Transcription pattern in Normal (NL) and Down's Syndrome (DS) Astrocytes
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ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Pablo Helguera
PROVIDER: E-GEOD-42772 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:We performed a broad-spectrum microarray analysis using mRNA from 3 NL and 5 DS astrocyte cultures. The microarray output was validated for several genes To explore the relation between gene expression and potential oxidative stress in DS samples, we also evaluated the transcription profile in NL astrocytes subjected to mild oxidative stress (50µM H2O2 for 24 hr).
2012-12-07 | GSE42772 | GEO
Project description:Title: Changes in gene expression affected by H2O2 in cardiac myocytes.<br/> Description: We aim to identify the changes in gene expression in response to <br/> oxidative stress in rat neonatal ventricular myocytes.<br/> Oxidative stress will be induced by dosing neonatal ventricular myocyte<br/> cultures with 0.2, 0.1 and 0.04mM hydrogen peroxide at 2, 4 and 8 hr time<br/> points using unstimulated myocytes as control.
2011-11-08 | E-MIMR-12 | biostudies-arrayexpress
Project description:Background: During gut colonization, the enteric pathogen C. jejuni has to surmount the toxic effects of reactive oxygen species produced by its own metabolism, by the host immune system and by the intestinal microflora. Elucidation of C. jejuni oxidative stress defense mechanisms is critical for understanding Campylobacter pathophysiology. Results: The mechanisms of oxidative stress defenses in Campylobacter jejuni were characterized by transcriptional profiling, genes mutagenesis, and phenotypic analysis. The transcriptome changes, in response to H2O2, cumene hydroperoxide, or menadione exposure, were found to be oxidant specific and revealed the differential expression of genes belonging to a variety of biological pathways, from the classical oxidative stress defense systems, to the heat shock response, DNA repair and metabolism, fatty acid and capsule biosynthesis, and multidrug efflux pumps. To define the peroxide sensing regulator PerR, an isogenic mutant was constructed and its transcriptome profile compared to the wild-type strain. Sixty-six genes were found to belong to the PerR regulon. PerR appear to regulate gene expression both dependently and independently of the presence of iron and/or H2O2. The perR mutant was affected in its motility and attenuated in the chick colonization model. Mutagenic and phenotypic studies of the superoxide disumutase SodB, the alkyl-hydroxyperoxidase AhpC, and the catalase KatA, revealed their role in oxidative stress defenses and chick gut colonization. Conclusion: This study reveals the interplay between PerR, the iron metabolism and the oxidative stress defenses and highlights their role in the colonization and/or survival of C. jejuni in the chick cecum. Keywords: Transcriptional response to 3 oxidants (H2O2, menadione and cumene hydroperoxide) and characterization of the perR regulon (comparison of the transciptomes from the wild-type and perR mutant). To investigate the transcriptional responses of C. jejuni to oxidant exposure, hydrogen peroxide (H2O2), cumene hydroperoxide (CHP), or menadione sodium bisulfite (MND) was added to the 50 ml broth at a final concentration of 1 mM. The same amount of water or DMSO was added to the bacterial culture that served as reference samples for the transcriptional profile study in response to H2O2, MND or CHP. Furthermore, to investigate the transcriptional response of C. jejuni to H2O2 exposure in the presence of excess iron, ferrous sulfate was added to the bacterial culture at a final concentration of 40 µM, 15 min prior to H2O2 exposure. Ten minutes after the addition of the oxidant, total RNA was extracted and processed for microarray hybridization. To identify the PerR regulon, the wild-type strain C. jejuni NCTC 11168 and the perR mutant were grown in 500 ml flasks containing 250 ml of MEMα medium. At mid-log phase, 50 ml of the cultures were transferred to 100 ml flasks and ferrous sulfate and/or H2O2 were added . Ten minutes following the addition of H2O2 the cells were collected and the total RNA extracted.
