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Links from GEO DataSets

Items: 20

1.

An interspecies analysis reveals sequence determinants of the bivalent chromatin state

(Submitter supplied) The sequence determinants of chromatin bivalency remain unclear. We analysed sequence determinants of chromatin bivalency genome-wide in several mammalian species and performed a series of transgenic experiments in mouse ES cells.
Organism:
Rattus norvegicus; Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL9185 GPL11282
2 Samples
Download data: SAM
Series
Accession:
GSE27580
ID:
200027580
2.

Dual functions of Tet1 in transcriptional regulation in mouse embryonic stem cells

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Mus musculus
Type:
Expression profiling by array; Genome binding/occupancy profiling by genome tiling array; Genome binding/occupancy profiling by high throughput sequencing; Methylation profiling by genome tiling array
6 related Platforms
38 Samples
Download data: CEL, PAIR, TXT
Series
Accession:
GSE26833
ID:
200026833
3.

Dual functions of Tet1 in transcriptional regulation in mouse embryonic stem cells (ChIP-Seq)

(Submitter supplied) Epigenetic modification of the mammalian genome by DNA methylation (5-methylcytosine) has a profound impact on chromatin structure, gene expression and maintenance of cellular identity. Recent demonstration that members of the Ten-eleven translocation (Tet) family proteins can convert 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) raised the possibility that Tet proteins are capable of establishing a distinct epigenetic state. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL9185
6 Samples
Download data: TXT
Series
Accession:
GSE26832
ID:
200026832
4.

Dual functions of Tet1 in transcriptional regulation in mouse embryonic stem cells (mRNA)

(Submitter supplied) Epigenetic modification of the mammalian genome by DNA methylation (5-methylcytosine) has a profound impact on chromatin structure, gene expression and maintenance of cellular identity. Recent demonstration that members of the Ten-eleven translocation (Tet) family proteins can convert 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) raised the possibility that Tet proteins are capable of establishing a distinct epigenetic state. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL1261
12 Samples
Download data: CEL
Series
Accession:
GSE26830
ID:
200026830
5.

Dual functions of Tet1 in transcriptional regulation in mouse embryonic stem cells (ChIP-chip and MeDIP-chip)

(Submitter supplied) Epigenetic modification of the mammalian genome by DNA methylation (5-methylcytosine) has a profound impact on chromatin structure, gene expression and maintenance of cellular identity. Recent demonstration that members of the Ten-eleven translocation (Tet) family proteins can convert 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) raised the possibility that Tet proteins are capable of establishing a distinct epigenetic state. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by genome tiling array; Methylation profiling by genome tiling array
4 related Platforms
20 Samples
Download data: PAIR, TXT
Series
Accession:
GSE26827
ID:
200026827
6.

Kdm2b maintains murine embryonic stem cell status by recruiting PRC1 complex to CpG islands of developmental genes

(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:
GPL13112 GPL6246
12 Samples
Download data: CEL, WIG
Series
Accession:
GSE41316
ID:
200041316
7.

Kdm2b maintains murine embryonic stem cell status by recruiting PRC1 complex to CpG islands of lineage genes [ChIP-Seq]

(Submitter supplied) Polycomb group (PcG) proteins play important roles in repressing lineage-specific genes and maintaining the undifferentiated state of mouse embryonic stem cells (mESCs). However, the mechanisms by which PcG proteins are recruited to their targets are largely unknown. Here, we show that the histone demethylase Kdm2b is highly expressed in mESCs and regulated by the pluripotent factors Oct4/Sox2 directly. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL13112
8 Samples
Download data: WIG
Series
Accession:
GSE41314
ID:
200041314
8.

Kdm2b maintains murine embryonic stem cell status by recruiting PRC1 complex to CpG islands of lineage genes [Expression profiling]

(Submitter supplied) Polycomb group (PcG) proteins play important roles in repressing lineage-specific genes and maintaining the undifferentiated state of mouse embryonic stem cells (mESCs). However, the mechanisms by which PcG proteins are recruited to their targets are largely unknown. Here, we show that the histone demethylase Kdm2b is highly expressed in mESCs and regulated by the pluripotent factors Oct4/Sox2 directly. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL6246
4 Samples
Download data: CEL
Series
Accession:
GSE41298
ID:
200041298
9.

