Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

69 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

EQTL Mapping of the Yeast Ethanol Response

ABSTRACT: 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. To understand the genetic basis for these expression differences, we performed eQTL mapping analysis of the response to acute ethanol stress in ~100 F2 strains from two crosses: DBY8268x M22 and DBY8268 x YPS163. We measured the gene expression response to acute ethanol stress (5% for 30 min) in 6 replicates for the parental strains, and in biological duplicate for the eQTL mapping population. Dye swaps were performed in the replicates to control for dye-specific effects.

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Jeffrey Lewis

PROVIDER: E-GEOD-54196 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Genetic architecture of ethanol-responsive transcriptome variation in Saccharomyces cerevisiae strains.

Lewis Jeffrey A JA Broman Aimee T AT Will Jessica J Gasch Audrey P AP

Genetics 20140626 1

Natural variation in gene expression is pervasive within and between species, and it likely explains a significant fraction of phenotypic variation between individuals. Phenotypic variation in acute systemic responses can also be leveraged to reveal physiological differences in how individuals perceive and respond to environmental perturbations. We previously found extensive variation in the transcriptomic response to acute ethanol exposure in two wild isolates and a common laboratory strain of ...[more]

PMID: 24970865

Similar Datasets

Comparison of the transcriptional response to ethanol in laboratory and wild yeast strains

Project description: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. The genomic expression response to 5% ethanol stress was measured in 3 different strain backgrounds, and 2 different mutant backgrounds. Basal gene expression was also compared in two non-lab strains to the S288c reference. A single replicate was performed for the time-course experiment. All of the single time-point experiments were performed using biological triplicates.

2010-12-17 | E-GEOD-22904 | biostudies-arrayexpress

Natural variation in the yeast glucose-signaling network reveals a new role for the Mig3p transcription factor

Project description:The Crabtree effect, in which fermentative metabolism is preferred at the expense of respiration, is a hallmark of budding yeast’s glucose response and a model for the Warburg effect in human tumors. While the glucose-responsive transcriptional repressors Mig1p and Mig2p play well-characterized roles in the Crabtree effect, little function for the related Mig3p transcription factor has been uncovered despite numerous investigations of laboratory yeast strains. Here we studied a wild isolate of Saccharomyces cerevisiae to uncover a critical role for Mig3p that has been lost in S288c-derived laboratory strains. We found that Mig3p affects the expression of hundreds of glucose-responsive genes in the oak strain YPS163, both during growth under standard conditions and upon ethanol treatment. Our results suggest that Mig3p may act as a multifunctional activator/repressor that plays separate roles under standard versus stress conditions, but this function has been largely lost in the lab strains. Population analysis suggests that the lab strain, and several wild strains, harbor mutations that diminish Mig3p function. Thus, by expanding our attention to multiple genetic backgrounds, we have uncovered an important missing link in a key metabolic response. We performed a series of microarray experiments comparing the gene expression response of unstressed or EtOH stressed wild-type or mig3∆ strains in either the BY4741 or YPS163 background (biological triplicates). We also compared gene expression for in reciprocal hemizygous strains (YPS163/BY4741mig3∆ and YPS163mig3∆/BY4742; biological duplicates). Lastly, we measured the gene expression of BY4741 over-expressing BY_MIG3 via galactose induction (biological triplicates).

2012-11-01 | E-GEOD-40153 | biostudies-arrayexpress

eQTL Mapping of the Yeast Ethanol Response

Project description: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. To understand the genetic basis for these expression differences, we performed eQTL mapping analysis of the response to acute ethanol stress in ~100 F2 strains from two crosses: DBY8268x M22 and DBY8268 x YPS163.

2014-10-02 | GSE54196 | GEO

Multiple means to the same end: The genetic basis of acquired stress resistance in yeast

Project description:A series of experiments comparing the gene expression response before and after 30 min 0.7M NaCl exposure in WT and mutant yeast strains. Mutant strains were identified as having a defect in acquiring resistance to H2O2 following mild NaCl pretreatment. The mutants in this study were taken from the Yeast Knock-Out Collection, mat a. Unstressed cells vs cells exposed to 0.7M NaCl for 30 min; 5 replicates for WT, 3 replicates for hog1∆, msn2∆, mck1∆, pde2∆, rim101∆, and 2 replicates for the remaining mutants.

