Gene expression analysis of murine pluripotent stem cells treated with myxothiazol for 12 h
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE107414 | GEO | 2017/11/29
SECONDARY ACCESSION(S): PRJNA420033
REPOSITORIES: GEO
Similar Datasets
Project description:This dataset is part of a study that aims to compare in vivo human trophoblast differentiation into EVTs to different in vitro trophoblast organoids using single-cell and single-nuclei RNA sequencing. This specific dataset includes scRNA-seq and snRNA-seq data from trophoblast stem cells (TSCs). Trophoblast stem cell (TSC) lines BTS5 and BTS11 derived by Okae and colleagues were grown as described previously (Okae et al. 2018) together with EVT differentiation media. This study shows that the main regulatory programs mediating EVT invasion in vivo are preserved in in vitro models of EVT differentiation from primary trophoblast organoids and trophoblast stem cells. Data for primary trophoblast organoids is available under E-MTAB-12650.
| EGAD00001010017 | EGA
Project description:Trophectoderm-specific expression of Angiomotin (AMOT) in pre-implantation embryos followed by its unique expression in the post-implantation ectoplacental cone that harbors the trophoblast stem cell niche prompted our investigation on the function of AMOT in trophoblast cells. Using the in vitro trophoblast stem cell culture model, we established differentiation dependent up-regulation of AMOT expression in trophoblast cells. To understand the function of AMOT in trophoblast cells mass spectrometry-based proteomic analysis was employed to identify the AMOT interactome within the trophoblast proteome. This approach utilized immunoprecipitation of endogenous AMOT followed by fractionation on SDS-PAGE and subsequently subjecting the tryptic digested excised gel bands to mass spectrometry.
2021-11-03 | PXD019391 | Pride
Project description:The aim of this study was to set up an in vitro model to highlight yet-unidentified mechanisms facilitating the escape of human colonic epithelial cells from chronic inflammation-induced senescence, and to define whether these mechanisms afford cells a resistance to oxidative stress thereby contributing to tumor initiation. By driving a specific genetic program (termed ALEP), as observed in ulcerative colitis and Crohn’s disease patients, transient expression of ZEB transcription factors buffers ROS deleterious effects and maintains intestinal stem cell (ISC) integrity. Nonetheless, as a perverse effect, maintenance of this program is likely to facilitate their neoplastic transformation and contribute to tumor initiation. We identified the quinolinate phosphoribosyltransferase enzyme (QPRT) as the main component of the ALEP-associated survival advantage. Here is mRNA expression data of second cohort of 50 sporadic primary colorectal carcinomas (CRC) resected from untreated patients used in conjunction with their QPRT values assessed by IHC. These 50 CRCs were scored for ALEP, Stem-like, Lgr5 and EphB2high signatures to test correlation with QPRT.
2021-05-06 | E-MTAB-4090 | biostudies-arrayexpress
Project description:In the process of evaluating teratogenic properties of xenobiotica, the consumption of laboratory animals is high and costly which makes the development of alternative methods desirable. The pluripotent embryocarcinoma cell line P19, which closely resembles the early stage of an embryo, may be relevant as an in vitro model of teratogenicity. The antiepileptic drug Valproic acid (VPA) is a potent inducer of neural tube defects (ntd:s) in both human and mouse, but its mechanism of teratogenicity is not know. P19 cells were here treated with sodium valproate in a both time and dose dependent matter to profile the gene expression response with Codelink UniSet Mouse 20K I Bioarrays. This profile may reveal biomarkers of ntd:s as well as give mechanistic input of the teratogenicity of VPA.
2008-01-23 | E-MEXP-981 | biostudies-arrayexpress
Project description:Ozone (O3) is a phytotoxic air pollutant that enters the plant through stomata and activates cell death programs leading to development of lesions in sensitive plant species. Exposure to O3 provokes the formation of reactive oxygen species (ROS) in the apoplast of plant cells. Imbalanced ROS homeostasis has deleterious toxic effects on DNA, proteins, lipids, and carbohydrates. However, ROS are not merely damaging molecules, as they also initiate signaling events that help plants acclimate to stress. Like under most abiotic and biotic stresses, apoplastic ROS signaling triggered by O3 induces massive changes in gene expression, enzyme activities and metabolic profiles. Thus, O3 is a very useful tool to study general mechanisms of ROS signaling and regulation of gene expression. Here we used a combination of transcriptome analysis and cell death assays to identify molecular mechanism initiated by apoplastic ROS signaling involved in the regulation of defense signaling and cell death in Arabidopsis thaliana.
