GEO DataSets

(Submitter supplied) Transcriptional profiling of four different yeast FZF1 alleles: S. cerevisiae, S. paradoxus and two reciprocal chimeras with the coding and 5' noncoding region from opposite species of S. cerevisiae and S. paradoxus, both before and 15 minutes after sulfite addition. FZF1 is a transcription factor that is known to be turned on in response to sulfite. Here we determine whether the FZF1 allele from two species leads to different transcriptional responses and the effect of the individual noncoding and coding regions on the transcriptional response.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL9825

24 Samples

Download data: GPR

(Submitter supplied) Transcriptional profiling of Candida albicans cells comparing control untreated C. albicans cells with sulfite-treated C. albicans cells. Sulfite is a toxic molecule that C. albicans encounters in its human host. Both wild type and ∆zcf2 mutant cells were used. The goal was to determine the effects of sulfite on C. albicans gene expression, and to determine which of the genes areZcf2-depedent.

Organism:

Candida albicans

Type:

Expression profiling by array

Platform:

GPL16243

8 Samples

Download data: TXT

(Submitter supplied) Determining the different sources of heritable variation underlying quantitative traits in nature is currently at the forefront of genetic studies. To this end, molecular profiling studies in S. cerevisiae have shown that individual gene expression levels are subject to genetic control and this variation can mediate genetic differences on phenotype. Thus, determining how natural variation influences allele specific expression (ASE) and ultimately complex traits represents a useful tool to determine the mechanisms leading to yeast niche adaptation. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13821

18 Samples

Download data: TXT

(Submitter supplied) A fundamental problem in biology is the molecular basis for divergence among related organisms. We have investigated the level of divergence of transcription factor binding sites for two key factors that regulate developmental processes in the budding yeasts. The genomic binding locations for the Ste12 and Tec1 transcription factors in S. cerevisiae, S. mikatae and S. bayanus were mapped by chromatin immunoprecipitation combined with microarrays (chIP chip)1, 2 and compared to one another. more...

Organism:

Candida albicans; Saccharomyces mikatae; Saccharomyces bayanus; Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

4 related Platforms

27 Samples

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

Organism:

Saccharomyces cerevisiae

Type:

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

Platforms:

GPL9134 GPL9825

222 Samples

Download data: TXT

(Submitter supplied) In this study, we mapped for the first time differences in transcription binding among individuals and elucidated the genetic basis of such variation. Whole-genome Ste12 binding profiles were determined using ChIP-Seq in pheromone-treated cells of 43 segregants of a cross between two highly diverged yeast strains, YJM789 and S288c as well as the parental lines. We identified extensive Ste12 binding variation among individuals and mapped underlying cis- and trans- acting loci responsible for such variation. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9134

174 Samples

Download data: TXT

(Submitter supplied) In this study, we mapped for the first time differences in transcription binding among individuals and elucidated the genetic basis of such variation. Whole-genome Ste12 binding profiles were determined using ChIP-Seq in pheromone-treated cells of 43 segregants of a cross between two highly diverged yeast strains, YJM789 and S288c, as well as the parental lines. We identified extensive Ste12 binding variation among individuals and mapped underlying cis- and trans- acting loci responsible for such variation. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL9825

48 Samples

Download data: TXT

(Submitter supplied) In this study, we constructed three isogenic strains of S96 yrr1Δ background (its native YRR1 gene was knocked out) carrying three different YRR1 alleles, YRR1_S96, YRR1_YJM789, YRR1_S96-I775E, respectively. We then conducted chromatin immuno-precipitation followed by high-throughput sequencing (ChIP-Seq) for Yrr1 protein on the three strains grown in Yeast Peptone Dextrose medium (YPD) and YPD + 4NQO.

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13821

24 Samples

Download data: XLSX

(Submitter supplied) In this study, we constructed three isogenic strains of S96 yrr1Δ background (its native YRR1 gene was knocked out) carrying three different YRR1 alleles, YRR1_S96, YRR1_YJM789 and YRR1_S96-I775E, respectively. We then conducted RNA deep sequencing (RNA-Seq) on the three strains grown in Yeast Peptone Dextrose medium (YPD), YPD + 4NQO and Yeast Peptone glycerol medium (YPglycerol).

