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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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JM43_Galactose_Air_N2_Air_Shift

ABSTRACT: The yeast cells were grown aerobically on galactose medium. At time zero (generation 0) the saprge gas was switched from air to O2-free N2 and samples were harvested after 0 (aerobic control), 0.04, 0.08, 0.13, 0.19, 0.25, 0.38, 0.5, 1, 2, 3, 4, 5 and 6 generations of anaerobic growth. After six generations, the saprge gas was switched back to air and samples were harvested at 6 (anaerobic control), 6.03, 6.06, 6.1, 6.13, 6.2, 6.3, 6.4, 6.6, 6.8, and 7.6 generations. Keywords: time-course

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Kurt Kwast

PROVIDER: E-GEOD-2246 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Metabolic-state-dependent remodeling of the transcriptome in response to anoxia and subsequent reoxygenation in Saccharomyces cerevisiae.

Lai Liang-Chuan LC Kosorukoff Alexander L AL Burke Patricia V PV Kwast Kurt E KE

Eukaryotic cell 20060901 9

We conducted a comprehensive genomic analysis of the temporal response of yeast to anaerobiosis (six generations) and subsequent aerobic recovery ( approximately 2 generations) to reveal metabolic-state (galactose versus glucose)-dependent differences in gene network activity and function. Analysis of variance showed that far fewer genes responded (raw P value of <or=10(-8)) to the O(2) shifts in glucose (1,603 genes) than in galactose (2,388 genes). Gene network analysis reveals that this diffe ...[more]

PMID: 16963631

Similar Datasets

JM43_Glucose_Air_N2_Air_Shift

Project description:The yeast cells were grown aerobically on glucose medium. At time zero (generation 0) the saprge gas was switched from air to O2-free N2 and samples were harvested after 0 (aerobic control), 0.04, 0.08, 0.13, 0.19, 0.25, 0.38, 0.5, 1, 2, 3, 4, 5 and 6 generations of anaerobic growth. After six generations, the saprge gas was switched back to air and samples were harvested at 6 (anaerobic control), 6.03, 6.06, 6.1, 6.13, 6.2, 6.3, 6.4, 6.6, 6.8, and 7.6 generations. Keywords: time-course

2006-06-30 | GSE2267 | GEO

JM43_Galactose_Air_N2_Air_Shift

Project description:The yeast cells were grown aerobically on galactose medium. At time zero (generation 0) the saprge gas was switched from air to O2-free N2 and samples were harvested after 0 (aerobic control), 0.04, 0.08, 0.13, 0.19, 0.25, 0.38, 0.5, 1, 2, 3, 4, 5 and 6 generations of anaerobic growth. After six generations, the saprge gas was switched back to air and samples were harvested at 6 (anaerobic control), 6.03, 6.06, 6.1, 6.13, 6.2, 6.3, 6.4, 6.6, 6.8, and 7.6 generations. Keywords: time-course

2006-06-30 | GSE2246 | GEO

JM43_Glucose_Air_N2_Air_Shift

2010-06-11 | E-GEOD-2267 | biostudies-arrayexpress

aerobic_to_anaerobic_shift

Project description:The wild-type (grown on galactose or glucose) or msn2/4 mutant (grown on galactose) strains were grown aerobically. At time zero (generation 0) the sparge gas was switched from air to O2-free N2 and samples were harvested after 0 (aerobic control), 0.04, 0.08, 0.19, and 2 generations of anaerobic growth. Keywords: time-course

