GEO DataSets

(Submitter supplied) Aneuploidy has a myriad of consequences for health and disease, yet models of aneuploidy toxicity are still widely debated. To distinguish the effects of specific genes from the generalized burden of chromosome amplification, we measured the effects of duplicating individual genes in euploid cells as well as in select aneuploids using a barcoded plasmid library. We analyzed the responses of cells with and without extra chromosomes, as well as those with and without RNA-binding protein Ssd1. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL21656

83 Samples

Download data: CSV

(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:

GPL13821 GPL17342

60 Samples

Download data: TXT

(Submitter supplied) Alteration of normal ploidy (aneuploidy) is an important mechanism of evolution of species. It has been linked to a rapid response to stress and is regarded as a hallmark of cancer. While increased genomic instability of aneuploid cells can accelerate genetic diversification and facilitate adaptation, these cells also face the adverse effects of gene imbalance, resulting in fitness cost. Here, to understand the mechanisms through which cells respond to aneuploidy and develop tolerance leading to fitness restoration, we subjected disomic (i.e. more...

Organism:

Saccharomyces cerevisiae W303

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25517

45 Samples

Download data: TSV

(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) Background. Most methods for constructing aneuploid yeast strains that have gained a specific chromosome rely on spontaneous failures of cell division fidelity. In Saccharomyces cerevisiae, extra chromosomes can be obtained when errors in meiosis or mitosis lead to nondisjunction, or when nuclear breakdown occurs in heterokaryons. We describe a strategy for constructing N+1 disomes that does not require such spontaneous failures. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome variation profiling by array

Platform:

GPL6273

24 Samples

Download data: DAT

(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 hallmark of tumor cells, and yet the precise relationship between aneuploidy and a cell’s proliferative ability, or cellular fitness, has remained elusive. In this study, we have combined a detailed analysis of aneuploid clones isolated from laboratory-evolved populations of Saccharomyces cerevisiae with a systematic, genome-wide screen for the fitness effects of telomeric amplifications to address the relationship between aneuploidy and cellular fitness. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome variation profiling by array

Platforms:

GPL4131 GPL10045

64 Samples

Download data: TXT

(Submitter supplied) Purpose: Monitor modulation of aneuploidy in Leishmania donovani during adaptation to different in vitro and in vivo environments, and its impact on gene expression Importance: Aneuploidy is usually detrimental in multicellular organisms, but in several micro-organisms (fungi being the best-studied) it can be tolerated and even beneficial. Leishmania – a protozoan parasite killing more than 30,000 persons each year – is emerging as a new model for aneuploidy studies: unexpectedly high levels of aneuploidy are found in clinical isolates. more...

Organism:

Leishmania donovani

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23261

11 Samples

Download data: TXT

(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) 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) Analysis of copy number variation in evolved haploid, diploid, tetraploid strains.

Organism:

Saccharomyces cerevisiae

Type:

Genome variation profiling by genome tiling array

Platform:

GPL4131

67 Samples

Download data: 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) 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) 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) Aneuploidy has profound effects on an organism, typically more so than polyploidy, and the basis of this contrast is not fully understood. A dosage series of maize chromosome arm 1L was used to compare relative global gene expression in different types and degrees of aneuploidy to gain insight into how the magnitude of genomic imbalance as well as hypoploidy affect global gene expression. While previously available methods required a selective examination of specific genes, RNA sequencing provides a whole-genome view of gene expression in aneuploids. more...

Organism:

Zea mays

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL17628 GPL20156

29 Samples

Download data: TXT, XLSX

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

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL17342

15 Samples

Download data

(Submitter supplied) In response to acute loss of the Ulp2 SUMO-specific protease, yeast become disomic for chromosome I (ChrI) and ChrXII. Here we report that ChrI disomy, which creates an adaptive advantage in part by increasing the dosage of the Ccr4 deadenylase, was eliminated by extended passaging. Loss of aneuploidy is often accompanied by mutations in essential SUMO-ligating enzymes, which reduced polySUMO-conjugate accumulation. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL17342

3 Samples

Download data: TXT

(Submitter supplied) In response to acute loss of the Ulp2 SUMO-specific protease, yeast become disomic for chromosome I (ChrI) and ChrXII. Here we report that ChrI disomy, which creates an adaptive advantage in part by increasing the dosage of the Ccr4 deadenylase, was eliminated by extended passaging. Loss of aneuploidy is often accompanied by mutations in essential SUMO-ligating enzymes, which reduced polySUMO-conjugate accumulation. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17342

12 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:

GPL14946 GPL14947

6 Samples

Download data: GPR