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17143

18 Samples

Download data: XLSX

(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) Microarray analysis was used to identify all cryptic promoters in the S. cerevisiae genome that are activated in spt6 and spt16 mutants. These experiments showed that cryptic initiation is widespread, occurring in approximately 1,000 genes.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL7078

6 Samples

Download data: GPR

(Submitter supplied) We measured mRNA levels of two yeast species (S.cerevisiae and S.paradoxus) and their hybrid, at four time-points (0, 20min, 40min, 60min) following transcription arrest using 1,10-Phenantroline (150ug/ml). This data was used to infer mRNA degradation rates of orthologous genes, study the divergence of mRNA degradation rates and the contribution of cis and trans mutations.

Organism:

Saccharomyces cerevisiae; Saccharomyces paradoxus; Saccharomyces cerevisiae x Saccharomyces paradoxus

Type:

Expression profiling by array

Platform:

GPL13449

16 Samples

Download data: TXT

(Submitter supplied) Genome wide interaction of mediator Keywords: Genome wide interaction of mediator

Organism:

Schizosaccharomyces pombe

Type:

Expression profiling by array; Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL2789 GPL2795 GPL3592

36 Samples

Download data

(Submitter supplied) DNA variants that alter gene expression contribute to variation in many phenotypic traits. In particular, trans-acting variants, which are often located on different chromosomes from the genes they affect, are an important source of heritable gene expression variation. However, our knowledge about the identity and mechanism of causal trans-acting variants remains limited. Here, we developed a fine-mapping strategy called CRISPR-Swap and dissected three expression quantitative trait locus (eQTL) hotspots known to alter the expression of multiple genes in trans in the yeast Saccharomyces cerevisiae. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26302

25 Samples

Download data: TXT

(Submitter supplied) We describe the genome-wide nucleosome profiles for S. bayanus under standard conditions

Organism:

Saccharomyces bayanus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL10782

1 Sample

Download data: WIG

(Submitter supplied) Genome-scale datasets have been used extensively in model organisms to screen for specific candidates or to predict functions for uncharacterized genes. However, despite the availability of extensive knowledge in model organisms, the planning of genome-scale experiments in poorly studied species is still based on the intuition of experts or heuristic trials. We propose that computational and systematic approaches can be applied to drive the experiment planning process in poorly studied species based on available data and knowledge in closely related model organisms. more...

Organism:

Saccharomyces cerevisiae; Saccharomyces bayanus

Type:

Expression profiling by array

7 related Platforms

343 Samples

Download data: GPR

(Submitter supplied) The abf1-1 mutant and wild type cells were grown at 30 degrees C in YPAD until OD600 reached 1.0-1.2. The same volume of 42 degrees C preheated YPAD was added for each flask. After 45 min incubation at 36 degrees C, cells were harvested and RNA was isolated. Four repeats of microarray results are in this series. Keywords: repeat sample

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL1300

4 Samples

Download data

(Submitter supplied) We compared the genome-wide expression profiles of two yeast species (S. cerevisiae and S. paradoxus) using a two-species microarray that contain species-specific probes and can thus measure the expression levels of the two species simultaneosly. In Addition, we used the array to measure expression levels of the interspecific hybrid of these yeast species, while discriminating between the alleles that correspond to the two parental species. more...

Organism:

Saccharomyces cerevisiae x Saccharomyces paradoxus; Saccharomyces paradoxus; Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL8157

20 Samples

Download data: ZIP

(Submitter supplied) Comparative-genomic studies have reported widespread variation in levels of gene expression within and between species. In the vast majority of cases, the phenotypic and evolutionary relevance of regulatory change is unknown. We haveu sed a wild Malaysian population of S. cerevisiae as a testbed in the search to identify organismal correlates of regulatory variation. Malaysian yeast, when cultured in standard medium, activated regulatory programs that protect cells from the toxic effects of high iron.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL13821 GPL9377

8 Samples

Download data: TXT

(Submitter supplied) Coordinated ribosomal protein (RP) gene expression is crucial for cellular viability, but the transcriptional network controlling this regulon has only been well characterized in the yeast Saccharomyces cerevisiae. We have used whole-genome transcriptional and location profiling to establish that, in Candida albicans, the RP regulon is controlled by the Myb-domain protein Tbf1 working in conjunction with Cbf1. more...

Organism:

Candida albicans

Type:

Expression profiling by array; Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL6475 GPL6474

16 Samples

Download data: TXT