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ChIP Seq of Oct4, Nanog, H3K27me3 in Oct4+/+ and Oct4 +/- mES cells

ABSTRACT: ChIP Seq of Oct4, Nanog, H3K27me3 in Oct4+/+ and Oct4 +/- mES cells

PROVIDER: PRJEB1833 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR263541.fastq.gz	Fastqsanger.gz
	ERR263542.fastq.gz	Fastqsanger.gz
	ERR263543.fastq.gz	Fastqsanger.gz
	ERR263544.fastq.gz	Fastqsanger.gz
	ERR263545.fastq.gz	Fastqsanger.gz

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ChIP Seq of Oct4, Nanog, H3K27me3 in Oct4+/+ and Oct4 +/- mES cells

Project description:Embryonic stem cell (ESC) pluripotency is governed by a gene regulatory network centred on the transcription factors Oct4 and Nanog. ESCs fluctuate between states of high and low Nanog expression that direct efficient or inefficient self-renewal. To date, robust self-renewing ESC states have only been attained by chemical inhibition of signalling pathways or enforced transgene expression. Here we show that ESCs expressing a reduced range of Oct4 concentrations, typified by Oct4 heterozygous ESCs exhibit stable robust pluripotency. Despite this reduced Oct4 concentration range, this state is characterised by increased genome-wide binding of Oct4, particularly at pluripotency-associated enhancers, homogeneous expression of pluripotency transcription factors, enhanced self-renewal efficiency and delayed differentiation kinetics. In this state, ESCs exhibit increased wnt expression, enhanced LIF-sensitivity, non-responsiveness to FGF signalling and can clonally maintain pluripotency without BMP but remain dependent upon LIF. Robust pluripotency is destabilised either by alteration of the Oct4 level or by removal of LIF. Our findings suggest that robust pluripotency originates from cells with a reduced Oct4 protein concentration and that the wild-type Oct4 range enables effective differentiation.

2013-05-07 | E-MTAB-1617 | biostudies-arrayexpress

Strome MES-4, H3K36me3 and H3K27me3 in mes-4 RNAi EEMB

Project description:ChIP-chip of MES-4, H3K36me3 and H3K27me3 in mes-4 RNAi C. elegans early embryo

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Genome-wide maps of histone marks, Sox2, Oct4 and PARP-1 in mES cells.

Project description:ChIP-seq was performed to analyze genome-wide distribution of PARP-1 and histone marks H3K4me3, H3K27me3 in mES cells, and examine the effect of PARP-1 knockout on Sox2 and Oct4 genome-wide distribution in ES cells.

2017-01-23 | GSE74112 | GEO

Strome MES-4, H3K36me3 and H3K27me3 in mes-4 RNAi EEMB

Project description:ChIP-chip of MES-4, H3K36me3 and H3K27me3 in mes-4 RNAi C. elegans early embryo EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: mes-4 RNAi; Developmental Stage: Early Embryo; Genotype: N2; Sex: population predominantly Hermaphrodites perhaps with some Males; NUMBER OF REPLICATES: 2; EXPERIMENTAL FACTORS: temperature 24

2012-05-29 | E-GEOD-38159 | biostudies-arrayexpress

Strome Mes-4, H3K36me3 and H3K27me3 in N2 EEMB

Project description:ChIP-chip of Mes-4, H3K36me3 and H3K27me3 in N2 C. elegans early embryo

2012-05-30 | GSE38180 | GEO

Auxin-degron system identifies immediate mechanisms of Oct4 [Nanog ChIP-seq]

Project description:Auxin-degron system identifies immediate mechanisms of Oct4 [Nanog ChIP-seq]

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Chromatin immunoprecipitation of Oct4 and nanog in mouse embryonic stem cells to enable comparison of regulatory networks obtained by ChIP-Chip and ChIP-PET

Project description:Genome-wide approaches have begun to elucidate the transcriptional and epigenetic regulatory networks responsible for pluripotency in embryonic stem (ES) cells. Chromatin Immunoprecipitation (ChIP) followed either by hybridization to a microarray platform (ChIP-chip), or by DNA sequencing (ChIP-PET), has identified the genomic-binding targets of the ES cell transcription factors Oct4 and Nanog in humans and mice, respectively. A central issue that remains to be resolved is the concordance of the data obtained by these methods, given the differences between the two techniques. Here, we report the identification of the Oct4 and Nanog genomic targets in mouse ES cells by ChIP-Chip and have compared the data with binding data identified previously by ChIP-PET. Binding data have also been combined with Oct4 and Nanog RNAi knockdown expression profiling data in ES cells. Surprisingly, we find a substantial difference between the regions that identified exclusively by one of the two techniques. In both studies, however, targets identified by either technique contain a number of genes that are differentially expressed on Oct4 or Nanog knockdown, and have been implicated in cell-fate determination events. This study provides a comparison between the data obtained by different genomic platform, and offers a more comprehensive picture of the stem cell transcriptional network.

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Project description:The pluripotency factor Oct4 is essential for the maintenance of naïve pluripotent stem cells in vitro and in vivo. However, the specific role of Oct4 in this process remains unknown. Here, we developed a rapid protein-level Oct4 depletion system that demonstrates that the immediate downstream response to loss of Oct4 is reduced expression of key pluripotency factors. Our data show a requirement for Oct4 for the efficient transcription of several key pluripotency factors, and suggest that expression of trophectoderm markers is a subsequent event. Additionally, we find that Nanog is competent to bind to the genome in the absence of Oct4, and this binding is in fact enhanced. Globally, however, active enhancer associated histone mark H3K27ac is depleted. Our work establishes that while Oct4 is required for the maintenance of the naïve transcription factor network, at a normal ESC level it antagonises this network through inhibition of Nanog binding

2021-06-17 | GSE168576 | GEO

NANOG-OCT4-SOX2 Regulatory Module in Human Embryonic Stem Cells

Project description:This SuperSeries is composed of the following subset Series: GSE34904: NANOG-OCT4-SOX2 Regulatory Module in Human Embryonic Stem Cells (dataset 1) GSE34912: NANOG-OCT4-SOX2 Regulatory Module in Human Embryonic Stem Cells (dataset 2) GSE34918: NANOG-OCT4-SOX2 Regulatory Module in Human Embryonic Stem Cells (dataset 3) GSE34920: NANOG-OCT4-SOX2 Regulatory Module in Human Embryonic Stem Cells (dataset 4) Refer to individual Series

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