GEO DataSets

(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) 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) An S288c-derived lab strain of Saccharomyces cerevisiae has lower ethanol resistance than either the vineyard strain M22 or the oak strain YPS163. We performed a 60 minute time-course experiment in the presence of 5% ethanol and compared the transcriptional response to ethanol between strains. We additionally analyzed the time-point of maximal response (30 min.) in wild type cells, YPS163 msn2D, and YPS163 hap1D cells.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL5915

36 Samples

Download data: GPR

(Submitter supplied) Organisms frequently experience environmental stresses that occur in predictable patterns and combinations. For wild Saccharomyces cerevisiae yeast growing in natural environments, cells may experience high osmotic stress when they first enter broken fruit, followed by high ethanol levels during fermentation, and then finally high levels of oxidative stress resulting from respiration of ethanol. Yeast have adapted to these patterns by evolving sophisticated “cross protection” mechanisms, where mild ‘primary’ doses of one stress can enhance tolerance to severe doses of a different ‘secondary’ stress. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21656

119 Samples

Download data: TXT, XLSX

(Submitter supplied) A six array study using total gDNA recovered from two separate cultures of each of three different strains of Saccharomyces cerevisiae (YB-210 or CRB, Y389 or MUSH, and Y2209 or LEP) and two separate cultures of Saccharomyces cerevisiae DBY8268. Each array measures the hybridization of probes tiled across the Saccharomyces cerevisiae genome.

Organism:

Saccharomyces cerevisiae

Type:

Genome variation profiling by array

Platform:

GPL15778

6 Samples

Download data: FTR

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

Organism:

Escherichia coli; Saccharomyces cerevisiae

Type:

Other

Platforms:

GPL18133 GPL17342

38 Samples

Download data: TXT

(Submitter supplied) Sequence variation in regulatory DNA alters gene expression and shapes genetically complex traits. However, the identification of individual, causal regulatory variants is challenging. Here, we used a massively parallel reporter assay to measure the cis-regulatory consequences of 5,832 natural DNA variants in the promoters of 2,503 genes in the yeast Saccharomyces cerevisiae. We identified 451 causal variants, which underlie genetic loci known to affect gene expression. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL17342

36 Samples

Download data: TXT

(Submitter supplied) Sequence variation in regulatory DNA alters gene expression and shapes genetically complex traits. However, the identification of individual, causal regulatory variants is challenging. Here, we used a massively parallel reporter assay to measure the cis-regulatory consequences of 5,832 natural DNA variants in the promoters of 2,503 genes in the yeast Saccharomyces cerevisiae. We identified 451 causal variants, which underlie genetic loci known to affect gene expression. more...

Organism:

Escherichia coli

Type:

Other

Platform:

GPL18133

2 Samples

Download data: TXT

(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) Expression analysis of BY4716(isogenic to S288c) and a wild isolate collected by R. Mortimer. Each strain was grown in culture 6 independent times and RNA from each culture was isolated. Each of these RNA samples was subjected to a dye-swap pair of arrays (except the "RM11" sample, which only got one array). All arrays used the same pool of reference BY4716 sample. In sample titles, "BY" alone signifies the reference sample and all other strings represent independent cultures. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Datasets:

GDS93 GDS94

Platform:

GPL118

23 Samples

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(Submitter supplied) Expression analysis of F1 haploid segregants from a cross between BY4716 (isogenic to S288c) and a wild isolate collected by R. Mortimer. Each segregant sample was subjected to a dye-swap pair of arrays. All arrays used the same pool of reference BY4716 sample. In sample titles, "BY" alone signifies the reference sample and all other strings represent segregants. All sample titles are of the form S1-S2. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Datasets:

GDS91 GDS92

Platform:

GPL118

80 Samples

Download data

Genetic linkage analysis of global expression levels in a cross between two budding yeast strains. Identification of cis-acting and trans-acting loci that modulate a total of 570 genes.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array, log ratio, 2 strain sets

Platform:

GPL118

Series:

GSE38

11 Samples

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Genetic linkage analysis of global expression levels in a cross between two budding yeast strains. Identification of cis-acting and trans-acting loci that modulate a total of 570 genes.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array, log ratio, 2 strain sets

Platform:

GPL118

Series:

GSE38

12 Samples

Download data

Genetic linkage analysis of global expression levels in a cross between two budding yeast strains. Identification of cis-acting and trans-acting loci that modulate a total of 570 genes.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array, log ratio, 7 other sets

Platform:

GPL118

Series:

GSE37

40 Samples

Download data

Genetic linkage analysis of global expression levels in a cross between two budding yeast strains. Identification of cis-acting and trans-acting loci that modulate a total of 570 genes.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array, log ratio, 7 other sets

Platform:

GPL118

Series:

GSE37

40 Samples

Download data

(Submitter supplied) This study is a quantitative trait linkage mapping study targeted at gene-environment interaction. A family of yeast derived from BY4716 and RM11-1a was grown in two carbon sources (glucose and ethanol) and expression profiled. The analysis revealed how the influence of genetic factors changes in different conditions. Abstract: The effects of genetic variants on phenotypic traits often depend on environmental and physiological conditions, but such gene–environment interactions are poorly understood. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platforms:

GPL2883 GPL884

246 Samples

Download data: TXT

(Submitter supplied) A quantitative genetic analysis of the yeast replicative life span was carried out by sampling the natural genetic variation

Organism:

Saccharomyces cerevisiae

Type:

Genome variation profiling by array

Platform:

GPL90

39 Samples

Download data: CEL, TXT