Expression data from B6C3F1 mice treated with reduced oxygen
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE17796 | GEO | 2010/01/11
SECONDARY ACCESSION(S): PRJNA123535
REPOSITORIES: GEO
Similar Datasets
Project description:Mice received decreasing oxygen concentrations from 21% to 6% O2 for ~ 30 minutes. Then, the mice remained an additional 120 minutes at 6% O2, control mice were placed insimilarchambers but recieved normal (21%) oxygen. Mice were euthanased by cervical dislocation under ketamine / acepromazine (100 mg/kg / 5 mg/kg, I.P) anesthesia. The bone marrow from the right humerus, a portion of the left lateral liver lobe and half a cross-section of the spleen were harvested and the RNA was isolated from these tissues using standard Qiagen reagents. Standard Affymetrix protocols were used for GeneChip probe preparations. 39 arrays.
2010-01-10 | E-GEOD-17796 | biostudies-arrayexpress
Project description:The iron sensing protein FBXL5 is the substrate adaptor for a SKP1-CUL1-RBX1 E3 ubiquitin ligase complex that regulates the degradation of iron regulatory proteins (IRPs). Here we describe a mechanism of FBXL5 regulation involving its interaction with the cytosolic Fe-S cluster assembly (CIA) targeting complex comprised of MMS19, FAM96B, and CIAO1. We demonstrate that the CIA targeting complex promotes the ability of FBXL5 to degrade IRPs. In addition, the FBXL5-CIA targeting complex interaction is regulated by oxygen tension displaying a robust association in 21% O2 that is severely diminished in 1% O2 and contributes to O2-dependent regulation of IRP degradation. Together, these data identify a novel oxygen-dependent signaling axis that links IRP-dependent iron homeostasis with the Fe-S cluster assembly machinery.
2019-05-02 | MSV000083739 | MassIVE
Project description:Transcriptomic analyses of the oxygen response of two glioma cell lines at 20% versus 0.3% O2, and 3% vs 0.3% O2 in the presence or absence of serum
2013-04-05 | GSE32100 | GEO
Project description:Commonly used monolayer cell cultures lack the capacity to provide a physiologically relevant environment for cell culture in terms of cell-cell architecture, extracellular matrix composition, and spatiotemporal delivery of key growth factors and small molecules, such as oxygen. Here, we describe a three-dimensional (3D) approach to cell culture in vitro, utilizing a bioreactor system designed to control oxygenation of 3D cancer cell cultures, in order to better mimic tumor microenvironments observed in vivo. We found transcriptomic differences in breast and ovarian cancer cell cultures grown in traditional monolayer cultures as compared to cultures grown in a Matrigel three-dimensional matrix. We also investigated the transcriptomes of 3D cultures grown in 21% O2, 3% O2, and a gradient of 3% O2 to 0% O2 using our bioreactor system. By controlling oxygen delivery, we observed differences in cell growth morphology and transcriptome regulation under the three conditions.
2019-04-02 | GSE129111 | GEO
Project description:PURPOSE: Tissue culture is traditionally performed at atmospheric oxygen concentration (21%), which induces hyperoxic stress, as endogenous physiologic oxygen tension found in tissues varies between 2% and 9%. This discrepancy may lead to misinterpretation of results and may explain why effects observed in vitro cannot always be reproduced in vivo and vice versa. Only a few studies have been conducted in low physiologic oxygen conditions to understand the development and differentiation of cells from the eye. METHODS: The aim of this study was to investigate the growth and gene expression profile of melanocytes from the choroid permanently exposed to 21% (hyperoxic) or 3% (physiologic) oxygen with proliferation assays and DNA microarray. The cellular behavior of the melanocytes was then compared to that of cancer cells. RESULTS: The gross morphology and melanin content of choroidal melanocytes changed slightly when they were exposed to 3% O2, and the doubling time was statistically significantly faster. There was an increase in the percentage of choroidal melanocytes in the active phases of the cell cycle as observed by using the proliferation marker Ki67. The caveolin-1 senescence marker was not increased in choroidal melanocytes or uveal melanoma cells grown in hyperoxia. In comparison, the morphology of the uveal melanoma cells was similar between the two oxygen levels, and the doubling time was slower at 3% O2. Surprisingly, gene expression profiling of the choroidal melanocytes did not reveal a large list of transcripts considerably dysregulated between the two oxygen concentrations; only the lactate transporter monocarboxylate transporter (MCT4) was statistically significantly upregulated at 3% O2. CONCLUSIONS: This study showed that the oxygen concentration must be tightly controlled in experimental settings, because it influences the subsequent cellular behavior of human choroidal melanocytes.
