GEO DataSets

(Submitter supplied) Yeast has proven to be a useful model system for aging studies, including CR effects. We report here that yeast adapted through in vitro evolution to the severe cellular stress caused by loss of the Ulp2 SUMO-specific protease exhibit both enhanced growth rates and replicative lifespan, and they have altered gene expression profiles similar to those observed in CR. Notably, in certain evolved ulp2Δ lines, a dramatic increase in the auto-sumoylation of Ubc9 E2 SUMO-conjugating enzyme results in altered regulation of multiple targets involved in energy metabolism and translation at both transcriptional and post-translational levels. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17342

12 Samples

Download data: CSV, XLSX

(Submitter supplied) Yeast has proven to be a useful model system for aging studies, including CR effects. We report here that yeast adapted through in vitro evolution to the severe cellular stress caused by loss of the Ulp2 SUMO-specific protease exhibit both enhanced growth rates and replicative lifespan, and they have altered gene expression profiles similar to those observed in CR. Notably, in certain evolved ulp2Δ lines, a dramatic increase in the auto-sumoylation of Ubc9 E2 SUMO-conjugating enzyme results in altered regulation of multiple targets involved in energy metabolism and translation at both transcriptional and post-translational levels. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL27812

8 Samples

Download data: BW

(Submitter supplied) Work summary: Full-transcriptome methods have brought versatile power to protein biosynthesis research, but remain difficult to apply for the quantification of absolute protein synthesis rates. Here we propose and, using modified translation complex profiling, confirm co-localisation of ribosomes on messenger(m)RNA resulting from the ribosomal diffusional dynamics. We demonstrate that the stochastically co-localised ribosomes are linked with the translation initiation rate and provide a robust variable to model and quantify specific absolute protein output from mRNA. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL17342

18 Samples

Download data: BED

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

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25927

60 Samples

Download data

(Submitter supplied) Gene expression was quantified in S. cerevisae cells after 48 hours of treatment with KCl. crz1 and crz1 cnb1 mutant strains were compared to allow the identification of calcineurin-dependent gene expression changes that are independent of the downstream transcription factor Crz1. We find that calcineurin has very little effect on gene expression in response to KCl.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25927

12 Samples

Download data: CSV

(Submitter supplied) Gene expression was quantified in S. cerevisae cells over a time course of three days of CaCl2 treatment to activate calcineurin. crz1 and crz1 cnb1 mutant strains were compared to allow the identification of calcineurin-dependent gene expression changes that are independent of the downstream transcription factor Crz1. We show that mitochondrial genes are downregulated in both geneotypes over time. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25927

24 Samples

Download data: CSV

(Submitter supplied) Gene expression was quantified in S. cerevisae cells over a time course of three days of CaCl2 treatment to activate calcineurin. Wild type (WT) and cnb1 mutant strains were compared to allow the identification of calcineurin-dependent gene expression changes. We show that mitochondrial genes are downregulated, and ribosome biogenesis genes are upregulated, in both geneotypes over time.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25927

24 Samples

Download data: CSV

(Submitter supplied) Formalin induces inter- and intra-molecular crosslinks within exposed cells. This cross-linking can be exploited to characterise chromatin state as in the FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) and MNase (micrococcal nuclease) assays. Our team aims to optimise these assays for application in museum preserved formalin-exposed specimens. To do so, we first sought to understand the effect of prolonged formalin fixation on the read alignment signatures resulting from FAIRE and MNase treatment. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27812

6 Samples

Download data: FPKM_TRACKING, TXT

(Submitter supplied) Formalin induces inter- and intra-molecular crosslinks within exposed cells. This cross-linking can be exploited to characterise chromatin state as in the FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) and MNase (micrococcal nuclease) assays. Our team aims to optimise these assays for application in museum preserved formalin-exposed specimens. To do so, we first sought to understand the effect of prolonged formalin fixation on the read alignment signatures resulting from FAIRE and MNase treatment. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL27812

58 Samples

Download data: WIG

(Submitter supplied) The response to proteotoxic stresses such as heat shock is an ancient and ubiquitous transcriptional program allowing organisms to maintain protein homeostasis under changing environmental conditions. We depleted or deleted the three stress-specific transcription factors, Hsf1, Msn2 and Msn4, in S. cerevisiae and determined the effects on the transcriptome and proteome. Msn2/4 are responsible for a broad transcriptional reprogramming which includes i. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18085

