Similar studies for GEO DataSets (Select 200038214) - GEO DataSets

Select item 2000382141.

Dynamic changes of DNA methylome and hydroxymethylome during neural differentiation of hES cell (hMeDIP-Seq and MBD-Seq)

(Submitter supplied) DNA methylation and hydroxymethylation have been implicated in normal development and differentiation, but our knowledge about the genome-wide distribution of 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) during cellular differentiation remains limited. Using in vitro model system of gradual differentiation of human embryonic stem (hES) cells into ventral midbrain-type neural precursor (NP) cells and terminally into dopamine (DA) neurons, we explored changes in 5mC or 5hmC patterns during lineage commitment. more...

Organism:: Homo sapiens

Type:: Methylation profiling by high throughput sequencing

Platform:: GPL13534
6 Samples

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Series

Accession:: GSE38214

ID:: 200038214

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Select item 2000382172.

Dynamic changes of DNA methylome and hydroxymethylome during neural differentiation of hES cells

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

Organism:: Homo sapiens

Type:: Methylation profiling by array; Methylation profiling by high throughput sequencing

Platform:: GPL9115
6 Samples

Download data: BED

Series

Accession:: GSE38217

ID:: 200038217

PubMed Similar studies

Select item 2000382163.

Dynamic changes of DNA methylome and hydroxymethylome during neural differentiation of hES cells (Methylation BeadChip)

(Submitter supplied) DNA methylation and hydroxymethylation have been implicated in normal development and differentiation, but our knowledge about the genome-wide distribution of 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) during cellular differentiation remains limited. Using in vitro model system of gradual differentiation of human embryonic stem (hES) cells into ventral midbrain-type neural precursor (NP) cells and terminally into dopamine (DA) neurons, we explored changes in 5mC or 5hmC patterns during lineage commitment. more...

Organism:: Homo sapiens

Type:: Methylation profiling by array

Platforms:: GPL13534 GPL9115
12 Samples

Download data: BED, TXT

Series

Accession:: GSE38216

ID:: 200038216

Select item 2000410714.

Integrated detection of both 5-mC and 5-hmC by high-throughput tag sequencing technology highlights methylation reprogramming of bivalent genes during cellular differentiation

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

Organism:: Homo sapiens

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

Platform:: GPL11154
16 Samples

Download data: WIG

Series

Accession:: GSE41071

ID:: 200041071

PubMed Full text in PMC Similar studies

Select item 2000410705.

Integrated detection of both 5-mC and 5-hmC by high-throughput tag sequencing technology highlights methylation reprogramming of bivalent genes during cellular differentiation [MeDIP_hMeDIP]

(Submitter supplied) 5-methylcytosine (5-mC) can be oxidized to 5-hydroxymethylcytosine (5-hmC). Genome-wide profiling of 5-hmC thus far indicated 5-hmC may not only be an intermediate form of DNA demethylation but could also constitute an epigenetic mark per se. We describe a cost-effective and selective method to detect both the hydroxymethylation and methylation status of cytosines in more than 1.8 million MspI sites in the human genome. more...

Organism:: Homo sapiens

Type:: Methylation profiling by high throughput sequencing

Platform:: GPL11154
2 Samples

Download data: WIG

Series

Accession:: GSE41070

ID:: 200041070

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2000410696.

Integrated detection of both 5-mC and 5-hmC by high-throughput tag sequencing technology highlights methylation reprogramming of bivalent genes during cellular differentiation [HMST-Seq]

(Submitter supplied) 5-methylcytosine (5-mC) can be oxidized to 5-hydroxymethylcytosine (5-hmC). Genome-wide profiling of 5-hmC thus far indicated 5-hmC may not only be an intermediate form of DNA demethylation but could also constitute an epigenetic mark per se. We describe a cost-effective and selective method to detect both the hydroxymethylation and methylation status of cytosines in more than 1.8 million MspI sites in the human genome. more...

Organism:: Homo sapiens

Type:: Methylation profiling by high throughput sequencing

Platform:: GPL11154
12 Samples

Download data: TXT

Series

Accession:: GSE41069

ID:: 200041069

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2000409537.

