GEO DataSets

(Submitter supplied) The protein homeostasis (proteostasis) network maintains balanced protein synthesis, folding, transport and degradation within a cell. Because failure to maintain proteostasis is associated with aging and disease, a concerted effort has been placed on studying how the proteostasis network responds to various stresses. Typically, this is accomplished using ectopic overexpression of well-characterized, model misfolded protein substrates; however, how cells tolerate large-scale, diverse burden to the proteostasis network is not understood. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13821

24 Samples

Download data: TXT

(Submitter supplied) These experiments were done to compare the transcriptional response to high temperature of disomic yeast to that of WT yeast.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL11488

20 Samples

Download data: TXT

(Submitter supplied) Life is resilient because living systems are able to respond to elevated temperatures with an ancient gene expression program called the heat shock response (HSR). Our global analysis revealed a modular HSR dependent on the severity of the stress in yeast. Interestingly, at all temperatures analyzed, the transcription of hundreds of genes is upregulated among them the molecular chaperones, which protect proteins from aggregation. more...

Organism:

Schizosaccharomyces pombe; Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL2529

45 Samples

Download data: CEL

(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) Transcriptional profiling of anreuploid yeast strains grown in rich medium YEPD

Organism:

Saccharomyces cerevisiae; Saccharomyces cerevisiae W303

Type:

Expression profiling by array

Platform:

GPL16244

24 Samples

Download data: TXT

(Submitter supplied) Aneuploidy, in which cells carry an abnormal chromosome count, is detrimental during development yet common in human cancers; why cells differ in tolerance remains unclear. We mapped the genetic basis of aneuploidy tolerance in wild Saccharomyces cerevisiae versus the sensitive lab strain to Ssd1, an RNA-binding protein involved in translation whose loss recapitulates aneuploidy signatures in laboratory yeast. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17143 GPL17342

52 Samples

Download data: TXT

(Submitter supplied) Aneuploidy is a condition frequently found in tumor cells but how it affects cellular physiology is not known. We have characterized one aspect of aneuploidy, the gain of extra chromosomes. We created a collection of haploid yeast strains that each bear an extra copy of one or more of almost all of the yeast chromosomes. Their characterization revealed that aneuploid strains share a number of phenotypes, including defects in cell cycle progression, increased glucose uptake and increased sensitivity to conditions interfering with protein synthesis and protein folding. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array; Genome variation profiling by array; Genome variation profiling by genome tiling array

Platforms:

GPL884 GPL2883

112 Samples

Download data: TXT

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

Organism:

Saccharomyces cerevisiae

Type:

Genome variation profiling by genome tiling array

Platforms:

GPL14947 GPL14946

6 Samples

Download data: GPR

(Submitter supplied) Aneuploidy, a state of having uneven numbers of chromosomes, is a form of large-effect mutation able to confer adaptive phenotypes under diverse stress conditions. Here we investigate whether pleiotropic stresses could in turn induce aneuploidy in budding yeast. Radicicol was shown to induce high level missegregation of an artificial chromosome (CF). This experiment examines possible aneuploidy of other (“natural”) chromosomes induced by radicicol.

Organism:

Saccharomyces cerevisiae

Type:

Genome variation profiling by genome tiling array

Platform:

GPL14947

3 Samples

Download data: GPR

(Submitter supplied) Aneuploidy, a state of having uneven numbers of chromosomes, is a form of large-effect mutation able to confer adaptive phenotypes under diverse stress conditions. Here we investigate whether pleiotropic stresses could in turn induce aneuploidy in budding yeast. Cells exposed to radicicol, an Hsp90 inhibitor, exhibit chromosomal instability. To assess the karyotype of cells with an acquired resistance to radicicol, array CGH was used to compare three stably resistant yeast colonies to a WT strain.

Organism:

Saccharomyces cerevisiae

Type:

Genome variation profiling by genome tiling array

Platform:

GPL14946

3 Samples

Download data: GPR

(Submitter supplied) Ribosome biogenesis is a complex and energy-demanding process requiring tight coordination of ribosomal RNA (rRNA) and ribosomal protein (RP) production. Alteration of any step in this process may impact growth by leading to proteotoxic stress. Although the transcription factor Hsf1 has emerged as a central regulator of proteostasis, how its activity is coordinated with ribosome biogenesis is unknown. more...

