GEO DataSets

(Submitter supplied) Alteration of growth condition or disruption of gene function are commonly used strategies to study cellular systems. Although widely appreciated that such experiments may result in indirect effects, these frequently remain uncharacterized. Here, genome-wide expression reanalysis of functionally unrelated Saccharyomyces cerevisiae deletion strains reveals a common expression signature. One property shared by these strains is slower growth, with increased presence of the signature in more slowly growing strains. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL11232

22 Samples

Download data: TXT

(Submitter supplied) Alteration of growth condition or disruption of gene function are commonly used strategies to study cellular systems. Although widely appreciated that such experiments may result in indirect effects, these frequently remain uncharacterized. Here, genome-wide expression reanalysis of functionally unrelated Saccharyomyces cerevisiae deletion strains reveals a common expression signature. One property shared by these strains is slower growth, with increased presence of the signature in more slowly growing strains. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL11232

12 Samples

Download data: TXT

(Submitter supplied) Alteration of growth condition or disruption of gene function are commonly used strategies to study cellular systems. Although widely appreciated that such experiments may result in indirect effects, these frequently remain uncharacterized. Here, genome-wide expression reanalysis of functionally unrelated Saccharyomyces cerevisiae deletion strains reveals a common expression signature. One property shared by these strains is slower growth, with increased presence of the signature in more slowly growing strains. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL11232

4 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL11232

2633 Samples

Download data: TXT

(Submitter supplied) This dataset consists of 700 responsive mutants (four or more significant mRNA expression changes as a result of the deletion) from a gene expression profile compendium of 1,484 deletion mutants that have a role or are implicated in mRNA transcription regulation, mRNA turnover, signaling or are located in the nucleus.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL11232

1387 Samples

Download data: TXT

(Submitter supplied) This dataset consists of 784 non-responsive mutants (three or less significant mRNA expression changes as a result of the deletion) from a gene expression profile compendium of 1,484 deletion mutants that have a role or are implicated in mRNA transcription regulation, mRNA turnover, signaling or are located in the nucleus.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL11232

1246 Samples

Download data: TXT

(Submitter supplied) We studied the relation between growth rate and genomewide gene expression, cell cycle progression, and glucose metabolism in 36 steady state continuous cultures limited by one of six different nutrients (glucose, ammonium, sulfate, phosphate, uracil or leucine). The expression of more than a quarter of all yeast genes is linearly correlated with growth rate, independently of the limiting nutrient. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL884

36 Samples

Download data: TXT

(Submitter supplied) The yeast Saccharomyces cerevisiae is able to adapt and in situ detoxify lignocellulose derived inhibitors such as furfural and HMF. The length of lag phase for cell growth in response to the inhibitor challenge has been used to measure tolerance of strain performance. Mechanisms of yeast tolerance at the genome level remain unknown. Using systems biology approache, this study investigated comparative transcriptome profiling, metabolic profiling, cell growth response and gene regulatory interactions of yeast strains and selective gene deletion mutations in response to HMF challenges during the lag phase of growth. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL10684

14 Samples

Download data: GPR

(Submitter supplied) 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. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL1535

227 Samples

Download data

(Submitter supplied) 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. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL1535

227 Samples

Download data

(Submitter supplied) The transcription factor Cst6p in Saccharomyces cerevisiae has been reported to play important roles in several biological processes. However, the genome-wide targets of Cst6p and the mechanisms for its physiological functions remain unknown. Here, we mapped the genome-wide binding sites of Cst6p with ChIP-exo at high resolution. Cst6p binds to the promoter regions of 59 genes with various biological functions when cells are grown on ethanol, but hardly binds to the genome on glucose. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19756

4 Samples

Download data: XLSX

(Submitter supplied) Continuous cultures assure the invariability of environmental conditions and the metabolic state of cultured microorganisms, whereas batch-cultured cells undergo constant changes in nutrients availability. For that reason, continuous culture is sometimes employed in the whole transcriptome, whole proteome, or whole metabolome studies. However, the typical method for establishing uniform growth of a cell population, i.e., by limited chemostat, results in the enrichment of the cell population gene pool with mutations adaptive for starvation conditions. more...

Organism:

Saccharomyces cerevisiae; Saccharomyces cerevisiae W303

Type:

Expression profiling by array

Platform:

GPL22543

3 Samples

Download data: TXT, XLSX

(Submitter supplied) Aneuploidy, a condition characterized by whole chromosome gains and losses, is often associated with significant cellular stress and decreased fitness. However, whether and how cells respond to the aneuploid state has remained controversial. In aneuploid budding yeast, two opposing gene expression patterns have been reported: an environmental stress response (ESR) and a “common aneuploidy gene-expression” (CAGE) signature, in which many ESR genes are oppositely regulated. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13821

176 Samples

Download data: FA, GTF, TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platforms:

GPL3244 GPL5031 GPL3245

69 Samples

Download data: SRR, TXT

(Submitter supplied) To study the signals and pathways underlying spore germination we examined the global changes in gene expression during this process. We find that the germination process can be divided into two distinct stages. During the first stage, the induced spores respond only to glucose. The transcription program during this stage recapitulates the general transcription response of yeast cells to glucose. Only during the second phase are the cells able to sense and respond to other nutritional components in the environment. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL5031

38 Samples

Download data: SRR

(Submitter supplied) To study the signals and pathways underlying spore germination we examined the global changes in gene expression during this process. We find that the germination process can be divided into two distinct stages. During the first stage, the induced spores respond only to glucose. The transcription program during this stage recapitulates the general transcription response of yeast cells to glucose. Only during the second phase are the cells able to sense and respond to other nutritional components in the environment. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platforms:

GPL3244 GPL3245

31 Samples

Download data: TXT

(Submitter supplied) Cells must adjust their gene expression in order to compete in a constantly changing environment. Two alternative strategies could in principle ensure optimal coordination of gene expression with physiological requirement. First, the internal physiological state itself could feedback to regulated gene expression. Second, the expected physiological state could be inferred from the external environment, using evolutionary-tuned signaling pathways. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL4567

95 Samples

Download data: XLS

(Submitter supplied) This data file contains all the data used to produce Figure 4 of Saldanha, Brauer and Bostein. The limiting nutrient is indicated by the letter followed by the timecourse number. S= sulfate, P=phosphate, U=uracil, L=leucine. The chemostat comparisons are prefixed by CC. Channels are as noted in the individual arrays, and are consistent for a given timecouse, but may vary between time courses. An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

4 related Platforms

124 Samples

Download data

(Submitter supplied) We are investigating the transcriptional response of yeast to treatment with enediynes or gamma radiation, which generate different extents of double or single strand breaks in DNA. We used microarrays to detail the global programme of gene expression underlying the DNA damage response in yeast Keywords: dose

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Dataset:

GDS2508

Platform:

GPL90

18 Samples

Download data

Analysis of cells exposed to the radiomimetic enediyne antibiotics calicheamicin, esperamicin A1, and neocarzinostatin. These enediynes bind specifically to DNA and generate single- and double-strand DNA breaks. Results provide insight into the response to DNA damage.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array, count, 6 agent sets

Platform:

GPL90

Series:

GSE5301

18 Samples

Download data