Genome-wide analysis identifies a functional association of Tet1 and Polycomb PRC2 in mouse embryonic stem cells but not in differentiated tissues

(Submitter supplied) Recent studies have analyzed the distribution and role of 5-hydroxymethylcytosin (5hmC) in Embryonic Stem Cells (ESC). However, DNA hydroxymethylation occurs also in differentiated cells and it is significantly deregulated in cancer. Here we mapped 5hmC genome-wide profile in pluripotent ES cells in comparison to embryonic and adult differentiated cells. Comparative analysis of 5hmC genomic distribution with respect to gene expression reveals that 5hmC is enriched on the gene body of genes expressed at medium/high level and on TSS of genes not expressed or expressed at low level independently from the cell type. more...
Organism:
Mus musculus
Type:
Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform:
GPL16173
8 Samples
Download data: BED, BEDGRAPH
Series
Accession:
GSE44566
ID:
200044566
10.

Gene expression and ChIP-seq analyses of mesenchymal stem cells, osteoblasts and the U2OS osteosarcoma cell line

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Homo sapiens
Type:
Expression profiling by array; Genome binding/occupancy profiling by high throughput sequencing
Platforms:
GPL4133 GPL9442
17 Samples
Download data: BED, GFF3, TXT
Series
Accession:
GSE35576
ID:
200035576
11.

ChIP-seq analysis of H3K4Me3- and H3K27Me3-marked chromatin in mesenchymal stem cells (MSCs), osteoblasts derived from MSCs and the osteosarcoma cell line U2OS

(Submitter supplied) Many DNA-hypermethylated cancer genes are occupied by the polycomb (PcG) repressor complex in embryonic stem cells (ESCs). Their prevalence in the full spectrum of cancers, the exact context of chromatin involved, and their status in adult cell renewal systems are unknown. Using a genome-wide analysis, we demonstrate that approximately 75% of hypermethylated genes are marked by PcG in the context of bivalent chromatin in both ESC and adult stem/progenitor cells. more...
Organism:
Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL9442
9 Samples
Download data: BED, GFF3
Series
Accession:
GSE35573
ID:
200035573
12.

Gene expression analysis of mesenchymal stem cells (MSC), osteoblasts and the U2OS (osteosarcoma) cell line

(Submitter supplied) Transcriptional profiling of MSC, Osteoblasts and U2OS cells. The aim was to quantitate relative gene expression in MSC, osteoblasts and U2OS. MSC and osteoblasts were used as normal cells in this study because osteosarcoma most likely originates from MSC or osteoblasts.
Organism:
Homo sapiens
Type:
Expression profiling by array
Platform:
GPL4133
8 Samples
Download data: TXT
Series
Accession:
GSE27900
ID:
200027900
13.

Expression data from wild type, Ring1B-/-, Eed-/-, and Ring1B/Eed double deficient mouse ES cells

(Submitter supplied) Polycomb complexes establish chromatin modifications for maintaining gene repression and are essential for embryonic development in mice. Here we use pluripotent embryonic stem (ES) cells to demonstrate an unexpected redundancy between Polycomb repressive complex 1 (PRC1) and PRC2 during the formation of differentiated cells. ES cells lacking the function of either PRC1 or PRC2 can differentiate into cells of the three germ layers, whereas simultaneous loss of PRC1 and PRC2 abrogates differentiation. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL1261
12 Samples
Download data: CEL, CHP
Series
Accession:
GSE19076
ID:
200019076
14.