2005-02-28 | GSE1879 | GEO

JM43_Galactose_N2_AntimycinA

Project description:In previous temporal studies, we found the anaerobic response was biphasic when cells growing in galactose medium were shifted from aerobiosis to anaerobiosis, consisting of an acute, transitory phase (<60 min) followed by a more chronic but delayed phase (> 1 generation), but largely monophasic (delayed, chronic phase only) when cells were shifted in glucose medium. Gene network and functional analyses revealed the acute phase was comprised of genes associated with the retooling of metabolism (respiro-fermentative to strictly fermentative) and balancing energy supply and demand. A similar pattern of gene expression is seen when cells encounter other “environmentally stressful” conditions. However, cells shifted to anaerobiosis on glucose, in which no catabolic rearrangement is required nor change in growth rate observed, do not exhibit this pattern, suggesting the “stress” encountered is one associated with the abrupt cessation of galactose-dependent respiration and slowing of growth, not oxygen deprivation per se. In order to test this hypothesis, we added the respiratory inhibitor, antimycin A, under aerobiosis for three generations then shifted to anaerobiosis, which no catabolic rearrangement is required. Keywords: time course Sparged, fermentor cultures of a wild-type yeast strain (JM43) were aerobically grown on galactose medium (SSG-TEA) in the presence of Antimycin A for three generations. After three generations, the sparge gas was switched from air to O2-free N2 and samples were harvested after 0.04, 0.08, 0.13, 0.19, 0.25, 0.38, 0.5, 1, 2, and 3 generations of anaerobic growth in the presence of Antimycin A. Total RNA was reverse transcribed (Cy3) and hybridized against a reference (Cy5). The full time series was repeated in triplicate.

2008-12-31 | E-GEOD-3706 | biostudies-arrayexpress

JM43 cells grown aerobically in galactose and treated with Antimycin A

Project description:In previous temporal studies, we found the anaerobic response was biphasic when cells growing in galactose medium were shifted from aerobiosis to anaerobiosis, consisting of an acute, transitory phase (<60 min) followed by a more chronic but delayed phase (> 1 generation), but largely monophasic (delayed, chronic phase only) when cells were shifted in glucose medium. Gene network and functional analyses revealed the acute phase was comprised of genes associated with the retooling of metabolism (respiro-fermentative to strictly fermentative) and balancing energy supply and demand. A similar pattern of gene expression is seen when cells encounter other “environmentally stressful” conditions. However, cells shifted to anaerobiosis on glucose, in which no catabolic rearrangement is required nor change in growth rate observed, do not exhibit this pattern, suggesting the “stress” encountered is one associated with the abrupt cessation of galactose-dependent respiration and slowing of growth, not oxygen deprivation per se. In order to test this hypothesis, we conducted this genomic study using the respiratory inhibitor, antimycin A, under aerobiosis, which mimicked the retooling of metabolism from respiro-fermentative to strictly fermentative growth. Keywords: time course Sparged, fermentor cultures of a wild-type yeast strain (JM43) were aerobically grown on galactose medium (SSG-TEA) for six generations of preconditioning. When cell density was ≈1 Klett unit, Antimycin A (1 μM) was added into medium. Samples were harvested after 0 (control), 0.04, 0.08, 0.13, 0.19, 0.25, 0.38, 0.5, 1, 2, and 3 generations of aerobic growth in the presence of Antimycin A. Total RNA was reverse transcribed (Cy3) and hybridized against a reference (Cy5). The full time series was repeated in triplicate.

2008-12-31 | E-GEOD-3705 | biostudies-arrayexpress

Transcriptional profiling of Escherichia coli after addition of CO gas to aerobically and anaerobically growing cells

Project description:Escherichia coli strain MG1655 was grown in a New Brunswick Scientific Bioflow III Biofermentor under continuous culture (chemostat) conditions. Cells were grown in Evans media containing 2 mM glucose as the sole and limiting source of energy and carbon. The working volume was 200 ml, and the dilution rate 0.2 h-1. For aerobic growth, the air-flow rate was 0.1 l/min, and the dissolved oxygen tension was maintained at ~7% air saturation by measuring oxygen dissolved in the culture using a Broadley James D140 OxyProbeÂ® electrode. For anaerobic growth, cells are grown on 100 % nitrogen gas bubbled at 0.1 l/min Cells were grown as above to steady-state, At steady-state, CO gas was bubbled through the culture at 0.1L/min. Samples were taken immediately prior to the addition of CO gas and over a time course of 2.5, 5, 10, 20, 40 and 80 min exposure to CO gas for subsequent analysis using microarrays. Cells were harvested directly into phenol:ethanol to stabilize RNA, and total RNA was purified using Qiagenâ??s RNeasy Mini kit as recommended by the suppliers. Time course experiment with samples taken immediately prior to or 2.5, 5, 10, 20, 40 or 80 minutes after addition of CO gas under either 0 or 100 % perceived aerobiosis. 2 biological repeats were performed for the aerobic condition with 2 technical (dye swap) repeats per biological repeat, and three biological repeats were perfomed for the anaerobic condition with 2 technical (dye swap) repeats per biological repeat.