Organism:

Saccharomyces cerevisiae W303

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL25517

63 Samples

Download data: BW

(Submitter supplied) Aneuploidy causes a proliferative disadvantage in all normal cells analyzed to date, yet this condition is associated with a disease characterized by unabated proliferative potential, cancer. The mechanisms that allow cancer cells to tolerate the adverse effects of aneuploidy are not known. To probe this question, we identified aneuploid yeast strains with improved proliferative abilities. Their molecular characterization revealed strain-specific genetic alterations as well as mutations shared between different aneuploid strains. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array; Genome variation profiling by array

Platforms:

GPL10045 GPL7542

121 Samples

Download data: TXT, ZIP

(Submitter supplied) Cells maintain proteostasis by selectively recognizing and targeting misfolded proteins for degradation. In Saccharomyces cerevisiae, the Hsp70 nucleotide exchange factor Fes1 is essential for the degradation of chaperone-associated misfolded proteins by the ubiquitin-proteasome system. Here we show that the FES1 transcript undergoes unique 3' alternative splicing that results in two equally active isoforms with alternative C-termini, Fes1L and Fes1S. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17342

18 Samples

Download data: TXT

(Submitter supplied) We characterized the mechanisms that allow yeast cells to survive under conditions of thiol peroxidase deficiency. Two thiol peroxidase null yeast (delta8) strains independently acquired a second copy of chromosome XI and increased expression of genes encoded by it. Delta-8 strains were compared to the Wt-M11 strain, which is characterized by duplication of chr-XI.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13821

6 Samples

Download data: TXT

(Submitter supplied) Ribosome profiling and high-throughput sequencing provide unprecedented opportunities for the analysis of mRNA translation. Using this novel method, several studies have demonstrated the widespread role of short upstream reading frames in translational control as well as slower elongation at the beginning of open reading frames in response to stress. Based on the initial studies, the importance of adding or omitting translation inhibitors, such as cycloheximide, was noted as it markedly affected ribosome coverage profiles. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL13821

24 Samples

Download data: TXT

(Submitter supplied) We show that aneuploidy is common in wild isolates of yeast, which are inherently tolerant to chromosome amplification and down-regulate expression at 40% of amplified genes.  To dissect the mechanism of this dosage response, we generated isogenic strain panels in which diploid cells carried either two, three, or four copies of the affected chromosomes.  Using a mixture of linear regression (MLR) model to classify genes, we find that expression is actively down regulated in proportion to increased gene copy at up to 30% of genes. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL17342 GPL13821

60 Samples

Download data: TXT

(Submitter supplied) The response to proteotoxic stresses such as heat shock is an ancient and ubiquitous transcriptional program allowing organisms to maintain protein homeostasis under changing environmental conditions. We depleted or deleted the three stress-specific transcription factors, Hsf1, Msn2 and Msn4, in S. cerevisiae and determined the effects on the transcriptome and proteome. Msn2/4 are responsible for a broad transcriptional reprogramming which includes i. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18085

60 Samples

Download data: TSV, TXT

(Submitter supplied) There are many different types and origins of aneuploidy, but whether there is a uniform cellular response to aneuploidy in human cells has not been addressed so far. To uncover a uniform transcriptional response to aneuploidy we evaluted the transcription profiles of trisomic and tetrasomic cell lines and cell lines with complex aneuploid karyotypes.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL13607 GPL4133

14 Samples

Download data: TXT, XLSX

(Submitter supplied) Extra chromosome copies markedly alter the physiology of eukaryotic cells, but the underlying reasons are not well understood. We created human trisomic and tetrasomic cell lines and determined the quantitative changes in their genome, transcriptome and proteome in comparison to their diploid counterparts.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL13607 GPL4133

18 Samples

Download data: TXT, XLSX

(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