Integrated detection of both 5-mC and 5-hmC by high-throughput tag sequencing technology highlights methylation reprogramming of bivalent genes during cellular differentiation [DGE]

(Submitter supplied) 5-methylcytosine (5-mC) can be oxidized to 5-hydroxymethylcytosine (5-hmC). Genome-wide profiling of 5-hmC thus far indicated 5-hmC may not only be an intermediate form of DNA demethylation but could also constitute an epigenetic mark per se. We describe a cost-effective and selective method to detect both the hydroxymethylation and methylation status of cytosines in more than 1.8 million MspI sites in the human genome. more...

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL11154
2 Samples

Download data: TXT

Series

Accession:: GSE40953

ID:: 200040953

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Select item 2000301738.

Integrating 5 Hydroxymethylcytosine into the Epigenetic Landscape of Human Embryonic Stem Cells

(Submitter supplied) Covalent modification of DNA distinguishes cellular identities and is crucial for regulating the pluripotency and differentiation of embryonic stem (ES) cells. The recent demonstration that 5-methylcytosine (5-mC) may be further modified to 5-hydroxymethylcytosine (5-hmC) in ES cells has revealed a novel regulatory paradigm to modulate the epigenetic landscape of pluripotency. To understand the role of 5-hmC in the epigenomic landscape of pluripotent cells, here we profile the genome-wide 5-hmC distribution and correlate it with the genomic profiles of 11 diverse histone modifications and six transcription factors in human ES cells. more...

Organism:: Homo sapiens

Type:: Methylation profiling by high throughput sequencing

Platform:: GPL9115
2 Samples

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Series

Accession:: GSE30173

ID:: 200030173

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Select item 2001045859.

Assessment and site-specific manipulation of DNA (hydroxy-)methylation during mouse corticogenesis

(Submitter supplied) Purpose: In this study we investigated the molecular role of cytosine modification in the developing cortex of mice. To this aim we isolated thee linage related cell populations of the developing cortex and mapped both, 5mC as well as 5hmC on a genome-wide scale. Furthermore we established a system to site-specifcally demethylate DNA by using a dCas9-Tet1 fusion protein. Methods: Neuronal stem cells (Btg2-/Tubb3-), neurogenic progenitors (Btg2+/Tubb3-) and neurons (Tubb3+) were isolated from E14.5 Btg2-RFP/Tubb3-GFP double heterozygous mouse embryos (Aprea et al. more...

Organism:: Mus musculus

Type:: Methylation profiling by high throughput sequencing

Platform:: GPL17021
12 Samples

Download data: BW, TXT

Series

Accession:: GSE104585

ID:: 200104585

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Select item 20002504810.

Identification of DNA Methylation Markers for Lineage Commitment of in vitro Hepatogenesis

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

Organism:: Homo sapiens

Type:: Expression profiling by array; Methylation profiling by array

Platforms:: GPL6947 GPL8490
21 Samples

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Series

Accession:: GSE25048

ID:: 200025048

Select item 20002504711.

Identification of DNA Methylation Markers for Lineage Commitment of in vitro Hepatogenesis [methylation profiling]

(Submitter supplied) Hepatocytes that have differentiated from human embryonic stem cells have great potential for the treatment of liver disease as well as for drug testing. Moreover, in vitro hepatogenesis is a powerful model system for studying the molecular mechanisms underlying liver development. DNA methylation is an important epigenetic mechanism that influences differential gene expression during embryonic development. more...

Organism:: Homo sapiens

Type:: Methylation profiling by array

Platform:: GPL8490
9 Samples

Download data: TXT

Series

Accession:: GSE25047

ID:: 200025047

Select item 20002504612.

Identification of DNA Methylation Markers for Lineage Commitment of in vitro Hepatogenesis [mRNA profiling]

(Submitter supplied) Hepatocytes that have differentiated from human embryonic stem cells have great potential for the treatment of liver disease as well as for drug testing. Moreover, in vitro hepatogenesis is a powerful model system for studying the molecular mechanisms underlying liver development. DNA methylation is an important epigenetic mechanism that influences differential gene expression during embryonic development. more...

Organism:: Homo sapiens

Type:: Expression profiling by array

Platform:: GPL6947
12 Samples

Download data: TXT

Series

Accession:: GSE25046

ID:: 200025046

Select item 20002207713.