2016-09-01 | E-GEOD-50713 | biostudies-arrayexpress

Transcriptional profiling of Escherichia coli after addition of CO gas to aerobically and anaerobically growing cells

Project description:Escherichia coli strain MG1655 was grown in a New Brunswick Scientific Bioflow III Biofermentor under continuous culture (chemostat) conditions. Cells were grown in Evans media containing 2 mM glucose as the sole and limiting source of energy and carbon. The working volume was 200 ml, and the dilution rate 0.2 h-1. For aerobic growth, the air-flow rate was 0.1 l/min, and the dissolved oxygen tension was maintained at ~7% air saturation by measuring oxygen dissolved in the culture using a Broadley James D140 OxyProbe® electrode. For anaerobic growth, cells are grown on 100 % nitrogen gas bubbled at 0.1 l/min Cells were grown as above to steady-state, At steady-state, CO gas was bubbled through the culture at 0.1L/min. Samples were taken immediately prior to the addition of CO gas and over a time course of 2.5, 5, 10, 20, 40 and 80 min exposure to CO gas for subsequent analysis using microarrays. Cells were harvested directly into phenol:ethanol to stabilize RNA, and total RNA was purified using Qiagen’s RNeasy Mini kit as recommended by the suppliers.

2016-09-01 | GSE50713 | GEO

E. coli Transcriptome Dynamics during the Transition from Anaerobic to Aerobic Conditions

Project description:Escherichia coli is a metabolically versatile bacterium that is able to grow in the presence and absence of oxygen. Several previous transcript-profiling experiments have compared separate anaerobic and aerobic cultures. Here, for the first time, the process of adaptation was investigated by determining changes in transcript profiles when anaerobic steady-state cultures were perturbed by the introduction of air. Escherichia coli strain MG1655 was grown in a New Brunswick Scientific Bioflow 1000 fermentation vessels (1.8 l capacity) with culture agitation speed constant at 400 rpm and the temperature maintained at 37 °C. Oxygen levels were monitored using galvanic oxygen electrodes while the pH was maintained at 7.2 ±0.2 by automatic titration with sterile KOH. Evans defined medium was used as the growth medium with glucose (30 mM) as the carbon source with the dilution rate being 0.2 h-1. Anaerobic cultures were maintained by sparging the chemostat with oxygen-free nitrogen (95 %) and carbon dioxide (5 %) (0.2 l min-1). The switch to aerobic conditions was achieved by sparging the culture with air (2.0 l min-1) in place of the above gas mix. After a period of 5, 10, 15 and 60 min exposure to air, cells were harvested directly into RNA Protect (Qiagen) to stabilize RNA before total RNA purification using Qiagen’s Rneasy Midi kit as recommended by manufacturer’s instructions. Keywords: time course response to air

2006-07-28 | GSE4735 | GEO

Transcriptional profiling of Escherichia coli after addition of CORM-401 to aerobically and anaerobically growing cells

Project description:Escherichia coli strain MG1655 was grown in a New Brunswick Scientific Bioflow III Biofermentor under continuous culture (chemostat) conditions. Cells were grown in Evans media containing 2 mM glucose as the sole and limiting source of energy and carbon. The working volume was 200 ml, and the dilution rate 0.2 h-1. For aerobic growth, the air-flow rate was 0.1 l/min, and the dissolved oxygen tension was maintained at ~7% air saturation by measuring oxygen dissolved in the culture using a Broadley James D140 OxyProbe® electrode. For anaerobic growth, cells are grown on 100 % nitrogen gas bubbled at 0.1 l/min Cells were grown as above to steady-state, At steady-state, CO gas was bubbled through the culture at 0.1L/min. Samples were taken immediately prior to the addition of CORM-401 and over a time course of 2.5, 5, 10, 20, 40 and 80 min exposure to CORM-401 for subsequent analysis using microarrays. Cells were harvested directly into phenol:ethanol to stabilize RNA, and total RNA was purified using Qiagen’s RNeasy Mini kit as recommended by the suppliers.

2017-05-31 | GSE71784 | GEO

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