GEO DataSets

(Submitter supplied) Saccharomyces cerevisiae is an established microbial host for the production of non-native compounds. The synthesis of these compounds typically demands energy and competes with growth for carbon and energy substrate. Uncoupling product formation form growth would benefit product yields and decrease formation of by-product biomass. Studying non-growing metabolically-active yeast cultures provides a first step towards developing S. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL90

13 Samples

Download data: CEL

(Submitter supplied) Transcriptional profiling of Pichia pastoris cultivated at different specific growth rates in carbon and energy-limited aerobic chemostats and retentostats

Organism:

Komagataella pastoris; Komagataella phaffii CBS 7435

Type:

Expression profiling by array

Platform:

GPL21808

54 Samples

Download data: TXT

(Submitter supplied) Saccharomyces cerevisiae has become a popular host for production of non-native compounds. The metabolic pathways involved generally require a net input of energy. To maximize the ATP yield on sugar in S. cerevisiae, industrial cultivation is typically performed in aerobic, sugar-limited fed-batch reactors which, due to constraints in oxygen transfer and cooling capacities, have to be operated at low specific growth rates. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL90

16 Samples

Download data: CEL

(Submitter supplied) Extremely low specific growth rates (below 0.01 h-1) represent a largely unexplored area of microbial physiology. Retentostats enable controlled, energy-limited cultivation at near-zero specific growth rates while avoiding starvation. In this study, anaerobic, glucose-limited retentostats were used to analyze physiological and genome-wide transcriptional responses of Saccharomyces cerevisiae to cultivation at near-zero specific growth rates. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL90

11 Samples

Download data: CEL

(Submitter supplied) Cultivation methods used to investigate microbial calorie restriction often result in carbon and energy starvation. This study aims to dissect cellular responses to calorie restriction and starvation in Saccharomyces cerevisiae by using retentostat cultivation. In retentostats, cells are continuously supplied with a small, constant carbon and energy supply, sufficient for maintenance of cellular viability and integrity but insufficient for growth. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL90

10 Samples

Download data: CEL

(Submitter supplied) The methylotrophic, thermotolerant yeast Ogataea parapolymorpha (formerly Hansenula polymorpha) is an industrially relevant production host and exhibits a respiratory metabolism in the presence of oxygen. It possesses a branched respiratory chain with multiple entry points for NADH-derived electrons that differ in complexity and degree of energy conservation: proton-translocating respiratory Complex I and three putative alternative NADH dehydrogenases. more...

Organism:

Ogataea parapolymorpha

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24265

16 Samples

Download data: CSV

(Submitter supplied) Prolonged cultivation of Saccharomyces cerevisiae in aerobic, glucose-limited chemostat cultures (dilution rate, 0·10 h–1) resulted in a progressive decrease of the residual glucose concentration (from 20 to 8 mg l–1 after 200 generations). This increase in the affinity for glucose was accompanied by a fivefold decrease of fermentative capacity, and changes in cellular morphology. These phenotypic changes were retained when single-cell isolates from prolonged cultures were used to inoculate fresh chemostat cultures, indicating that genetic changes were involved. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL90

6 Samples

Download data: CEL, EXP

(Submitter supplied) Time course of exponentially growing yeast cells Fermenting glucose in the presence of enough oxygen to support respiration, known as aerobic glycolysis, is believed to maximize growth rate. We observed increasing aerobic glycolysis during exponential growth, suggesting additional physiological roles for aerobic glycolysis. We investigated such roles in yeast batch cultures by quantifying O2 consumption, CO2 production, amino acids, mRNAs, proteins, posttranslational modifications, and stress sensitivity in the course of nine doublings at constant rate. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL13340

8 Samples

Download data: TXT

(Submitter supplied) Saccharomyces cerevisiae is unique among yeasts for its ability to grow rapidly in the complete absence of oxygen. S. cerevisiae is therefore an ideal eukaryotic model to study physiological adaptation to anaerobiosis. Recent transcriptome analyses have identified hundreds of genes that are transcriptionally regulated by oxygen availability but the relevance of this cellular response has not been systematically investigated at the key control level of the proteome. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL4992

1 Sample

Download data: XLS

(Submitter supplied) B. subtilis was cultured in a retentostat at extremely low growth rates and the adaptation of B. subtilis to these near-zero growth conditions was studied by analysis of the transcriptome and genome. During retentostat culturing the specific growth rate decreased to a minimum of 0.00006 h-1, corresponding to a doubling time of 470 days. Transcriptome analysis shows that while cells under near-zero growth conditions exhibit many characteristics of stationary phase cells, they are also fundamentally different. more...