2016-09-10 | GSE86789 | GEO
Project description:Transcriptomic analyses of the oxygen response of two glioma cell lines at 20% versus 0.3% O2, and 3% vs 0.3% O2 in the presence or absence of serum 22 samples are analysed with three or more biological replicates in different O2 concentrations.
2013-04-05 | E-GEOD-32100 | biostudies-arrayexpress
Project description:To systematically address the role of different Fnr proteins in the transcription regulation in response to varying oxygen levels, we have established an oxygen switch protocol to study the transcriptional changes directly or indirectly associated with these oxygen-sensitive regulatory proteins. To ensure an efficient oxygen switch, cells were grown to the mid log phase (O.D600nm = 0.36±0.02) at high aeration rates (350 rpm) to ensure truly aerobic conditions and then switched to oxygen-limiting conditions (120 rpm) for 30 minutes prior to RNA extraction. Under these conditions, the switch in oxygen availability has minimal impact on growth rates of either the wild-type or the single fnr mutant strains, whilst allowing the detection of Fnr-dependent promoter activation. This enabled the comparison of the transcript profiles among the different strains under “high O2” (350 rpm or control) and “low O2” (120 rpm or switch) conditions.
2018-02-26 | E-MTAB-5741 | biostudies-arrayexpress
Project description:This study investigates the processes of angiogenesis and lymphangiogenesis in an in vitro mouse Embryoid Body (EB) model while maintaining as closely as possible an in vivo environment that is observed in human and murine placental development. Several studies have documented that human placental development is profoundly influenced by oxygen tension. Further the developing murine embryo also experiences hypoxic conditions prior to parturition, which regulates early organogenesis and embryonic blood vessel formation in vivo. Embryonic stem (ES) cells derived from 129/SvJ mice were differentiated into embryoid bodies (EBs) and were subjected to two oxygen treatments: normoxia (21% O2) and hypoxia (2.6%). Hypoxia was achieved in a humidified chamber flushed with 95% N2/5% CO2 until the oxygen level was stably maintained at 2.6%. EBs were transferred on days E8, E12, E15 and E18 to hypoxia or maintained in normoxia. After 2 days of differential oxygen treatments, these EBs were analyzed at E10, E14, E17 and E20 respectively.
2012-08-12 | GSE17613 | GEO
Project description:Purpose: Oxygen (O2) levels in cell culture conditions is typically 2-5 fold higher than the physiological O2 levels that most tissues experience in vivo. The ambient atmospheric O2 (21%) is known to induce cell proliferation defects and cellular senescence in stem cell and primary cell cultures. Therefore, culturing these cells under lower O2 levels (2-9%) is currently a standard practice. However, the non-cancerous immortalized cells and cancer cells, which evade cellular senescence are normally cultured under 21% O2 levels and the effects of higher O2 levels on these cells are not fully understood. Methods: Gene expression (RNA seq transcriptomics) analysis of immortalized human bronchial epithelial (BEAS-2B) cells cultured at ambient 21% O2 and lower 10% O2 levels for 3 days and 3 weeks. Further the beneficial effects of cuturing cells under lower oxygen tension is evalulated Results: Our results show NF-κB/RelA mediated activation of pro-inflammatory cytokines as a major outcome of cells being cultured 21% O2. Moreover, we demonstrate increased RelA binding at the NF-κB1/RelA target gene promoters at 21% O2. Interestingly, contrary to cells cultutred at 21% O2, external stress induced by H2O2 exposure did not induce inflammatory response in cells grown at 10% O2, suggesting increased ability to handle external stress in cells cultured at lower O2 levels.
2016-01-26 | GSE68378 | GEO
Project description:Expression profiling of A. thaliana, A. stelleri, R. islandica, and T. salsuginea under the low-oxygen treatment(0.1% O2/99.9% N2, various time points at 0, 1, 3, 8, 24, 72h) Comparative analysis of transcriptional responses to low-oxygen stress with Arabidopsis and its related species to gain comprehensive insights into low-oxygen responses of the species.
2019-05-15 | GSE129468 | GEO