Saccharomyces cerevisiae
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA239467 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1177160.fastq.gz | Fastqsanger.gz | |||
| SRR1177161.fastq.gz | Fastqsanger.gz | |||
| SRR1177162.fastq.gz | Fastqsanger.gz | |||
| SRR1177163.fastq.gz | Fastqsanger.gz | |||
| SRR1177156.fastq.gz | Fastqsanger.gz |
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Project description:Heritable differences in gene expression between individuals are an important source of phenotypic variation. The question of how closely the effects of genetic variation on protein levels mirror those on mRNA levels remains open. Here, we addressed this question by using ribosomal footprinting to examine how genetic differences between two strains of the yeast S. cerevisiae affect translation. Strain differences in translation were observed for hundreds of genes, more than half as many as showed genetic differences in mRNA levels. Similarly, allele specific measurements in the diploid hybrid between the two strains found roughly half as many cis-acting effects on translation as were observed for mRNA levels. In both the parents and the hybrid, strong effects on translation were rare, such that the direction of an mRNA difference was typically reflected in a concordant footprint difference. The relative importance of cis and trans acting variation on footprint levels was similar to that for mRNA levels. Across all expressed genes, there was a tendency for translation to more often reinforce than buffer mRNA differences, resulting in footprint differences with greater magnitudes than the mRNA differences. Finally, we catalogued instances of premature translation termination in the two yeast strains. Overall, genetic variation clearly influences translation, but primarily does so by subtly modulating differences in mRNA levels. Translation does not appear to create strong discrepancies between genetic influences on mRNA and protein levels. Ribsosomal footprinting and RNASeq in the two yeast strains BY and RM as well as their diploid hybrid. We generated one library each for the BY and RM parents, and two libraries (biological replicates) for the hybrid data.
2014-03-31 | E-GEOD-55400 | biostudies-arrayexpress
Project description:Growth assay in the presence of a toxic chemical (sr7575) that uses the barcoded collections of yeast gene deletions (haploid, diploid, DamP) to identify deletion strains that are hypersensitive to the drug.
2015-12-09 | GSE60934 | GEO
Project description:Growth assay in the presence of a toxic chemical that uses the barcoded collections of yeast gene deletions (haploid, diploid, DamP) to identify deletion strains that are hypersensitive to the drug.
2019-12-31 | GSE125353 | GEO
Project description:Heritable differences in gene expression between individuals are an important source of phenotypic variation. The question of how closely the effects of genetic variation on protein levels mirror those on mRNA levels remains open. Here, we addressed this question by using ribosomal footprinting to examine how genetic differences between two strains of the yeast S. cerevisiae affect translation. Strain differences in translation were observed for hundreds of genes, more than half as many as showed genetic differences in mRNA levels. Similarly, allele specific measurements in the diploid hybrid between the two strains found roughly half as many cis-acting effects on translation as were observed for mRNA levels. In both the parents and the hybrid, strong effects on translation were rare, such that the direction of an mRNA difference was typically reflected in a concordant footprint difference. The relative importance of cis and trans acting variation on footprint levels was similar to that for mRNA levels. Across all expressed genes, there was a tendency for translation to more often reinforce than buffer mRNA differences, resulting in footprint differences with greater magnitudes than the mRNA differences. Finally, we catalogued instances of premature translation termination in the two yeast strains. Overall, genetic variation clearly influences translation, but primarily does so by subtly modulating differences in mRNA levels. Translation does not appear to create strong discrepancies between genetic influences on mRNA and protein levels.
2014-03-31 | GSE55400 | GEO
Project description:Xylose-utilizing yeasts with tolerances to fermentation inhibitors (such as weak organic acids) and high temperature are needed for cost-effective simultaneous saccharification and co-fermentation (SSCF) of lignocellulosic materials. We constructed a novel xylose-assimilating Saccharomyces cerevisiae strain with improved fermentation performance under heat and acid co-stress using the genome shuffling technique. Two xylose-utilizing diploid yeasts with different genetic backgrounds were used as the parental strains for genome shuffling. The hybrid strain Hyb-8 showed significantly higher xylose fermentation ability than both parental strains (Sun049T-Z and Sun224T-K) under co-stress conditions of heat and acids. To screen for genes that might be important for fermentation under heat and acid co-stress, a transcriptomic analysis of hybrid strain Hyb-8 and its parental strains was performed.
2017-07-25 | GSE101786 | GEO
Project description:Yeast mannoproteins contribute to several aspects of wine quality by protecting wine against protein haze, reducing astringency, retaining aroma compounds and stimulating growth of lactic-acid bacteria. The selection of a yeast strain simultaneously overproducing mannoproteins and showing good fermentative characteristics is a difficult task. In this work, a Saccharomyces cerevisiae x Saccharomyces cerevisiae hybrid bearing the two oenologically relevant features was constructed and a reduction in the amount of bentonite necessary for wine stabilization was observed for wines fermented with the generated strain. Additionally, different copy numbers of some genes probably related with these physiological features were detected in this hybrid. Hybrid share with parental Sc1 similar copy number of genes SPR1, SWP1, MNN10 and YPS7 related to cell wall integrity and with parental Sc2 similar copy number of some glycolytic genes as GPM1 and HXK1 as well as genes involved in hexose transport as HXT9, HXT11 and HXT12. This work demonstrates that artificial hybridization and stabilization in winemaking conditions constitute an effective approach to obtain yeast strains with desirable physiological features as mannoprotein overproducing capacity and improved fermentation performance, characteristics genetically depending on the coordinated expression of a multitude of different genes. In this work, genetically stable mannoprotein overproducing Saccharomyces cerevisiae strains simultaneously showing excellent fermentation capacities were obtained by hybridization methods giving rise to non-GMO strains. The potential relationship between the copy number of specific genes and the improved features was also evaluated by means of aCGH analysis of parental and hybrid strains.
2015-03-30 | GSE48117 | GEO
Project description:Comparison of 3 yeast strains grown under nitrogen starvation, nitrogen rich conditions, with and without quorum sensing molecule 2-phenylethanol
2025-07-08 | PXD061716 | JPOST Repository
Project description:Resurvey of nuclear and mitochondrial recombination in hybrid diploid yeast with third-generation sequencing technology
| PRJNA742490 | ENA
Project description:In response to limited nitrogen and abundant carbon sources, diploid Saccharomyces cerevisiae strains undergo a filamentous transition in cell growth as part of pseudohyphal differentiation. Use of the disaccharide maltose as the principal carbon source, in contrast to the preferred nutrient monosaccharide glucose, has been shown to induce a hyper-filamentous growth phenotype in a strain deficient for GPA2 which codes for a Galpha protein component that interacts with the glucose-sensing receptor Gpr1p to regulate filamentous growth. In this report, we compare the global transcript and proteomic profiles of wild-type and Gpa2p deficient diploid yeast strains grown on both rich and nitrogen starved maltose media. We find that deletion of GPA2 results in significantly different transcript and protein profiles when switching from rich to nitrogen starvation media. The results are discussed with a focus on the genes associated with carbon utilization, or regulation thereof, and a model for the contribution of carbon sensing/metabolism-based signal transduction to pseudohyphal differentiation is proposed. Keywords: Saccharomyces cerevisiae, nitrogen starvation, maltose, pseudohyphal differentiation, yeast, expression profiling
2007-12-21 | GSE7820 | GEO
Project description:Comparative genome-wide gene expression analysis between two industrial wine yeast hybrid strains belonging to the species S. cerevisiae x S. Kudriavzevii, in natural must fermentations.
2016-12-03 | GSE90793 | GEO