Organism:

Bacillus subtilis; Bacillus subtilis subsp. subtilis str. 168

Type:

Expression profiling by array

Platform:

GPL18393

24 Samples

Download data: GPR, TXT

(Submitter supplied) Engineered strains of Saccharomyces cerevisiae are used for industrial production of succinic acid. Optimal process conditions for dicarboxylic-acid yield and recovery include slow growth, low pH and high CO2. To quantify and understand how these process parameters affect yeast physiology, this study investigates individual and combined impacts of low pH (3.0) and high CO2 (50 %) on slow-growing chemostat and retentostat cultures of the reference strain S. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17342

26 Samples

Download data: CSV

(Submitter supplied) Abstract: We studied the physiological response to glucose limitation in batch and steady-state (chemostat) cultures of Saccharomyces cerevisiae by following global patterns of gene expression. Glucose-limited batch cultures of yeast go through two sequential exponential growth phases, beginning with a largely fermentative phase, followed by an essentially completely aerobic use of residual glucose and evolved ethanol. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL2638

20 Samples

Download data

(Submitter supplied) Time course of batch growth. Reference (channel 1) was a culture grown in MD medium with 2.4 g/L glucose, with 5 slpm air-flow, stirring at 400 rpm and a constant 300C temperature, dilution 0.25 volumes/hour. The experimental (channel 2) samples were grown in batch for the indicated time. Groups of assays that are related as part of a time series. FactorCategory: Elapsed Time; name: Elapsed Time; Measurement: time(absolute) 6 h; name: 34357_Elapsed Time; Measurement: time(absolute) 10.5 h; name: 34365_Elapsed Time; Measurement: time(absolute) 8 h; name: 34358_Elapsed Time; Measurement: time(absolute) 9 h; name: 34359_Elapsed Time; Measurement: time(absolute) 11 h; name: 34368_Elapsed Time; Measurement: time(absolute) 9.5 h; name: 34360_Elapsed Time; Measurement: time(absolute) 10 h; name: 34362_Elapsed Time Keywords: time_series_design

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL2638

7 Samples

Download data

(Submitter supplied) Time course of batch growth. Reference (channel 1) was a culture grown in MD medium with 2.4 g/L glucose, with 5 slpm air-flow, stirring at 400 rpm and a constant 300C temperature, dilution 0.25 volumes/hour. The experimental (channel 2) time course samples were grown in batch for the indicated time. The "Low-D chemostat vs. High-D chemostat" hybridization's channel 2 sample was grown in a chemostat, with a dilution rate of 0.05 volumes/hour; it is most similar to the time course samples taken between 8 and 9 hours. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL2638

13 Samples

Download data

(Submitter supplied) The present study aims to explore the role of Rim15 in both physiology and genome wide expression in S. cerevisiae under severe caloric restriction. Non-growing but metabolically active cultures of S. cerevisiae are of major interest for application in industry and as model systems for aging in higher eukaryotes. Using retentostat cultivations, almost non-growing but metabolic active cultures can be obtained resulting from the severe caloric restriction, yet not starvation, yeast experiences. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL90

11 Samples

Download data: CEL

(Submitter supplied) In contrast to batch cultivation, chemostat cultivation allows the identification of carbon source responses without interference by carbon-catabolite repression, accumulation of toxic products, and differences in specific growth rate. This study focuses on the yeast Saccharomyces cerevisiae, grown in aerobic, carbon-limited chemostat cultures. Genome-wide transcript levels and in vivo fluxes were compared for growth on two sugars, glucose and maltose, and for two C2-compounds, ethanol and acetate. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL90

12 Samples

Download data: CEL, EXP

(Submitter supplied) In Saccharomyces cerevisiae, glycogen and trehalose are important reserve carbohydrates that accumulate under nutrient limitation in batch cultures. An inherent draw-back of batch studies is that specific growth rate and substrate and product concentrations are variable over time and between cultures. The aim of this present study was to identify the nutritional requirements associated with high accumulation of reserve carbohydrates at a fixed specific growth rate (0.10 h-1) in anaerobic chemostat cultures that were limited by one of five different nutrients (carbon, nitrogen, sulfur, phosphorus or zinc). more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL90

21 Samples

Download data: CEL, CHP, EXP

(Submitter supplied) Raw expression values (CHP data) for transcriptional profiling of the response of Saccharomyces cerevisiae to challenges with lactic acid at pH 3 and pH 5. Keywords: response to lactic acid

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL90

12 Samples

Download data: CEL, CHP

(Submitter supplied) Saccharomyces cerevisiae is currently widely used as a model to study chronological aging of metazoan cells. Chronological aging is typically studied in aerobic stationary phase (SP) cultures, i.e. the final stage of batch cultures in which growth is arrested due to exogenous carbon source exhaustion. Survival of yeast cells in SP defines their chronological lifespan (CLS). S. cerevisiae SP cultures have strongly contributed to the understanding of cellular mechanisms involved in aging and indicated a key role for oxygen. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL90

20 Samples

Download data: CEL

(Submitter supplied) Diurnal temperature cycling is an intrinsic characteristic of many exposed microbial ecosystems. However, its influence on yeast physiology and transcriptome has not been studied in detail. In this study, 24-h sinoidal temperature cycles, oscillating between 12 and 30°C, were imposed on anaerobic, glucose-limited chemostat cultures of Saccharomyces cerevisiae. After three diurnal temperature cycles (DTC), concentrations of glucose, and extracellular metabolites, as well as CO2-production rates showed regular, reproducible circadian rhytms. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL90

17 Samples

Download data: CEL