2020-07-01 | GSE117052 | GEO
Project description:Chemosynthetic symbioses occur worldwide in marine habitats, but comprehensive physiological studies of chemoautotrophic bacteria thriving on animals are scarce. Stilbonematinae are coated by monocultures of thiotrophic Gammaproteobacteria. As these nematodes migrate through the redox zone, their ectosymbionts experience varying oxygen concentrations. Here, by applying omics, Raman microspectroscopy and stable isotope labeling, we investigated the effect of oxygen on the metabolism of Candidatus Thiosymbion oneisti. Unexpectedly, sulfur oxidation genes were upregulated in anoxic relative to oxic conditions, but carbon fixation genes and incorporation of 13C-labeled bicarbonate were not. Instead, several genes involved in carbon fixation, organic carbon assimilation and polyhydroxyalkanoate (PHA) biosynthesis, as well as nitrogen fixation and urea utilization were upregulated in oxic conditions. Furthermore, in the presence of oxygen, stress-related genes were upregulated together with vitamin biosynthesis genes likely necessary to withstand its deleterious effects, and fewer symbionts were detected to divide. Based on this first global physiological study of an uncultured chemosynthetic ectosymbiont, we propose that, in anoxic sediment, its proliferation is powered by anaerobic sulfur oxidation coupled to denitrification, whereas in upper layers it makes use of aerobic respiration to facilitate assimilation of carbon and nitrogen, and to survive oxidative stress. The ectosymbiont’s versatile metabolism is thus well-adapted to exploiting a highly changeable environment.
2020-04-30 | GSE146081 | GEO
Project description:Chromosomal instability (CIN) is thought to be a source of mutability in human cancer. However, CIN is highly deleterious for the cell, and the resulting aneuploidy induces metabolic stress and compromises cell fitness. Here we utilized the X-chromosome dosage compensation mechanism and changes in X-chromosome number to demonstrate in Drosophila epithelial cells the causal relationship between CIN, aneuploidy, gene dosage imbalance and tumorigenesis. Whereas the harmful effects of CIN can be buffered by resetting the X-chromosome dosage compensation to compensate for changes in X-chromosome number, interfering with the mechanisms of dosage compensation suffices to induce tumorigenesis. In addition, multiple mechanisms buffer the deleterious effects of CIN including DNA-damage repair, activation of the p38 signalling pathway, and induction of cytokine expression to promote compensatory cell proliferation. These data reveal a key role of gene dosage imbalances to CIN-induced programmed cell death and tumorigenesis and the existence of robust compensatory mechanisms.
2016-05-23 | GSE71242 | GEO
Project description:Pericardial sac surrounding the heart contains pericardial fluid (PF), which is rich in exosomes. PF exosomes increase angiogenesis in hypoxic endothelial cells and in animal model of hindlimb ischemia by passing the proangiogenic miRNAs to recipient cells. However, under pathological conditions such as diabetes, exosome cargo composition changes and harmful miRNAs can be transferred to the recipient cells and induce more deleterious effects in target tissues. In order to check cargo composition of different PF exosomes, we used PF exosomes from non-diabetic aortic valve replacement (AVR), mitral valve replacement (MVR), coronary artery bypass grafting (CABG) patients and CABG patients with diabetes.
2020-12-31 | GSE118103 | GEO
Project description:Neural stem cell (NSC) maintenance and functions are regulated by reactive oxygen species (ROS). However, the mechanisms by which ROS control NSC behavior remain unclear. Here we report that ROS-dependent Igfbp2 signaling controls DNA repair pathways which balance NSC self-renewal and lineage commitment. Ncf1 or Igfbp2 deficiency constrained NSCs to a self-renewing state and prevented neurosphere formation due to absent Igfbp2 cysteine-43 oxidation. Ncf1-dependent oxidation of Igfbp2 promoted neurogenesis by NSCs in vitro and in vivo, while repressing Brca1 DNA damage response genes and inducing DNA double-strand breaks (DDSBs). By contrast, Ncf1–/– and Igfbp2–/– NSCs favored the formation of oligodendrocytes in vitro and in vivo. Notably, transient repression of Brca1 DNA repair pathway genes induced DDSBs and was sufficient to rescue the ability of Ncf1–/– and Igfbp2–/– NSCs to lineage-commit to form neurospheres and neurons. Our study highlights the role of DNA damage/repair in orchestrating NSC fate decisions downstream of redox-regulated Igfbp2.
2023-01-17 | GSE221955 | GEO
Project description:We profiled trophoblast stem cell replication-timing in order to compare these data to our data on underrepresented (UR) domainss in trophoblast giant cells (polyploid cells derived from 2N trophoblast stem cells). We found that UR domains are formed from late-replicating regions in tropoblast stem cells. Profile of early and late replicating regions in cultured trophoblast stem cells.
2014-05-29 | E-GEOD-50207 | biostudies-arrayexpress