Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA198855 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Genome-wide analysis of gene expression in LIF and LIF plus CHIR99021 in C57BL/6 mouse embryonic stem cells(B6 mESCs)
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Project description:Analysis of genes induced by 2I condition 2i contains glycogen synthase kinase 3 (GSK3) and mitogen-activated protein kinase kinase (MEK) inhibitors: 3uM Chir99021 and 1uM PD0325901 Total RNA obtained from B6 mESCs treated with LIF or LIF/2I for 12 hours.
2013-04-26 | E-GEOD-46369 | biostudies-arrayexpress
Project description:Enhancers are distal regulators of gene expression that shape cell identity and regulate cell fate transitions. Mouse embryonic stem cells (mESCs) are a typical example of cells whose pluripotent identity is maintained by a complex enhancer landscape, that is drastically altered upon differentiation. Genome-wide chromatin accessibility and histone modification assays are commonly used as a proxy for enhancer location, strength and dynamics. Here, we applied STARR-seq, a genome-wide plasmid-based assay, to measure the enhancer potential of genomic loci in a plasmid context in “ground-state” (2i+LIF; 2iL-ESCs) and “metastable” (serum+LIF; SL-ESCs) embryonic stem cells.
2020-08-16 | GSE143541 | GEO
Project description:Enhancers are distal regulators of gene expression that shape cell identity and regulate cell fate transitions. Mouse embryonic stem cells (mESCs) are a typical example of cells whose pluripotent identity is maintained by a complex enhancer landscape, that is drastically altered upon differentiation. Genome-wide chromatin accessibility and histone modification assays are commonly used as a proxy for enhancer location, strength and dynamics. Here, we applied STARR-seq, a genome-wide plasmid-based assay, to measure the enhancer potential of genomic loci in a plasmid context in “ground-state” (2i+LIF; 2iL-ESCs) and “metastable” (serum+LIF; SL-ESCs) embryonic stem cells.
2020-08-16 | GSE143545 | GEO
Project description:Enhancers are distal regulators of gene expression that shape cell identity and regulate cell fate transitions. Mouse embryonic stem cells (mESCs) are a typical example of cells whose pluripotent identity is maintained by a complex enhancer landscape, that is drastically altered upon differentiation. Genome-wide chromatin accessibility and histone modification assays are commonly used as a proxy for enhancer location, strength and dynamics. Here, we applied STARR-seq, a genome-wide plasmid-based assay, to measure the enhancer potential of genomic loci in a plasmid context in “ground-state” (2i+LIF; 2iL-ESCs) and “metastable” (serum+LIF; SL-ESCs) embryonic stem cells.
2020-08-16 | GSE143544 | GEO
Project description:Enhancers are distal regulators of gene expression that shape cell identity and regulate cell fate transitions. Mouse embryonic stem cells (mESCs) are a typical example of cells whose pluripotent identity is maintained by a complex enhancer landscape, that is drastically altered upon differentiation. Genome-wide chromatin accessibility and histone modification assays are commonly used as a proxy for enhancer location, strength and dynamics. Here, we applied STARR-seq, a genome-wide plasmid-based assay, to measure the enhancer potential of genomic loci in a plasmid context in “ground-state” (2i+LIF; 2iL-ESCs) and “metastable” (serum+LIF; SL-ESCs) embryonic stem cells.
2020-08-16 | GSE143543 | GEO
Project description:Activin/Nodal/TGF-β signaling pathway plays a major role in maintaining mouse epiblast stem cells (mEpiSCs). The mEpiSC medium which contains Activin A and bFGF induces differentiation of mouse embryonic stem cells (mESCs) to mEpiSC. Here we show that Activin A also has an ability to efficiently propagate mESCs without differentiation to mEpiSCs when combined with a MEK inhibitor PD0325901. mESCs cultured in Activin+PD retained high-level expression of naive pluripotency-related transcription factors. Genome-wide analysis revealed that the gene expression profile of mESCs cultured in Activin+PD resembles that of mESCs cultured in 2i. mESCs cultured in Activin+PD also showed features which are related to naive pluripotency of mESCs, including the preferential usage of the Oct4 distal enhancer and the self-renewal response to Wnt pathway activation. Our finding reveals a role of Activin/Nodal/TGF-β signaling in stabilizing self-renewal gene regulatory networks in mESCs. To compare the gene expression patterns of mESCs cultured in Activin+PD, 2i and LIF+BMP4 and mEpiSCs, we performed genome-wide gene expression analysis by using Affymetrix GeneChip oligonucleotide microarrays
2019-07-11 | GSE84679 | GEO
Project description:Mouse embryonic stem cells (mESCs) can convert to a ground state by dual inhibition of MEK and GSK3β signalling in defined media in the presence of LIF (2i). The cellular transition in 2i leads to uniform expression of pluripotency markers and global DNA hypomethylation. Whether hypomethylation is required for achieving ground state or is an outcome of the conversion process is still not clear. Here we show that J1 wild type and hypomethylated mESCs (dnmt3a-/-, dnmt3b-/-, dnmt1-/- [TKO]) lacking DNA methyltransferases undergo similar morphological and expression changes upon culturing in 2i that are consistent with conversion of both to a more naive state. Maintenance of global DNA methylation levels in 2i media by constitutive expression of de novo methyltransferases is also not a barrier to conversion. Hence, signalling pathways in mES cells regulate pluripotency networks and cell state independently of their global DNA methylation status. Indicated mESCs were cultured in 2i/LIF for 2 weeks and then harvested along with serum/LIF counterparts for microarray analysis. 1ug of total RNA was used to prepare Cy3 labelled aRNA using an Amino Allyl MessageAmp II aRNA kit (Ambion) following manufacturers protocol. The samples were hybridised to SurePrint G3 mouse GE 8x60k microarrays (Agilent) and were scanned using NimbleGen MS 200 (Roche). Results were analysed with custom-written scripts implemented in the statistical programming language R (http://www.R-project.org).
2020-06-16 | GSE72302 | GEO
Project description:Mouse embryonic stem cells (mESCs) cultured in 2i (MEK and GSK3 kinase inhibitor)/LIF and serum/LIF that we called 2i-ESCs and serum-ESCs represent ground and confused pluripotent states, respectively. However, the transcription factors that regulate ground pluripotency through chromatin-associated characteristics are not yet fully understood. By mapping chromatin accessibility and transcription factor regulatory networks during the interconversion of 2i-ESCs and serum-ESCs, we have identified TEAD2 as highly enriched in 2i-specific peaks. While Tead2 knockout did not affect the pluripotency or differentiation ability of either 2i-ESCs or serum-ESCs, it did prevent the establishment of the 2i-specific state and the exit from the serum-specific state. TEAD2 binds to active regions in 2i-specific genes and activates their expression by regulating enhancer-promoter (EP) interactions during serum-to-2i transition. Remarkably, TEAD2-mediated EP interactions were independent of chromatin architecture proteins YY1 and CTCF, but instead appear to be facilitated by TEAD2 homodimer formation.
2024-03-03 | GSE226316 | GEO
Project description:This study describes the transcriptome profiling of: 1) Mof fl/fl mESCs cultured in 2i/LIF medium with Ethanol (WT) or 4-OHT (Mof-/-); 2) E14 mESCs cultured in 2i/LIF medium treated with H2O (control) or Etomoxir treatment (ETO, FAO inhibition) and ETO-released (Released).
2020-07-02 | GSE137138 | GEO