ABSTRACT: Validation of an in vitro model of hypoxia using a primary cell culture of mouse embryonic fibroblasts (MEF) exposed to 1% oxygen at 37 degrees celsius. Control cells were exposed to atmospheric oxygen.
Project description:Validation of an in vitro model of hypoxia using a primary cell culture of mouse embryonic fibroblasts (MEF) exposed to 1% oxygen at 37 degrees celsius. Control cells were exposed to atmospheric oxygen. Hypoxic and normoxic MEF (in 100 mm dishes, four replicates per group) were submitted to gene expression analysis using Affymetrix Exon microarrays. Differential gene expression analysis was performed with R package DEMI (http://biit.cs.ut.ee/demi/).
Project description:Protein synthesis belongs to the most energy consuming processes in the cell. Lowering oxygen tension below normal (hypoxia) causes a rapid inhibition of global mRNA translation due to the decreased availability of energy. Interestingly, subsets of mRNAs pursue active translation under such circumstances. In human fibrosarcoma cells (HT1080) exposed to prolonged hypoxia (36 h, 1% oxygen) we observed that transcripts are either increasingly or decreasingly associated with ribosomes localized at the endoplasmic reticulum (ER). In a global setting it turned out that only 31% of transcripts showing elevated total-RNA levels were also increasingly present at the ER in hypoxia. These genes, regulated by its expression as well as its ER-localization, belong to the gene ontology’s “hypoxia response”, “glycolysis” and “HIF-1 transcription factor network” supporting the view of active mRNA translation at the ER during hypoxia. Interestingly, a large group of RNAs was found to be unchanged at the expression level, but translocate to the ER in hypoxia. Among these are transcripts encoding translation factors and >180 ncRNAs. In summary, we provide evidence that protein synthesis is favoured at the ER and, thus, partitioning of the transcriptome between cytoplasmic and ER associated ribosomes mediates adaptation of gene expression in hypoxia. Human fibrosarcoma HT1080 cells were cultured for 36 h under control/atmospheric (21% O2, 5% CO2, 37 °C) or hypoxic (1% O2, 5% CO2, 37°C) conditions. Total RNA (representing expression level) and ER (endoplasmatic reticulum)-RNA (representing transcript localization at ER) was isolated for both conditions. Pooled RNA samples from 5 independent biological experiments were used for microarray analysis.
Project description:Tendon fascicles were extracted from tails of freshly euthanized mice and cultured for 6 days ex vivo in serum containing medium (10%) at either 3% oxygen and 29 degrees celsius or 21% oxygen and 37 degrees celsius.
Project description:To obtain a global view of the response of S. flexneri at the expression level induced by temperature up-shift, we compared the expression profiles of log-phase and stationary-phase cells grown at 30 degrees and 37 degrees Celsius.
2010-06-02 | GSE16535 | GEO
Project description:Transcriptome sequencing of Riemerella anatipestifer CH-1 under 37 degrees Celsius/42 degrees Celsius
Project description:B. cenocepacia J2315 was grown on LB medium to mid-stationary phase at OD 0.3 under full aeration and then transferred into a 50 ml centrifuge tube and placed upright into a CampyGen Compact (Oxoid, Basingstoke, UK) plastic pouch containing the gas generating paper sachet. The pouch was sealed immediately and then the cap of the centrifuge tube loosened to allow exchange of atmosphere between centrifuge tube and pouch. <br>The culture was further incubated at 37 degrees centigrade and 150 rpm for 2-3 hours until it reached OD 0.5. The centrifuge tube was sealed before opening the pouch and then snap-cooled before harvest to minimise exposure to atmospheric oxygen and to ensure expression profiles reflect the lower oxygen concentration.<br>The expression profile was compared to cells grown to OD 0.5 at atmospheric oxygen concentrations.<br>
Project description:Tendon fascicles were analysed directly after isolation from the tail of freshly euthanized mice and after of after ex vivo culture for 6 days. Fascicles were cultured in either serum containing medium (10%) or in serum-free medium at 21% oxygen and 37 degrees celsius.
Project description:The aim of this study was to investigate the effects of hypoxia on human macrophages Experiment Overall Design: Cultured macrophages from 4 donors were exposed to normoxia (21% oxygen) or hypoxia (0% oxygen) for 24 h. Two μg RNA from 4 donors incubated at normoxia and 4 donors at hypoxia was pooled respectively and these 2 pools were used for the target preparation and analyzed on duplicate DNA microarrays. Comparisons were made between the expression profile from macrophages exposed to hypoxia and the expression profile from the control normoxic macrophages to identify genes regulated during hypoxia.
Project description:PDAC(pancreatic ductal adenocarcinoma) cell lines- MiaPaca and 8988T were exposed to normoxic (20% Oxygen, 2 replicates each for MiaPaca and 8988T) or Hypoxia (0.1% Oxygen,3 replicates each for MiaPaca and 8998T) for 24 hrs
Project description:Pancreatic ductal adenocarcinoma (PDAC) is characterized by an extensive fibroinflammatory stromal reaction, which contributes to its hypovascular and hypoxic microenvironment. To assess the effects of hypoxia on fibroblast phenotype in an unbiased fashion, we performed RNA-sequencing profiling of mouse pancreatic stellate cells (PSCs) cocultured with mT3 PDAC cells exposed to normoxia (21% oxygen) or hypoxia (1% oxygen).