Ofd2+/-hypoxia
Ontology highlight
ABSTRACT:
ORGANISM(S): Schizosaccharomyces pombe 972h- Schizosaccharomyces pombe
PROVIDER: GSE31236 | GEO | 2011/08/06
SECONDARY ACCESSION(S): PRJNA146037
REPOSITORIES: GEO
Similar Datasets
Project description:Investigation of mRNA expression level changes in S. pombeOfd2 (SPAP8A3.02c) deletion strain compared to wild-type strain at both normal oxygen (normoxia) and low oxygen (hypoxia) growth conditions. Four samples in total consisting of two S. pombeyeast strains, wild type (WT) and a gene deleted strain for Ofd2 (SPAP8A3.02c), analysed for gene expression under two growth conditions, normal oxygen (normoxia) and low oxygen (hypoxia). Five micrograms of total RNA from two independent experiments were pooled and mRNA levels were quantified by Roche NimbleGen using the S. pombe 72K array service
2011-08-05 | E-GEOD-31236 | biostudies-arrayexpress
Project description:The goal of the study was to identify hypoxia-induced gene expression changes in C. elegans and to determine which of these responses to hypoxia were regulated by hif-1. Towards these aims, we analyzed mRNA expression patterns in synchronized populations of wild-type worms that were cultured in standard lab conditions (normoxia) or in hypoxia. We also assayed mRNA from two mutant strains: (i) animals carrying the strong loss-of-function mutation in hif-1 and (ii) C. elegans that carry a deletion in vhl-1 and express the HIF-1 protein at constitutively high levels. In the microarray experiments, 3 strains were assayed: wild type N2, hif-1 (ia04), and vhl-1 (ok161). Worms were incubated for 4 hours in 21% oxygen or 0.1% oxygen at 210C. Animals were quickly harvested in ice cold M9 buffer, and poly (A) RNA was isolated using established procedures. No more than 3 minutes elapsed between the removal of plates from the hypoxic chamber and the addition of Trizol. RNA was isolated from three independent experiments for each experimental condition (3 genotypes; normoxia vs hypoxia). mRNAs were hybridized to whole-genome microarrays which contained probes for 17,817 predicted genes (94% of the genome). Ch1 in the array represents the data for the worms growed under hypoxia; and Ch2 in the array reprents the data for the worms growed under normoxia. Keywords: Biological Replicates
2005-06-25 | GSE2836 | GEO
Project description:(1) The identification of genes that are transcriptionally regulated in response to exposure to hypoxia (~0.2% oxygen) in H99 (WT) and strains CM092 and CM098. (2) The identification of genes that are differentially-regulated in the strain CM093 compared to H99 (WT) Keywords: hypoxia response, comparative transcriptional hybridization 8 cultures for each strain (4 grown in normoxia and 4 grown in hypoxia) are analyzed on 4 microarrays for each strain (normoxia hybridized against hypoxia). Two out of four microarrays contain dye-swaps.
2010-06-12 | E-GEOD-6226 | biostudies-arrayexpress
Project description:Purpose: The goal of this study is to investigate the role of interplay between circadian clock and oxygen-sensing pathways in determining myogenic progenitor cell fate. Methods: Total RNAs were extracted from wild-type and Bmal1-/- myoblasts following exposure to normoxia (21% O2) or hypoxia (1% O2) for 6 hours, and subjected to RNA-sequencing. Results: There were significantly up-regulated (443 in normoxia versus 477 in hypoxia) and down-regulated (745 in normoxia versus 796 in hypoxia) genes in Bmal1-/- cells compared to wild-type, with a large degree of overlap between hypoxia and normoxia, although the fold change of differential gene expression was generally greater under hypoxia versus normoxia. Conclusion: Loss of Bmal1 in myoblasts leads to a premature differentiation-prone transcriptome, which was exaggerated following exposure to hypoxia.
2022-07-01 | GSE184741 | GEO
Project description:The goal of the study was to identify hypoxia-induced gene expression changes in C. elegans and to determine which of these responses to hypoxia were regulated by hif-1. Towards these aims, we analyzed mRNA expression patterns in synchronized populations of wild-type worms that were cultured in standard lab conditions (Snormoxia) or in hypoxia. We also assayed mRNA from two mutant strains: (i) animals carrying the strong loss-of-function mutation in hif-1 and (ii) C. elegans that carry a deletion in vhl-1 and express the HIF-1 protein at constitutively high levels. In the microarray experiments, 3 strains were assayed: wild type N2, hif-1 (ia04), and vhl-1 (ok161). Worms were incubated for 4 hours in 21% oxygen or 0.1% oxygen at 210C. Animals were quickly harvested in ice cold M9 buffer, and poly (A) RNA was isolated using established procedures. No more than 3 minutes elapsed between the removal of plates from the hypoxic chamber and the addition of Trizol. RNA was isolated from three independent experiments for each experimental condition (3 genotypes; normoxia vs hypoxia). mRNAs were hybridized to whole-genome microarrays which contained probes for 17,817 predicted genes (94% of the genome). Ch1 in the array reprents the data for the worms growed under hypoxia; and Ch2 in the array reprents the data for the worms growed under normoxia.
