GEO DataSets

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

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL17342

135 Samples

Download data: TXT

(Submitter supplied) Genetic variation that underlies phenotypic differences provides the material on which evolutionary selection acts. Gene duplication/amplification is one type of genetic variation that can allow an organism to rapidly respond to environmental changes by increasing gene dosage. While the potential benefits afforded by gene amplification during evolution are well known, there is also a significant fitness cost to increasing gene dosage including resource shortages and burdening cellular systems. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL17342

90 Samples

Download data: TXT

(Submitter supplied) We used RNA-Seq to measure transcript abundance in 15 Saccharomyces cerevisiae strains from a diverse range of genetic lineages when growing in rich media (YPD) to characterize differential expression across strains.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17342

45 Samples

Download data: TXT

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

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL17342 GPL21656

59 Samples

Download data

(Submitter supplied) Free-living cells live in fluctuating environments and must be able to respond rapidly in order to survive. Genetic background can influence how an individual responds to a changing environment, including stressful changes. Changes in gene copy number can influence stress tolerance and responses, presumably due to corresponding changes in gene expression. However, we recently showed that strains vary in their ability to tolerate gene copy number differences; how this influences variation in stress tolerance is relatively unknown. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL21656

24 Samples

Download data: TXT

(Submitter supplied) We used RNA-Seq to measure transcript abundance in 4 Saccharomyces cerevisiae strains (BY4743, BC187, NCYC3290, and YPS128) from a diverse range of genetic lineages when growing in rich media (YPD) with 0.7M NaCl to characterize differential expression across strains in response to osmotic and ionic stress.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17342

35 Samples

Download data: TXT

(Submitter supplied) Evolutionary outcomes depend not only on the selective forces acting upon a species, but also on the genetic background. However, large timescales and uncertain historical selection pressures can make it difficult to discern such important background differences between species. Experimental evolution is one tool to compare evolutionary potential of known genotypes in a controlled environment. Here we utilized a highly reproducible evolutionary adaptation in Saccharomyces cerevisiae to investigate whether experimental evolution of other yeast species would select for similar adaptive mutations. more...

Organism:

Saccharomyces cerevisiae; Saccharomyces bayanus

Type:

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

6 related Platforms

52 Samples

Download data: GPR, TXT

(Submitter supplied) The environmental stresses and inhibitors encounted by Saccharomyces cerevisiae strains are main limiting factors in bioethanol fermentation. Investigation of the molecular mechanisms underlying the stresses-related phenotypes diversities within and between S. cerevisiae populations could guide the construction of yeast strains with improved stresses tolerance and fermentation performances. Here, we explored the genetic characteristics of the bioethanol S. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome variation profiling by genome tiling array

Platform:

GPL7699

2 Samples

Download data: PAIR

(Submitter supplied) We report the application of single-molecule-based sequencing technology for transcription profile analysis of S. cerevisiae strains with different genetic background. By combining the whole genome sequence of these strains, we sought to explore the effects of genome mutations on the transcription diversities.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13821

3 Samples

Download data: RPKM

(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) Variation in gene expression arises from cis- and trans-regulatory mutations, which contribute differentially to expression divergence. Here, we compare the impacts on gene expression and fitness for cis- and trans-regulatory mutations affecting expression of the TDH3 gene in Saccharomyces cerevisiae. We use the effects of cis-regulatory mutations to isolate effects of trans-regulatory mutations caused by impacts on TDH3 from pleiotropic impacts on other genes, providing a rare distribution of pleiotropic effects. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21656

188 Samples

Download data: SF, TXT

(Submitter supplied) Microarray karyotyping (aCGH) of three independent isolates each of four different commerical wine yeast strains was performed. Duplicate arrays (labeled "A" and "B") were performed for each isolate. An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract. Keywords: all_pairs

Organism:

Saccharomyces cerevisiae

Type:

Genome variation profiling by array

Platforms:

GPL2634 GPL2633

24 Samples

Download data

(Submitter supplied) Adaptive evolution is generally assumed to progress through the accumulation of beneficial mutations. However, deleterious mutations may also have an important role by promoting adaptive genetic changes that are otherwise inaccessible. Here we study the capacity of the baker’s yeast genome to compensate the complete loss of genes during evolution, and explore the long-term consequences of this process. more...

Organism:

Saccharomyces cerevisiae BY4741; Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL11232

34 Samples

Download data: TXT

(Submitter supplied) Each strain was grown overnight then diluted in fresh rich media. After three hours strains were again rediluted into either rich media or rich media supplemented with copper sulfate. After another three hours cultures were sampled, cells lysed and flash frozen using liquid nitrogen. RNA was extrated using hot phenol-chloroform, reverse transcripbed using amino-allyle dUTP and labelled with either Cy3 or Cy5 flourescent dye. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL1007

60 Samples

Download data: JPG, TIFF

(Submitter supplied) In a previous study, we identified extensive natural variation in the response to acute ethanol treatment in three yeast strains: a lab strain derived from the commonly used S288c (DBY8268), vineyard isolate M22, and oak soil strain YPS163. Many expression differences persisted across several modules of co-regulated genes, implicating trans-acting systemic differences in ethanol sensing and/or response. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL13254

196 Samples

Download data: FTR, PAIR

(Submitter supplied) We created a multi-species microarray platform, containing probes to the whole genomes of seven different Saccharomyces species, with very dense coverage (one probe every ~500 bp) of the S. cerevisiae genome, including non-S288c regions, mitochondrial and 2 micron circle genomes, plus probes at fairly dense coverage (one probe every ~2,100 bp) for each of the genomes of six other Saccharomyces species: S. more...

Organism:

Saccharomyces cerevisiae; Saccharomyces bayanus

Type:

Genome variation profiling by array

Platform:

GPL11575

98 Samples

Download data: TXT

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

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array; Genome variation profiling by array

Platform:

GPL5915

69 Samples

Download data: GPR

(Submitter supplied) Gene expression variation was measured in 17 non-laboratory strains compared to the sequenced S288c lab strain Keywords: Gene expression comparisons in different yeast strains

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL5915

54 Samples

Download data: GPR

(Submitter supplied) Gene expression variation was measured in 17 non-laboratory strains compared to the sequenced S288c lab strain Keywords: comparative genomic hybridizations (CGH) comparing different yeast strains

Organism:

Saccharomyces cerevisiae

Type:

Genome variation profiling by array

Platform:

GPL5915

15 Samples

Download data: GPR

(Submitter supplied) We report the application of next-generation sequencing technology for transcription profile analysis of S. cerevisiae strains with different genetic background. By combining the whole genome sequence of these strains, we sought to explore the effects of genome mutations on the transcription diversities.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13821

2 Samples

Download data: TXT