Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Analysis of genes differentially expressed depending on Oct4/Nanog induction and of chromatin interactions to define the HoxB landscape in ESCs and mouse embryos

ABSTRACT: Analysis of genes differentially expressed depending on Oct4/Nanog induction and of chromatin interactions to define the HoxB landscape in ESCs and mouse embryos

PROVIDER: PRJNA374895 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR5260230.fastq.gz	Fastqsanger.gz
	SRR5260240.fastq.gz	Fastqsanger.gz
	SRR5260250.fastq.gz	Fastqsanger.gz
	SRR5260260.fastq.gz	Fastqsanger.gz
	SRR5260231.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 32

Similar Datasets

Analysis of genes differentially expressed depending on Oct4/Nanog induction

Project description:The goal is to examine the transcriptome of Oct4 and Nanog conditional expressing mouse embryos at different developmental stages.

2020-01-01 | GSE94952 | GEO

Analysis of chromatin interactions to define the HoxB landscape in ESCs and mouse embryos

Project description:The goal is to examine the interactions at chromatin level between two specific Oct4/Nanog binding-sites in the vicinity of Hoxb1 in ESCs and E9.5 mouse embryos.

2020-01-01 | GSE94953 | GEO

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

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

| PRJEB1833 | ENA

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

2012-04-05 | E-GEOD-34921 | biostudies-arrayexpress

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

An enhancer cluster promotes NPCs formation from ESCs through maintaining HoxB activation by long-range chromatin interaction

Project description:Homeobox B cluster genes (HoxB) are important marker genes for neural progenitor cells (NPCs) formation from embryonic stem cells (ESCs). However, mechanisms of HoxB activation in NPCs remain largely unknown. Here, we find an enhancer cluster (EnC) interacting with the HoxB locus by PLAC-seq analysis. CRISPR/Cas9-mediated EnC deletion significantly inhibited HoxB expression, indicating that the EnC is required for HoxB activation in NPCs. Transcriptome analysis revealed that differentiation-related master control genes and NPCs formation-related signaling pathways were significantly inhibited suggesting that the EnC is essential for NPCs formation. In summary, our results reveal a new mechanism about HoxB activation depending on EnC is crucial for NPCs formation.

2020-10-13 | GSE159378 | GEO

Analysis of genes differentially expressed depending on Oct4/Nanog induction and of chromatin interactions to define the HoxB landscape in ESCs and mouse embryos

Project description:This SuperSeries is composed of the SubSeries listed below.

2020-01-01 | GSE94954 | GEO

NANOG-OCT4-SOX2 Regulatory Module in Human Embryonic Stem Cells (dataset 4)

Project description:The transcription factors Nanog, Oct4 and Sox2 are the master regulators of pluripotency in mouse embryonic stem cells (mESCs), however, their functions in human ESCs (hESCs) have not been rigorously defined. Here we show that the requirements for NANOG, OCT4 and SOX2 in hESCs differ from those in mESCs. Both NANOG and OCT4 are required for self-renewal and repress differentiation. OCT4 controls both extraembryonic and epiblast-derived cell fates in a BMP4-dependent manner. OCT4-depleted hESCs commit to trophectoderm and primitive endoderm in the presence of BMP4, but undergo neuroectoderm differentiation in the absence of BMP4. NANOG represses neuroectoderm and neural crest commitment, but has little or no effect on the other lineages. We find that SOX2 is not required for self-renewal because it is redundant with SOX3, which is induced in SOX2-depleted hESCs. Simultaneous depletion of both SOX2 and SOX3 induces differentiation into the primitive streak. Unexpectedly, we identify significant variability in the usage of pluripotency factors by individual hESC lines, suggesting that the pluripotency network is remodelled to support a continuum of developmental states. Our study revises the general view of how NANOG, OCT4 and SOX2 orchestrate self-renewal in hESCs.

2012-04-06 | GSE34920 | GEO

NANOG-OCT4-SOX2 Regulatory Module in Human Embryonic Stem Cells (dataset 3)

2012-04-06 | GSE34918 | GEO

NANOG-OCT4-SOX2 Regulatory Module in Human Embryonic Stem Cells (dataset 2)

2012-04-06 | GSE34912 | GEO