification of a specific reprogramming-associated epigenetic signature in human induced pluripotent stem cells

(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
Series
Accession:
GSE40372
ID:
200040372
15.

Gene Expression of ESC and iPSC lines after specific differentiation

(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
Series
Accession:
GSE39210
ID:
200039210
16.

DNA Methylation Dynamics in Human Induced Pluripotent Stem Cells over Time (Agilent)

(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
Series
Accession:
GSE24677
ID:
200024677
17.

DNA Methylation Dynamics in Human Induced Pluripotent Stem Cells over Time

(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
Series
Accession:
GSE24676
ID:
200024676
18.

Gene expression signatures for human iPS cell lines

(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
Series
Accession:
GSE20750
ID:
200020750
19.
Full record GDS3842

Transcription factor-induced pluripotent stem cells

Analysis of induced pluripotent stem cells (iPSC) and their parental somatic cells (SC) from amniotic mesodermal (AM), placental artery endothelial (PAE), uterine endometrium (UtE), and MRC sources. Results identify potential candidates for linkage between inner and outer cellular states in iPSCs.
Organism:
Homo sapiens
Type:
Expression profiling by array, count, 13 cell line, 2 cell type, 14 other sets
Platform:
GPL4133
Series:
GSE20750
51 Samples
Download data: TXT
20.

Defining Differentiated Methylation Regions Especial for Pluripotency Acquisition and Maintenance in Human Stem Cell

(Submitter supplied) Here, we determined the DNA methylation profiles of 12 human cell lines, including 2 ESC lines, 2 pESC lines,4 virally-delivered iPSC lines, 2 episomal-delivered iPSC lines, and 2 parent cell lines that iPSCs derived from using Illumina’s Infinium HumanMethylation450. The iPSCs exhibited a hypermethylation status similarly to ESCs but distinct differences from the parent cells. Genes of common methylation pattern between iPSCs and ESCs were regarded as critical factors for stemness, while differences existing between iPSCs and ESCs implied that iPSCs partly retained the parental characteristics and gained de novo methylation aberrances during cell reprogramming. more...
Organism:
Homo sapiens
Type:
Non-coding RNA profiling by genome tiling array
Platform:
GPL13534
12 Samples
Download data: IDAT, TXT
Series
Accession:
GSE57992
ID:
200057992
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