2010-09-07 | E-GEOD-13126 | biostudies-arrayexpress
Project description:H2O2 is considered to function as a ubiquitous intracellular messenger in addition to oxidative stress molecule. This dual role of H2O2 is based on the distinct responses against the different concentration, which is low dose (sub-toxic) and high dose (toxic). In this study we performed the transcription response of low and high dosage of H2O2 on Candida albicans
2010-12-03 | E-MEXP-2680 | biostudies-arrayexpress
Project description:To identify the respective roles of light and ROS in the photoinhibition process and detect a possible light-driven tolerance to oxidative stress, we compared the transcriptomic responses of Synechococcus sp. WH7803 acclimated to low (LL) or high light (HL) to oxidative stress, induced by hydrogen peroxide (H202) or methylviologen (MV). Cultures were acclimated during many generations to continuous low light (LL, 18 ?mol photons m-2 s-1, hereafter LL cells) and high light (HL, 250 ?mol photons m-2 s-1, hereafter HL cells) provided by Sylvania Daylight 58W/154 fluorescent bulbs. For all stress experiments performed in this study, exponentially growing cultures (1 to 3 x 107 cells mL-1), were split into subcultures and submitted to oxidative stress by addition of H2O2 or MV and harvested when PSII quantum yield fell to half of the initial value. For H2O2 experiments, this level of PSII photoinactivation was reached 2 h after submitting LL and HL cultures to 750 M and 25 M respectively. Because of the large divergence in dose and kinetics responses to MV between LL- and HL cells, it was not possible to find MV concentrations leading to 50 % decrease of quantum yield at the same time for both light acclimations. Thus, array analyses for MV were performed on HL and LL cultures incubated at the same MV concentration (50 M) but harvested once PSII quantum yield was halved, i.e. after 1 and 3.5 h of stress respectively. All hybridizations were performed on 4 independent biological replicates and using as reference sample a pool of RNA from all samples investigated in this study. Pairwise comparison were performed to analyze the stress induced by either H2O2 or MV on both LL- and HL cultures (i.e. LL-Ct vs. LL+MV, LL-Ct vs. LL+H2O2, HL-Ct vs. HL+MV, HL-Ct vs. HL+H2O2) as well as to compare the steady state acclimation to different light conditions (i.e. LL-Ct vs. HL-Ct).
2011-08-18 | E-MTAB-681 | biostudies-arrayexpress
Project description:50mM H2O2 was added to mid-log phase Halobacterium NRC-1 cultures. After constant stress of H2O2 for 30 minutes, cultures were spun down and pellets were resuspended in same volume of GN101 media. Samples for RNA preparation were collected during recovery time points at 0, 10, 20, 30, 40, 60 and 120 minutes. 16 samples (8 exposed to H2O2 and 8 non-exposed controls) were each hybridized on duplicate arrays (as dye-flips) against the same standard control sample.