60 Samples

Download data: TSV, TXT

(Submitter supplied) Cotranslational protein folding depends on general chaperones that engage highly diverse nascent chains at the ribosomes. Here we find that the universal cotranslational machinery adapts to accommodate the challenging biogenesis of abundantly expressed eukaryotic translation elongation factor 1A (eEF1A). During eEF1A synthesis, chaperone Chp1 is recruited to the ribosome with the help of the nascent polypeptide-associated complex (NAC), where it safeguards eEF1A biogenesis. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL26302

16 Samples

Download data: H5

(Submitter supplied) Earlier investigations have associated mammalian eIF2A with Met-tRNAi binding to the 40S subunit and its recruitment to specialized mRNAs in a GTP-independent manner. Additionally, eIF2A has been implicated in non-AUG start codon initiation, particularly under conditions where eIF2 function is attenuated by phosphorylation of its α-subunit during stress or starvation. However, the precise role of eIF2A in vivo translation remains unclear. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL17342

16 Samples

Download data: XLSX

(Submitter supplied) Nuclear mRNA export via nuclear pore complexes is an essential step in eukaryotic gene expression. Although factors involved in mRNA transport have been characterized, a comprehensive mechanistic understanding of this process and its regulation is lacking. Here, we use single-RNA imaging in yeast to show that cells use mRNA retention to control mRNA export during stress. We demonstrate that upon glucose withdrawal the essential RNA-binding factor Nab2 forms RNA-dependent condensate-like structures in the nucleus. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL31112

21 Samples

Download data: TXT

(Submitter supplied) The SAM1 and SAM2 genes encode for S-AdenosylMethionine (AdoMet) synthetase enzymes, with AdoMet serving as the main cellular methyl donor. We have previously shown that independent deletion of these genes alters chromosome stability and AdoMet concentrations in opposite ways in Saccharomyces cerevisiae. To characterize other changes occurring in these mutants, we grew wildtype, sam1∆/sam1∆, and sam2∆/sam2∆ strains in 15 different Phenotypic Microarray plates with different components and measured growth variations. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19756

9 Samples

Download data: TSV

(Submitter supplied) We attempted to improve the resistance of taxadiene-producing yeast strain to oxidative stress to develop a more robust yeast cell factory for improved Taxol® drug oxyenated taxanes precursors production from taxadiene. To this end, we evolved a yeast strain on H2O2-containing defined growth medium, supplemented with galactose as carbon source to induce the heterologous taxadiene biosynthesis pathway genes in that strain. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21656

12 Samples

Download data: TXT

(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) Transcription of transfer-RNA genes (tDNAs) by RNA Polymerase III (RNAPIII) is tightly regulated upon nutrient and stress signaling. However, identical tDNAs across the genome are differentially regulated, suggesting regulation at the chromatin-level plays a crucial role. This study aimed to identify such mechanisms by decoding the chromatin proteome of a native tDNA locus in yeast using Epi-Decoder. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19756

4 Samples

Download data: BEDGRAPH

(Submitter supplied) Intrinsically disordered regions (IDRs) are abundant within eukaryotic proteins, but their sequence-function relationship remains poorly understood. IDRs of transcription factors (TFs) can direct promoter selection and recruit coactivators, as exemplified by the budding-yeast TF- Msn2. To examine how low-complexity IDRs encode multiple functions, we compared genomic binding preferences, gene induction, and coactivator recruitment amongst a large set of designed Mns2-IDR mutants. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27812

336 Samples

Download data: TXT

(Submitter supplied) The process of sulfate uptake plays a crucial role in cellular metabolism and growth. SUL1, a plasma membrane transporter responsible for regulating the entry of extracellular sulfate in S. cerevisiae. Our previous work verified SUL1 as a fundamental gene involved in the regulation of lifespan. This study aimed to undertake a more comprehensive analysis of the role of SUL1 in regulating longevity. Our data showed that that sulfate transport is not required for the effect of SUL1 deletion on increased longevity. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25927

5 Samples

Download data: TXT

(Submitter supplied) The essential stress-responsive chaperone Hsp90 impacts development and adaptation from microbes to humans. Yet despite evidence of its role in evolution, pathogenesis, and oncogenic transformation, the molecular mechanisms by which Hsp90 alters the consequences of mutations remain vigorously debated. Here we exploit the power of nucleotide-resolution genetic mapping in Saccharomyces cerevisiae to uncover more than 1,000 natural variant-to-phenotype associations governed by this molecular chaperone. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30266

18 Samples

Download data: CSV