Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

ORGANISM(S): Mus musculus

PROVIDER: GSE94953 | GEO | 2020/01/01

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

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

| PRJNA374895 | ENA

Reprogramming by Sall4, Nanog, Esrrb and Lin28 produces high quality iPSCs with a molecular signature of developmental potency that resembles ESCs.

Project description:To reveal a gene expression signature associated with developmental competence, we selected the following groups of iPSC lines for microarray analysis. i) “Poor quality” iPSCs: This group included the three OSKM-iPSC lines Nanog-GFP OSKM#2, Oct4-GFP OSKM#2 and KH2 OSKM27, that either did not produce fully developed pups or produced very low number of pups; ii) “Good quality” iPSCs: This group included BC_2 OSKM28 and Nanog-GFP SNEL#3, both of which gave rise to live, normal pups that survived only few hours; iii) “High quality” iPSCs consisting of Nanog-GFP SNEL#2 and Oct4-GFP SNEL#1, both of which generated live pups that survived postnatally (representative pups from each iPSC group are shown in Figure S5). iv) As controls we used Nanog-GFP, Oct4-GFP and KH229 ESCs.

2014-09-08 | GSE45173 | GEO

OCT4 IP-MS in Naive and Primed Human ESCs

Project description:Understanding the molecular underpinnings of pluripotency is a prerequisite for optimal maintenance and application of embryonic stem cells (ESCs). While the protein-protein interactions of core pluripotency factors have been identified in mouse ESCs, their interactome in human ESCs (hESCs) has not to date been explored. Here we mapped the OCT4 interactomes in naïve and primed hESCs, revealing extensive connections to mammalian ATP-dependent nucleosome remodeling complexes.

2021-09-12 | PXD026556 | Pride

Reprogramming by Sall4, Nanog, Esrrb and Lin28 produces high quality iPSCs with a molecular signature of developmental potency that resembles ESCs.

2014-09-08 | E-GEOD-45173 | biostudies-arrayexpress

Genome-wide maps of Tbx3 binding sites in mouse ESCs

Project description:Induced pluripotent stem (iPS) cells can be obtained through the introduction of defined factors into somatic cells. The combination of Oct4, Sox2 and Klf4 (OSK) constitutes the minimal requirement for generating iPS cells from mouse embryonic fibroblasts (MEFs). Through the genomic analyses of ESC genes that have roles in pluripotency and fusion-mediated somatic cell reprogramming, we identified Tbx3 as a transcription factor that significantly improves the quality of iPS cells. Induced-PS cells generated with OSK + Tbx3 (OSKT) are superior in both germ cell contribution to the gonads and germ-line transmission frequency. However, global gene expression profiling could not distinguish between OSK and OSKT iPS cells. Genome-wide ChIP-sequencing analysis of Tbx3 binding sites in ESCs suggests that Tbx3 regulates pluripotency-associated and reprogramming factors, in addition to sharing many common downstream regulatory targets with Oct4, Sox2, Nanog and Smad1. ChIP-seq of Tbx3 binding in mouse ESCs

2009-12-04 | E-GEOD-19219 | biostudies-arrayexpress

ChIP-Seq of Sox2 and Brn2 in ESCs, NPCs, and differentiating ESCs

Project description:We analyzed the genome-wide binding of Sox2 and POU factor partner factors, Oct4 in ESCs (using published datasets PMID:18692474 and GSM307137, GSM307154, GSM307155) and Brn2 in NPCs. We found that Sox2 and Oct4 co-occupied a large subset of promoters and enhancers in ESCs, but that Sox2 and Brn2 co-occupy predominantly enhancers. Further, we overexpressed Brn2 in differentiating ESCs and showed that ectopic Brn2 recruited Sox2 to NPC-specific targets, resulting in skewed differentiation towards the neural lineage. Examination of transcription factor binding in ESCs, NPCs, and differentiating ESCs by ChIP-Seq.

2013-02-20 | E-GEOD-35496 | biostudies-arrayexpress

ChIP-Seq of Sox2 and Brn2 in ESCs, NPCs, and differentiating ESCs

2013-02-20 | GSE35496 | GEO

Esrrb extinction triggers dismantling of naïve pluripotency and marks commitment to differentiation [Microarray]

Project description:Self-renewal of embryonic stem cells (ESCs) cultured in serum-LIF is incomplete with some cells initiating differentiation. While this is reflected in heterogeneous expression of naive pluripotency transcription factors (TFs), the link between TF heterogeneity and differentiation is not fully understood. Here we purify ESCs with distinct TF expression levels from serum-LIF cultures to uncover early events during commitment from naïve pluripotency. ESCs carrying fluorescent Nanog and Esrrb reporters show Esrrb downregulation only in NANOGlow cells. Independent Esrrb reporter lines demonstrate that ESRRBnegative ESCs cannot effectively self-renew. Upon ESRRB loss, pre-implantation pluripotency gene expression collapses. ChIP-Seq identifies different regulatory element classes that bind both OCT4 and NANOG in ESRRBhigh cells. Class I elements lose NANOG and OCT4 binding in ESRRBnegative ESCs and associate with genes expressed preferentially in naïve ESCs. In contrast, class II elements retain OCT4 but not NANOG binding in ESRRBnegative cells and associate with more broadly expressed genes. Therefore, mechanistic differences in TF function act cumulatively to restrict potency during exit from naïve pluripotency.

2018-09-13 | GSE118906 | GEO

Esrrb extinction triggers dismantling of naïve pluripotency and marks commitment to differentiation [ChIP-seq]

2018-09-13 | GSE118905 | GEO

Mouse ESCs (ES-D3) with Ash2l depletion

Project description:We showed a novel mechanism in which Ash2l directly binds to super-enhancers of several stemness genes to regulate pluripotency and self-renewal in pluripotent stem cells. Ash2l recruits Oct4/Sox2/Nanog (OSN) to form Ash2l/OSN complex at the super-enhancers of Jarid2, Nanog, Sox2, and Oct4, and further drives enhancer activation, upregulation of stemness genes, and maintains the pluripotent circuitry. Ash2l knockdown abrogates the OSN recruitment to all super-enhancers and further hinders the enhancer activation.

2020-01-24 | GSE136870 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data