Impact of substrate adhesiveness on embryonic stem cell pluripotency
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA516917 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8483120.fastq.gz | Fastqsanger.gz | |||
| SRR8483111.fastq.gz | Fastqsanger.gz | |||
| SRR8483121.fastq.gz | Fastqsanger.gz | |||
| SRR8483112.fastq.gz | Fastqsanger.gz | |||
| SRR8483122.fastq.gz | Fastqsanger.gz |
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Project description:GOAL: We developed novel hydrogel substrates for stem cell culture, in which we independently vary substrate stiffness and adhesiveness. Substrate adhesiveness is here defined by the density of matrix tethering sites on the hydrogel surface (not by protein concentration). Any extra-cellular matrix protein can be covalently bonded to the gel at those tethering sites. The density of matrix tethering sites is controlled by the concentration of a co-factor added to the polyacrylamide hydrogel premix. The goal of this study was to assess the impact of varying matrix tethering on the gene expression of pluripotent embryonic stem cells, and to determine whether the potential effect would be dependent on substrate stiffness.
2021-08-31 | GSE125611 | GEO
Project description:Genome-wide impact of substrate stiffness on embryonic stem cell pluripotency and the signalling pathways controlling it
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Project description:GOAL: The goal of this study was to assess the impact of substrate stiffness on the gene expression of pluripotent embryonic stem cells, in different heterogeneous conditions. Embryonic stem cells cultured on tissue culture plastic have heterogeneous gene expression when cultured in serum+LIF. We investigated whether culturing cells on soft fibronectin-coated StemBond hydrogels has genome-wide effects and in particular improves the homogeneity of naive pluripotent gene expression. To assess the interplay with multiple signalling pathways, we used multiple pluripotent conditions or differentiating conditions, by adding or removing the MEK inhibitor PD03, and the cytokine LIF.
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Project description:mouse embryonic fibroblasts, embryonic stem cells, and induced pluripotent stem cells were compared via metabolomic analysis
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Project description:Genomic integrity safeguards pluripotency in embryonic stem cells
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Project description:Protein kinase signalling is a major mechanism by which embryonic stem cell pluripotency and differentiation is controlled. However, the pathways and components that regulate embryonic stem cell identity have not been systematically defined. Here, we employ FGF4 signalling as a model system to investigate phosphoproteome dynamics in differentiating mouse embryonic stem cells. We report identification and quantitation of more than 10,000 phosphopeptides, of which hundreds of phosphophoylation sites are regulated more than 2-fold by acute FGF4 stimulation. We hypothesise that phosphorylation sites in this dataset are relevant for regulating the transition of mouse embryonic stem cells from pluripotency towards lineage specific differentiation.
2020-02-24 | PXD012069 | Pride
Project description:This SuperSeries is composed of the following subset Series: GSE30995: An Alternative Splicing Switch Regulates Embryonic Stem Cell Pluripotency and Reprogramming [RNA-Seq] GSE31006: An Alternative Splicing Switch Regulates Embryonic Stem Cell Pluripotency and Reprogramming [ChIP-Seq] GSE31007: An Alternative Splicing Switch Regulates Embryonic Stem Cell Pluripotency and Reprogramming [protein binding microarray] GSE31948: An Alternative Splicing Switch Regulates Embryonic Stem Cell Pluripotency and Reprogramming [AS microarray] Refer to individual Series
2011-09-14 | E-GEOD-30992 | biostudies-arrayexpress
Project description:Mouse embryonic stem (ES) cells are locked into self-renewal by shielding from inductive cues. Release from this ground state in minimal conditions offers a system for delineating developmental progression from naive pluripotency. Here we examined the initial transition process. The ES cell population behaves asynchronously. We therefore exploited a short-half-life Rex1::GFP reporter to isolate cells either side of exit from naive status. Differentiation of Rex1-GFPd2 ES cells was initiated by withdrawing 2i (Kalkan et al., 2016). Undifferentiated 2i-cells and post-2i withdrawal differentiating populations (16h, 25h-Rex1-High, 25h-Rex1-Low) were subjected to proteomic analysis by Mass Spectrometry.
