GEO DataSets

Analysis of catabolite-derepressed (galactose) wildtype JM43 and isogenic msn2/4 mutant KKY8 cells shifted to short-term anaerobiosis (2 generations). Msn2 and 4 are key stress factors. Results suggest Msn2/4 involvement in metabolic remodeling during acclimatization to short-term anaerobiosis.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array, log2 ratio, 2 genotype/variation, 2 protocol, 5 time sets

Platform:

GPL1535

Series:

GSE1879

30 Samples

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(Submitter supplied) 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

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Datasets:

GDS2002 GDS2003

Platform:

GPL1535

45 Samples

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Analysis of catabolite-repressed (glucose) or derepressed (galactose) wildtype JM43 cells shifted from aerobiosis to anaerobiosis (2 generations). Results identify metabolic remodeling that occurs during acclimatization to short-term anaerobiosis in galactose but not in glucose.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array, log2 ratio, 2 growth protocol, 2 protocol, 5 time sets

Platform:

GPL1535

Series:

GSE1879

30 Samples

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(Submitter supplied) 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. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL1535

74 Samples

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(Submitter supplied) 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. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL1535

75 Samples

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(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

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(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

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(Submitter supplied) Two time courses after pulses of 0.2 g/l and 2 g/l glucose on cells growing in chemostat with galactose as the carbon source. The reference is sample from the chemostat at time 0. Groups of assays that are related as part of a time series. Keywords: time_series_design

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Dataset:

GDS1752

Platform:

GPL3415

26 Samples

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Analysis of steady state cultures growing on galactose following a pulse of 0.2 or 2 grams of glucose per liter. Gene expression examined at various time points up to 4 hours after glucose addition. Results provide insight into the dynamics of the transcriptional response to changing environments.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array, log2 ratio, 2 dose, 18 time sets

Platform:

GPL3415

Series:

GSE4158

26 Samples

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(Submitter supplied) Expression microarray experiments were performed to identify all of the aerobic and hypoxic transcripts in wild-type cells. The role of Hap1 in the regulation of transcription was examined by monitoring gene expression in hap1 deletion cells. Keywords: gene expression, strain comparison, response to hypoxic conditions

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL4625

6 Samples

Download data: GPR

(Submitter supplied) Abf1 and Reb1, two general regulatory factors playing roles at promoters and other genome functional sites in budding yeast, were mapped genome-wide by ChIP-sequencing using strains expressing TAP-tagged versions of the proteins. As expected on the basis of previous in silico analysis of promoter regions, we found that these factors are enriched at the promoters of ribosome biogenesis (Ribi) genes, a large regulon of more than 200 genes required for ribosome biosynthesis and assembly, and known to be coordinately regulated in response to nutrient availability and cellular growth rate.

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17342

4 Samples

Download data: BED

(Submitter supplied) The FAR1 gene encodes a large protein, whose major function is inhibition of cyclin-dependent kinase complexes involved in the G1/S transition. It has been proposed that Far1, together with the G1 cyclin Cln3, may be part of a cell sizer mechanism that controls the entry into S phase. A genome-wide transcriptional analysis of FAR1-overexpressing and far1 deleted cells grown in ethanol- or glucose-supplemented minimal media indicates that FAR1 overexpression induces strong transcriptional remodelling, metabolism being the most affected cellular property. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL90

18 Samples

Download data: CEL

(Submitter supplied) We used RNA-seq to monitor mRNA levels of all genes in response to hypoxia of wild-type yeast, S. cerevisiae (strain yMH914 with wildtype HAP1). To gain insights into how gene expression changes over time, cells were subjected to 100% nitrogen gas and collected after 0,5,10,30,60,120,180, and 240 minutes. Total RNA was extracted and mRNAs were enriched by polyA selection. The cDNA was prepared into a sequencing library, multiplexed and single-end sequenced by an Illumina HiSeq 2500 sequencer. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17342

24 Samples

Download data: TAB

(Submitter supplied) Analysis of the transcriptome of the wild-type strain BY4741 and its isogenic derivative ixr1 null, grown in aerobic, hypoxic conditions and after a hypoxic shift

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL13727

12 Samples

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(Submitter supplied) The yeast PP2A-Cdc55 Serine/Threonine phosphatase regulates transcription under certain conditions. It is required for full activation of the environmental stress response mediated by the transcription factors Msn2 and Msn4. PP2A-Cdc55 contributes to sustained nuclear accumulation of Msn2 and Msn4 and extended chromatin recruitment under stress conditions such as hyperosmolarity stress. Transcript profiles of Msn2 and Msn4 double mutants are similar to cdc55 and the corresponding triple mutants. more...

Organism:

Saccharomyces cerevisiae W303; Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL16244

8 Samples

Download data: TXT

(Submitter supplied) The yeast PP2A-Cdc55 Serine/Threonine phosphatase regulates transcription under certain conditions. It is required for full activation of the environmental stress response mediated by the transcription factors Msn2 and Msn4. PP2A-Cdc55 contributes to sustained nuclear accumulation of Msn2 and Msn4 and extended chromatin recruitment under stress conditions such as hyperosmolarity stress. Transcript profiles of Msn2 and Msn4 double mutants are similar to cdc55 and the corresponding triple mutants. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL9825

16 Samples

Download data: TXT

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

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array; Other

Platforms:

GPL7662 GPL8546

60 Samples

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(Submitter supplied) In this study, we systematically identified RNAs associated with ribosomes. To identify ribosome associated RNAs, C-terminal ZZ-tagged Rpl16a or Rpl16b, expressed under control of thier native promoter, were affinity purified from whole cell extracts of cultures grown to mid-log phase in minimal medium. Extracts were incubated with immunoglobulin G (IgG) coupled microbeads, washed, and ribosomes were eluted by tobacco etch virus (TEV) protease treatment. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL8546

8 Samples

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(Submitter supplied) In this study, we systematically identified ribosome associated RNAs. To identify ribosome associated RNAs, C-terminal ZZ-tagged Rpl16a, expressed under control of its native promoter, was affinity purified from whole cell extracts of cultures grown to mid-log phase. Extracts were incubated with immunoglobulin G (IgG) coupled microbeads, washed, and ribosomes were eluted by tobacco etch virus (TEV) protease treatment. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array; Other

Platform:

GPL7662

52 Samples

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(Submitter supplied) Biological processes are usually associated with genome-wide remodeling of transcription driven by transcription factors (TFs). Identifying key TFs and their spatiotemporal binding patterns are indispensable to understanding how dynamic processes are programmed. We present a computational method, dynamic motif occupancy (DynaMO), which exploits random forest modeling and clustering based enrichment analysis. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17342

30 Samples

Download data: FPKM_TRACKING, TXT