2014-03-06 | E-GEOD-27819 | biostudies-arrayexpress

Transient Genotype-by-Environment Interactions in the Yeast Genomic Expression Response to Heat Shock

Project description:Microarray time courses followed the response of 5 yeast strains to heat shock. Expression variation due to genetic, environmental, and genotype-by-environment interactions were identified. Keywords: Timecourse and single timepoint expression studies of stress response in yeast The genomic expression response to heat shock was measured in 5 different yeast strains over the course of 2 hours. Basal expression at 25C was also compared in 4 non-lab strains to the S288c refernce. All experiments were done in duplicate, for a total of 68 Samples.

2010-05-18 | E-GEOD-15147 | biostudies-arrayexpress

An integrated model of stress-dependent gene expression in yeast

Project description:Microarray timecourses followed the gene expression response of Saccharomyces cereviciae to osmotic shock, over 4 hours. Data was compared to timecourses of quantitative proteomic data to understand the dynamic relationship between RNA and protein The dynamic genomic expression response to osmotic shock (0.7M NaCl) was measured in Saccharomyces cereviciae, over the course of 4 hours in biological triplicate. Six timepoints were taken for each time course, for a total of 18 tiled-genomic Nimblegen arrays against the S288c yeast genome.

2011-08-17 | E-GEOD-23798 | biostudies-arrayexpress

Variations in stress sensitivity and genomic expression in diverse S. cerevisiae strains (gene expression)

Project description: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 Each strain was grown in at least biological triplicate to log phase in rich (YPD) medium. Extracted total RNA was compared to that collected from the diploid S288C strain, DBY8268 (ura3-52/ura3-delta, ho/ho, GAL2/GAL2)

2010-06-19 | E-GEOD-10268 | biostudies-arrayexpress

Variations in stress sensitivity and genomic expression in diverse S. cerevisiae strains

Project description:This SuperSeries is composed of the following subset Series: GSE10267: Variations in stress sensitivity and genomic expression in diverse S. cerevisiae strains (CGH) GSE10268: Variations in stress sensitivity and genomic expression in diverse S. cerevisiae strains (gene expression) Keywords: SuperSeries Refer to individual Series

2008-09-05 | E-GEOD-10269 | biostudies-arrayexpress

Variations in stress sensitivity and genomic expression in diverse S. cerevisiae strains (CGH)

Project description: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 Each strain was grown in at least biological triplicate to log phase in rich (YPD) medium. Extracted total RNA was compared to that collected from the diploid S288C strain, DBY8268 (ura3-52/ura3-delta, ho/ho, GAL2/GAL2)

2010-06-19 | E-GEOD-10267 | biostudies-arrayexpress

Cells pretreated with NaCl have an altered gene expression in response to H2O2.

Project description:BY4741 (S288c haploid) cells have different gene expression in response to 0.4mM H2O2 when pretreated with 0.7M NaCl compared to cells that are not pretreated with NaCl (mock cells). BY4741 cells were grown in log phase for 3 doublings (t0) and then the genomic expression of mock cells to 0.4mM H2O2 was assessed every 10 mins for 40 mins. To study the effects of NaCl treatement on H2O2 response, BY4741 cells were grown in log phase for 3 doublings (t0) and then the genomic expression of cells was measured in response to 0.7M NaCl over the course of 60 min every 15 mins. The cells were then removed from stress and grown in stress free media for four hours (T240). Then these cells were exposed to 0.4mM H2O2 and the genomic expression was measured every 10 minutes during the H2O2 timecourse of 40 minutes. To see if the handling of cells had an affect on gene expression, BY4741 cells were grown for exponentially for 3 doublings (t0), received a mock YPD treatment for 60 mins, grown for 4 hours (T240) and then collected to asses genomic expression. Duplicates were done for at 30 and 45 minutes for the NaCl timecourse, triplicate were done for 0, 10 and 20 minutes in H2O2 timecourse and duplicates were done for 30 and 40 minutes in the H2O2 timecourse.

2011-09-17 | E-GEOD-32196 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data