2017-02-22 | PXD005581 | Pride
Project description:Chavez2009 - a core regulatory network of OCT4 in human embryonic stem cells
A core OCT4-regulated network has been identified as a test case, to analyase stem cell characteristics and cellular differentiation.
This model is described in the article:
In silico identification of a core regulatory network of OCT4 in human embryonic stem cells using an integrated approach.
Chavez L, Bais AS, Vingron M, Lehrach H, Adjaye J, Herwig R
BMC Genomics, 2009, 10:314
Abstract:
BACKGROUND: The transcription factor OCT4 is highly expressed in pluripotent embryonic stem cells which are derived from the inner cell mass of mammalian blastocysts. Pluripotency and self renewal are controlled by a transcription regulatory network governed by the transcription factors OCT4, SOX2 and NANOG. Recent studies on reprogramming somatic cells to induced pluripotent stem cells highlight OCT4 as a key regulator of pluripotency.
RESULTS: We have carried out an integrated analysis of high-throughput data (ChIP-on-chip and RNAi experiments along with promoter sequence analysis of putative target genes) and identified a core OCT4 regulatory network in human embryonic stem cells consisting of 33 target genes. Enrichment analysis with these target genes revealed that this integrative analysis increases the functional information content by factors of 1.3 - 4.7 compared to the individual studies. In order to identify potential regulatory co-factors of OCT4, we performed a de novo motif analysis. In addition to known validated OCT4 motifs we obtained binding sites similar to motifs recognized by further regulators of pluripotency and development; e.g. the heterodimer of the transcription factors C-MYC and MAX, a prerequisite for C-MYC transcriptional activity that leads to cell growth and proliferation.
CONCLUSION: Our analysis shows how heterogeneous functional information can be integrated in order to reconstruct gene regulatory networks. As a test case we identified a core OCT4-regulated network that is important for the analysis of stem cell characteristics and cellular differentiation. Functional information is largely enriched using different experimental results. The de novo motif discovery identified well-known regulators closely connected to the OCT4 network as well as potential new regulators of pluripotency and differentiation. These results provide the basis for further targeted functional studies.
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2005-01-01 | MODEL1305010000 | BioModels
Project description:The mammalian BRG1-associated factors (BAF) complex is a multi-subunit chromatin remodeling complex that is an important component of the embryonic stem cell (ESC) transcriptional regulatory network. However, the role of individual subunits in BAF complex targeting and function needs to be elucidated. Here, we find that the Bromodomain containing protein 9 (BRD9) defines a smaller, non-canonical BAF complex in mouse ESCs that is distinct from the canonical embryonic stem cell BAF (esBAF) and the polybromo-associated BAF (PBAF) complexes. This BRD9-containing BAF complex, or BBAF complex, uniquely incorporates the BRD4-interacting chromatin remodeling associated protein-like (BICRAL) or its paralog BICRA and lacks several esBAF subunits including BAF47, ARID1A and BAF57. We demonstrate that BBAF and esBAF complexes are targeted to different features of the genome and are co-bound with different sets of pluripotency transcription factors. Specifically, BBAF complexes co-localize with key regulators of naïve pluripotency, KLF4 and Sp5, on the genome. Consistent with this, we provide evidence that BBAF’s specific function is to regulate the transcription of genes involved in the maintenance of naïve pluripotency, including Nanog and Prdm14. Additionally, we show that BRD9 is displaced from chromatin by the selective BRD9 bromodomain inhibitor, I-BRD9, and that this leads to changes in target gene expression. Together, our results provide evidence for the identification of a new BAF complex, and demonstrate functionally specific roles for BAF complex assemblies in maintaining the transcriptional network of pluripotency.
2018-10-18 | PXD010670 | Pride