MeDIP-on-chip and Pol-II ChIP-on-chip during C2C12 myogenic and BMP2-induced osteogenic differentiation

(Submitter supplied) Differentiation of pluripotent embryonic stem cells, via more restricted multipotent adult stem cells, towards the multitude of terminally differentiated, specialized cell types that make up the adult body is a multi-step process characterized by a progressive restriction of differentiation potential. Previous studies have demonstrated tissue-specific differences in DNA methylation patterns that might play a role in lineage restriction and tissue-specific gene expression. more...

Organism:: Mus musculus

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

Platform:: GPL5811
14 Samples

Download data: BAR, BED, CEL

Series

Accession:: GSE22077

ID:: 200022077

PubMed Similar studies

Select item 20006933314.

TET-catalyzed 5-hydroxymethylcytosine regulates gene expression in differentiating colonocytes and colon cancer

(Submitter supplied) 5-hydroxymethylcytosine (5-mC) and gene expression profiling of T84 cell differentiation; 5-hmC profiling of colon cancer colonocyte fractions

Organism:: Homo sapiens

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

Platform:: GPL11154
12 Samples

Download data: TXT, WIG

Series

Accession:: GSE69333

ID:: 200069333

PubMed Full text in PMC Similar studies Analyze with GEO2R SRA Run Selector

Select item 20004679315.

An epigenetic signature of developmental potential in neural stem cells and early neurons

(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 GPL6885
14 Samples

Download data: BED, CSV

Series

Accession:: GSE46793

ID:: 200046793

Select item 20004679216.

An epigenetic signature of developmental potential in neural stem cells and early neurons [ChIP-seq]

(Submitter supplied) A cardinal property of neural stem cells (NSCs) is their ability to adopt multiple fates upon differentiation. The epigenome is widely seen as a read-out of cellular potential and a manifestation of this can be seen in embryonic stem cells (ESCs), where promoters of many lineage-specific regulators are marked by a bivalent epigenetic signature comprising trimethylation of both lysine 4 and lysine 27 of histone H3 (H3K4me3 and H3K27me3, respectively). more...

Organism:: Mus musculus

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL9185
6 Samples

Download data: BED, CSV

Series

Accession:: GSE46792

ID:: 200046792

PubMed Similar studies SRA Run Selector

Select item 20004679117.

An epigenetic signature of developmental potential in neural stem cells and early neurons [expression]

(Submitter supplied) A cardinal property of neural stem cells (NSCs) is their ability to adopt multiple fates upon differentiation. The epigenome is widely seen as a read-out of cellular potential and a manifestation of this can be seen in embryonic stem cells (ESCs), where promoters of many lineage-specific regulators are marked by a bivalent epigenetic signature comprising trimethylation of both lysine 4 and lysine 27 of histone H3 (H3K4me3 and H3K27me3, respectively). more...

Organism:: Mus musculus

Type:: Expression profiling by array

Platform:: GPL6885
8 Samples

Download data: TXT

Series

Accession:: GSE46791

ID:: 200046791

Select item 20003840718.

Genome-wide mapping of 5-hydroxymethylcytosine (5hmC) during differentiation of P19.6 and 3T3-L1 cells

(Submitter supplied) Enhancers are developmentally-controlled transcriptional regulatory regions whose activities are modulated through histone modifications or histone variant deposition. Here, we show by genome-wide mapping that the newly discovered DNA modification 5-hydroxymethylcytosine (5hmC) is dynamically associated with transcription factor binding to distal regulatory sites during neural differentiation of mouse P19 cells as well as during adipocyte differentiation of mouse 3T3-L1 cells. more...

Organism:: Mus musculus

Type:: Methylation profiling by high throughput sequencing

Platform:: GPL9250
4 Samples

Download data: WIG

Series

Accession:: GSE38407

ID:: 200038407

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20003306719.

Whole-genome mapping of MEIS1, TET1, H3K4me2 and H3K27ac in P19.6 mouse embryonal carcinoma cells and P19.6 cells treated for 48 hours with all-trans retinoic acid

(Submitter supplied) Enhancers are developmentally-controlled transcriptional regulatory regions whose activities are modulated through histone modifications or histone variant deposition. Here, we show by genome-wide mapping that the newly discovered DNA modification 5-hydroxymethylcytosine (5hmC) is dynamically associated with transcription factor binding to distal regulatory sites during neural differentiation of mouse P19 cells as well as during adipocyte differentiation of mouse 3T3-L1 cells. more...