Single Cell based genomewide gene expression analysis of murine bone-marrow derived Very Small Embryonic-Like Stem Cells (VSELs)

(Submitter supplied) Recently, we identified a population of Oct4+Sca-1+Lin-CD45- very small embryonic-like stem-cells (VSELs) in adult tissues. Open chromatin structure of pluripotency genes and genomic imprinting-related epigenetic mechanisms maintain pluripotency and quiescence of VSELs, respectively. However, global transcriptome signature of this rare stem-cell population remains elusive. Here, we demonstrate by genomewide gene-expression analysis with a small number of highly purified murine bone-marrow (BM)-derived VSELs, that Oct4+ VSELs i) express a similar, yet nonidentical, transcriptome as embryonic stem-cells (ESCs), ii) up-regulate cell-cycle checkpoint genes, iii) down-regulate genes involved in protein turnover and mitogenic pathways, and iv) highly express Ezh2, a polycomb group protein. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL1261
9 Samples
Download data: CEL
Series
Accession:
GSE29281
ID:
200029281
15.

GC-rich Sequence Elements Recruit Polycomb Repressive Complex 2 (PRC2) in ES cells

(Submitter supplied) Polycomb proteins are epigenetic regulators that localize to developmental loci in the early embryo where they mediate lineage-specific gene repression. In Drosophila, these repressors are recruited to sequence elements by DNA binding proteins associated with Polycomb repressive complex 2 (PRC2). However, the sequences that recruit PRC2 in mammalian cells have remained obscure. To address this, we integrated a series of engineered bacterial artificial chromosomes into embryonic stem (ES) cells and examined their chromatin. more...
Organism:
Mus musculus
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL9250
2 Samples
Download data: BED, WIG
Series
Accession:
GSE25197
ID:
200025197
16.

Mapping Promoter CpG Methylation in mESCs

(Submitter supplied) DNA methylation and histone modifications influence gene activities in a variety of mammalian cells. We report here the large scale mapping of DNA methylation patterns at proximal promoter regions in mouse embryonic stem cells (mESCs). A majority of methylated genes represent cell differentiation-associated genes that are repressed in mESCs. In contrast, unmethylated genes include many housekeeping and pluripotency genes such as STAT3 and Oct4/Nanog/Sox2, which are essential for ESC self-renewal. more...
Organism:
Mus musculus
Type:
Expression profiling by array; Methylation profiling by genome tiling array
Platforms:
GPL5806 GPL2872 GPL5805
15 Samples
Download data: TXT
Series
Accession:
GSE9172
ID:
200009172
17.

FBXL10 Protects Polycomb-bound Genes from Hypermethylation

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platform:
GPL13112
7 Samples
Download data: TXT
Series
Accession:
GSE65583
ID:
200065583
18.

FBXL10 and the Protection of Polycomb-bound Genes from Hypermethylation (RNA-Seq)

(Submitter supplied) Nearly all CpG-dense promoters are occupied by the multi-domain chromosomal protein FBXL10. We show here that complete inactivation of the Fbxl10 gene leads to dense de novo methylation only of the promoters that are co-occupied by both FBXL10 and by Polycomb Repressive Complexes; this results in pervasive defects in embryonic development and death of homozygous Fbxl10 mutant embryos at midgestation. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL13112
2 Samples
Download data: TXT
Series
Accession:
GSE65582
ID:
200065582
19.

FBXL10 and the Protection of Polycomb-bound Genes from Hypermethylation (RRBS)

(Submitter supplied) Nearly all CpG-dense promoters are occupied by the multi-domain chromosomal protein FBXL10. We show here that complete inactivation of the Fbxl10 gene leads to dense de novo methylation only of the promoters that are co-occupied by both FBXL10 and by Polycomb Repressive Complexes; this results in pervasive defects in embryonic development and death of homozygous Fbxl10 mutant embryos at midgestation. more...
Organism:
Mus musculus
Type:
Methylation profiling by high throughput sequencing
Platform:
GPL13112
5 Samples
Download data: TXT
Series
Accession:
GSE65580
ID:
200065580
20.

A Cbx8-containing Polycomb complex facilitates gene activation during ES cell differentiation

(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:
GPL9185 GPL13912
11 Samples
Download data: TXT, WIG
Series
Accession:
GSE54053
ID:
200054053
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