Saccharomyces cerevisiae
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PROVIDER: PRJNA92429 | ENA |
REPOSITORIES: ENA
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Project description:Transcriptional response of steady-state yeast cultures to transient perturbations in carbon source
| PRJNA95005 | ENA
Project description:Background Microorganisms adapt their transcriptome by integrating multiple chemical and physical signals from their environment. Shake-flask cultivation does not allow precise manipulation of individual culture parameters and therefore precludes a quantitative analysis of the (combinatorial) influence of these parameters on transcriptional regulation. Steady-state chemostat cultures, which do enable accurate control, measurement and manipulation of individual cultivation parameters (e.g. specific growth rate, temperature, identity of the growth-limiting nutrient) appear to provide a promising experimental platform for such a combinatorial analysis. Results A microarray compendium of 170 steady-state chemostat cultures of the yeast Saccharomyces cerevisiae is presented and analyzed. The 170 microarrays encompass 55 unique conditions, which can be characterized by the combined settings of 10 different cultivation parameters. By applying a regression model to assess the impact of (combinations of) cultivation parameters on the transcriptome, most S. cerevisiae genes were shown to be influenced by multiple cultivation parameters, and in many cases by combinatorial effects of cultivation parameters. The inclusion of these combinatorial effects in the regression model led to higher explained variance of the gene expression patterns and resulted in higher function enrichment in subsequent analysis. We further demonstrate the usefulness of the compendium and regression analysis for interpretation of shake-flask-based transcriptome studies and for guiding functional analysis of (uncharacterized) genes and pathways. Conclusions Modeling the combinatorial effects of environmental parameters on the transcriptome is crucial for understanding transcriptional regulation. Chemostat cultivation offers a powerful tool for such an approach. Keywords: chemostat steady state samples
2009-02-05 | GSE11452 | GEO
Project description:We combined the nuclear run-on (NRO) assay which labels and captures nascent transcripts with high throughput DNA sequencing to examine transcriptional activity in Saccharomyces cerevisiae. Examination of nascent transcripts and steady-state transcripts in exponentially growing and heat-shock treated yeast.
2011-11-01 | E-GEOD-33136 | biostudies-arrayexpress
Project description:Saccharomyces cerevisiae chemostat steady state microarray compendium
| PRJNA106367 | ENA
Project description:The first aim was to investigate the suitability of FSCF to analyze yeast physiology during the stationary phase of wine making. In this way, a comparative transcriptomic analysis was performed on mRNA samples collected from the third stage of FSCF and from batch culture, at the same fermentation progress (164 g/L residual glucose). In a second part, FSCF device was used to study the impact at the transcriptomic level of nitrogen addition performed at the beginning of the stationary phase. Gene expression profiles were compared at steady state between cells from the third stage of FSCF operating in presence or absence of continuous valine or ammonium perfusion.
2016-04-29 | GSE40526 | GEO
Project description:transcriptional profiling of yeast meiotic culture
2016-11-18 | GSE90006 | GEO
Project description:transcriptional profiling of yeast meiotic culture
2016-11-18 | GSE90005 | GEO
Project description:Yeast zeta-crystallin: An AU-Rich Element Binding Protein Involved in the Nutritional Stress Response
| PRJNA193429 | ENA
Project description:Study of the short term (within the first 330 seconds) transcriptional response of S.cerevisiae upon a sudden addition of glucose. Experiment Overall Design: Chemostat cultivation â Saccharomyces cerevisiae (CEN PK 113-7D) was cultivated in an aerobic carbon-limited chemostat culture in a 7-litres fermentor (Applikon, The Netherlands) with a working volume of 4-l on the adapted doubled mineral medium (Verduyn et al., 1992) with 27.1 g.l-1 of glucose and 1.42 g.l-1 of ethanol, to support a biomass concentration of about 15 g dry weight.l-1. The dilution rate was set to be 0.05 hr-1 and the airflow rate was set to be 200 l.hr-1. Other fermentation parameters are: a pH controlled at 5, a temperature controlled at 30ËC, an overpressure of 0.3 bar and stirrer speed of 600 rpm. The chemostat was considered to obtain its stable steady state condition 5 resident times after the end of its batch phase. Experiment Overall Design: Glucose pulse experiment - At the age of 7 dilution times, the steady state chemostat culture was perturbed by the addition of 20 ml of glucose solution (200 g/l) to the fermentor so that the residual glucose concentration was suddenly increased to about 1 g/l (5.56 mM). The glucose solution was rapidly injected by a pneumatic system (< 1 s). Samples were taken prior to the glucose pulse (steady state samples) and within 360 s transient after the perturbation. Experiment Overall Design: Verduyn,C., Postma,E., Scheffers,W.A., and van Dijken,J.P. (1992). Effect of benzoic acid on metabolic fluxes in yeasts: a continuous-culture study on the regulation of respiration and alcoholic fermentation. Yeast 8, 501-517.
2008-06-12 | E-GEOD-3821 | biostudies-arrayexpress