2010-05-27 | E-GEOD-7610 | biostudies-arrayexpress
Project description:The fungus Ustilago maydis is a biotrophic pathogen of corn. In its genome we have identified an ortholog of YAP1 from Saccharomyces cerevisae which regulates the oxidative stress response in this organism. yap1 mutants of U. maydis displayed higher sensitivity to H2O2 than wild type cells and their virulence was significantly reduced. U. maydis yap1 could partially complement the H2O2 sensitivity of a yap1 deletion mutant of S. cerevisiae and a Yap1-GFP fusion protein showed nuclear localization after H2O2 treatment, suggesting that Yap1 in U. maydis functions as a redox sensor. Mutations in two cysteine residues prevented accumulation in the nucleus and the respective mutant strains showed the same virulence phenotype as Dyap1 mutants. DAB staining revealed an accumulation of H2O2 around yap1 mutant hyphae which was absent in wild type. Inhibition of the plant NADPH oxidase prevented this accumulation and restored virulence. During the infection Yap1 showed nuclear localization after penetration up to 2-3 days after infection. Through array analysis a large set of yap1 regulated genes were identified and these included two peroxidase genes. Deletion mutants of these genes were attenuated in virulence. These results suggest that U. maydis is using its yap1 controlled H2O2 detoxification system for coping with early plant defense responses. Keywords: Oxidative stress, yap1 dependent genes, Ustilago maydis Two independent overnight cultures of U. mayidis FB1 and FB1Dyap1 grown in CM-glucose (OD600 0.8) were diluted in 100 ml of the same medium (OD600 0.2) and growth at 28° C until an OD600 0.6. The cultures were divided and one half was supplemented with 5mM H2O2. After one hour of exposition to H2O2, cells were harvested by centrifugation and frozen in liquid nitrogen. RNA extraction, purification, cDNA generation, purification and labeling were performed according to standard protocols (Affymetrix). DNA array analysis was performed performed on two biological replicates each, using custom-designed Affymetrix chips (MPIUstilagoA). Data were analysed using a GeneArray Scanner (Agilent/Affymetrix) and the GeneChip Expression Analysis software (GCOS)
2010-06-11 | E-GEOD-7518 | biostudies-arrayexpress
Project description:We aimed to identify putative H2O2-regulated miRNAs expressed in rice seedlings under oxidative stress by using a deep sequencing approach developed by Solexa (Illumina). Two small RNA libraries were constructed from H2O2-treated and control rice seedlings, and more than five million small RNA sequence reads were generated for each library. We identified seven H2O2-responsive miRNA families via expression profiling of the miRNAs based on a comparative miRNAomic analysis in combination with experimental validation. Furthermore, 32 miRNAs, 17 from known miRNA loci and 15 from novel miRNA loci, were also newly identified from the sequencing data. To the best of our knowledge, this is the first report of a systematic investigation of H2O2-regulated miRNAs and their targets in plants. Examination of 2 different small RNA expression profilings in the control and H2O2 treated rice samples.
2010-08-15 | E-GEOD-23217 | biostudies-arrayexpress
Project description:Microarray analysis of the effect of L-carnitine supplementation on global expression of Sachharomyces cerevisiae cultures in logarithmic growing conditions and after exposure to H2O2 induced oxidative stress; L-Carnitine plays a well documented role in eukaryotic energy homeostasis by acting as a shuttling molecule for activated acyl residues across intracellular membranes. This activity is supported by carnitine acyl-transferases and transporters, and is referred to as the carnitine shuttle. However, several pleiotropic and often beneficial effects of carnitine in humans have been reported that appear to be unrelated to the shuttling activity, but little conclusive evidence regarding the molecular networks that would be affected by carnitine exist. We have recently demonstrated a protective role of carnitine in oxidative stress in yeast that is independent of the carnitine shuttle. A DNA microarray-based global gene expression analysis identified Cyc3p, a cytochrome c heme lyase, as being important for carnitine's protective impact in oxidative stress conditions. These findings establish a direct genetic link to a carnitine-related phenotype that is independent of the shuttle system. The data suggest that the yeast Saccharomyces cerevisiae should provide a useful model for further elucidation of carnitine's physiological roles. Experiment Overall Design: Yeast cultures was grown to mid-log phase with and without carnitine supplementation to a final concentration of 100 mg/L. A second set was grown to mid log phase, with and without carnitine supplementation and exposed to 0.4 mM H2O2 for 30 min. The experiments were performed using biological duplicate.
2009-07-04 | E-GEOD-16346 | biostudies-arrayexpress
Project description:We undertook a transcriptional profiling to identify genes coping with H2O2-induced oxidative stress in S. oneidensis. The data revealed that the well conserved scavenging genes such as as ahpCF, katB, and katG formed the first line of defense while iron-sulfur protecting proteins may not play a significant role. Experimental cells collected 5 min after H2O2 treatment; Control cells collected just before H2O2 treatment. In total, 8 samples were studied (4 for wild type and 4 for arcA mutant, 4 replicates).
2012-07-31 | E-GEOD-31053 | biostudies-arrayexpress