2005-06-20 | E-SMDB-3266 | biostudies-arrayexpress
Project description:Purpose: Mutations in several genetic loci lead to cardiac anomalies, with mutations in transcription factor NKX2-5 gene being one of the largest mutations known. Gestational hypoxia, such as seen in high-altitude pregnancy, has been known to affect cardiac development, and this paper aims to uncover information about the underlying mechanisms of this phenomena. Methods: Wild-type female mice were mated with Nkx2-5 mutant males, to produce offsprings. The pregnant females were then separated into two groups, one left in normal air and one breathing hypoxic, 14% oxygen, air from gestation day 10.5 to 12.5. Hearts were dissected from E12.5 embryos, subjected to RNA purification followed by RNA-seq. Wild-hypoxia and mutant-normoxia were compared to control wild-normoxia. Conclusions: The results of our study provide insights into a common molecular mechanism underlying non-genetic/epigenetic and genetic cardiac anomalies.
2018-08-30 | GSE114532 | GEO
Project description:To investigate the effect of chronic continuous hypoxia (11%) oxygen on lifespan and neurological function in Ercc1 ∆/- mice. We performed bulk RNA-seq of the cerebellum from mice that were Ercc1 ∆/- normoxia, Ercc1 ∆/- hypoxia, wildtype normoxia, wildtype hypoxia.
2023-04-10 | GSE219203 | GEO
Project description:We used HeLa cells that overexpress GFP-tagged SRSF6 (4-fold) were grown in normal conditions (Normoxia, 21% oxygen) or hypoxic conditions (Hypoxia, 0.2% oxygen). compared the binding pattern of SRSF6 between normoxia, 4h hypoxia and 24h hypoxia.
2023-01-03 | GSE198308 | GEO
Project description:Adult zebrafish (Tübingen strain, sex not specified) at approximately 1 year of age were analysed. For experiments conducted under low oxygen conditions, nitrogen gas was bubbled through water to deplete oxygen before exposure of individual fish to the medium. Oxygen concentrations were measured using a dissolved oxygen meter (DO 6+, EUTECH instruments, Singapore). The dissolved oxygen level for hypoxia treatment was measured to be 1.20 ± 0.6 mg/l, whereas normal ambient oxygen levels were 6.6 ± 0.45 mg/l. Zebrafish were exposed to the hypoxic medium for 3 hours. Briefly, after each hypoxia trial, the animals were euthanized by hypothermic shock and then decapitated to remove the brain. Total RNA was extracted from samples mentioned above using the QIAGEN RNeasy mini kit (QIAGEN, GmbH, Hilden, Germany) and stored at â??80°C before further analysis. RNA concentration was determined with a NanoVueâ?¢ UVâ??vis spectrophotometer (GE Healthcare Life Sciences, Fairfield, USA). RNA integrity and quality were then estimated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA) and the RNA integrity number (RIN) index was calculated for each sample. Only RNAs with a RIN number >7.0 were processed further. Microarray analysis of gene expression was performed using the Zebrafish Gene 1.0 ST Array (Affymetrix Inc. Santa Clara, CA). Briefly, 300ng of total RNA derived from a single adult brain was converted to amplified sense strand cDNA using the Ambion WT Expression Kit (Life Technologies, Carlsbad, CA). The resulting sense cDNA was fragmented and Biotin end-labelled using the Affymetrix Genechip WT Terminal Labeling Kit prior to hybridisation to the array at 45 °C for 16 hours. Two treatments including hypoxia and normoxia were studied. Each treatment had three biological replicates (i.e. three fish exposed to hypoxia and three fish exposed to normoxia). Six samples were analysed. Microarray analysis of gene expression was performed using the Zebrafish Gene 1.0 ST Array. The signal intensity of the chip was scanned using a GeneChipR Scanner 3000TG and analysed using Expression Console software (www. Affymetrix.com). CEL files were imported and intensities adjusted by RMA background correction and quantile normalization.
2016-08-04 | E-GEOD-85149 | biostudies-arrayexpress
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.
2008-06-13 | E-GEOD-4630 | biostudies-arrayexpress