GEO DataSets

(Submitter supplied) The FAR1 gene encodes a large protein, whose major function is inhibition of cyclin-dependent kinase complexes involved in the G1/S transition. It has been proposed that Far1, together with the G1 cyclin Cln3, may be part of a cell sizer mechanism that controls the entry into S phase. A genome-wide transcriptional analysis of FAR1-overexpressing and far1 deleted cells grown in ethanol- or glucose-supplemented minimal media indicates that FAR1 overexpression induces strong transcriptional remodelling, metabolism being the most affected cellular property. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL90

18 Samples

Download data: CEL

(Submitter supplied) Here we show that the ChEC-Seq technique is able to differentiate the binding specificities of Esa1 and Gcn5 two chromatin-binding factors displaying widespread genome-wide associations. We also show that the ChEC-Seq technique reveals strong binding of the transcription factor Sfp1 at Ribi gene promoters. Furthermore, our data provide the first evidence that a specific DNA motif previously identified by ChEC-Seq (Albert 2019 PMID: 30804227) is in fact an in vivo binding site for Sfp1.

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17342

10 Samples

Download data: BW

(Submitter supplied) Understanding how transcriptional programs help to coordinate cell growth and division is an important unresolved problem. Here we report that the nutrient- and stress-regulated transcription factor Sfp1 is rate-limiting for expression of a large suite of genes involved in yeast cell growth, including ribosomal protein, ribosome biogenesis, and snoRNA genes. Remarkably, the spectrum of Sfp1 transcription effects is concordant with a combination of chromatin immunoprecipitation and chromatin endogenous cleavage binding analyses, which together provide evidence for two distinct modes of Sfp1 promoter binding, one requiring a co-factor and the other a specific DNA-recognition motif. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17342

32 Samples

Download data: BIGWIG, BW

(Submitter supplied) The wild-type (grown on galactose or glucose) or msn2/4 mutant (grown on galactose) strains were grown aerobically. At time zero (generation 0) the sparge gas was switched from air to O2-free N2 and samples were harvested after 0 (aerobic control), 0.04, 0.08, 0.19, and 2 generations of anaerobic growth. Keywords: time-course

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Datasets:

GDS2002 GDS2003

Platform:

GPL1535

45 Samples

Download data

Analysis of catabolite-derepressed (galactose) wildtype JM43 and isogenic msn2/4 mutant KKY8 cells shifted to short-term anaerobiosis (2 generations). Msn2 and 4 are key stress factors. Results suggest Msn2/4 involvement in metabolic remodeling during acclimatization to short-term anaerobiosis.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array, log2 ratio, 2 genotype/variation, 2 protocol, 5 time sets

Platform:

GPL1535

Series:

GSE1879

30 Samples

Download data

Analysis of catabolite-repressed (glucose) or derepressed (galactose) wildtype JM43 cells shifted from aerobiosis to anaerobiosis (2 generations). Results identify metabolic remodeling that occurs during acclimatization to short-term anaerobiosis in galactose but not in glucose.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array, log2 ratio, 2 growth protocol, 2 protocol, 5 time sets

Platform:

GPL1535

Series:

GSE1879

30 Samples

Download data

(Submitter supplied) The Saccharomyces cerevisiae SFP1 is required for proper regulation of ribosome biogenesis and cell size in response to nutrients. A mutant deleted for SFP1 shows specific traits among which a slow growth phenotype, which is particularly evident during growth on glucose. To assess the effects of nutrients on the activity of Sfp1 independent by growth rate related feedback we grew an sfp1Δ mutant and its isogenic reference strain in chemostat cultures, at the same specific growth rate, under glucose/ethanol-limitation. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL90

26 Samples

Download data: CEL

(Submitter supplied) The budding yeast Saccharomyces cerevisiae alters its gene expression profile in response to a change in nutrient availability. The PHO-system is a well-studied case in the transcriptional regulation responding to nutritional changes in which a set of genes (PHO genes) is expressed to activate phosphate (Pi) metabolism for adaptation to Pi-starvation. Pi-starvation triggers an inhibition of Pho85 kinase, leading to migration of unphosphorylated Pho4 transcriptional activator into the nucleus enabling expression of PHO genes. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL3723

8 Samples

Download data: CEL

(Submitter supplied) In Saccharomyces cerevisiae growth, size control and cell cycle progression are strictly coordinated and regulated according to the nutritional conditions. In particular, ribosome biogenesis appears a key event in this regulatory network. SFP1 encodes a zinc-finger protein promoting the transcription of a large cluster of genes involved in ribosome biogenesis. It has been suggested that Sfp1 is a cell size modulator acting at Start. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL90

12 Samples

Download data

(Submitter supplied) In previous temporal studies, we found the anaerobic response was biphasic when cells growing in galactose medium were shifted from aerobiosis to anaerobiosis, consisting of an acute, transitory phase (<60 min) followed by a more chronic but delayed phase (> 1 generation), but largely monophasic (delayed, chronic phase only) when cells were shifted in glucose medium. Gene network and functional analyses revealed the acute phase was comprised of genes associated with the retooling of metabolism (respiro-fermentative to strictly fermentative) and balancing energy supply and demand. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL1535

227 Samples

Download data

(Submitter supplied) In previous temporal studies, we found the anaerobic response was biphasic when cells growing in galactose medium were shifted from aerobiosis to anaerobiosis, consisting of an acute, transitory phase (<60 min) followed by a more chronic but delayed phase (> 1 generation), but largely monophasic (delayed, chronic phase only) when cells were shifted in glucose medium. Gene network and functional analyses revealed the acute phase was comprised of genes associated with the retooling of metabolism (respiro-fermentative to strictly fermentative) and balancing energy supply and demand. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL1535

227 Samples

Download data

(Submitter supplied) Sfp1p is known to form the [ISP+] prion in Saccharomyces cerevisiae. Interestingly enough, the consequences and phenotypes of Sfp1p prionization and its absence are quite different. In order to understand the origin of this difference, we compared transcription profiles of an [ISP+], sfp1delta strains against the control strain (SFP1 [isp-]).

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL16244

12 Samples

Download data: TXT

(Submitter supplied) Commitment to cell division at the end of G1 phase, termed Start in the budding yeast Saccharomyces cerevisiae, is strongly influenced by nutrient availability. To identify new dominant activators of Start that might operate under different nutrient conditions, we screened a genome-wide ORF overexpression library for genes that bypass a Start arrest caused by absence of the G1 cyclin Cln3 and the transcriptional activator Bck2. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19756

42 Samples

Download data: TXT

(Submitter supplied) Analysis of gene expression across the cell cycle from wild type cells, and cells expressing alleles of Yox1, Yhp1, Hcm1, and Tos4 that cannot be phosphorylated by Cdk1. Expression of S-phase and M/G1 transcripts are downregulated when phosphorylation of these factors is blocked, demonstrating that Cdk1 promotes expression of late cell cycle genes.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL16244

32 Samples

Download data: TXT

(Submitter supplied) To study the TORC1-mediated transcriptional regulation of the genes involved in ribosome biosynthesis in fission yeast

Organism:

Schizosaccharomyces pombe

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16192

4 Samples

Download data: XLSX

(Submitter supplied) Whi3 associated mRNAs were identified by immunoprecipitation of TAP-tagged Whi3 followed by microarray analysis

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL17846

4 Samples

Download data: TXT

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

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array; Other; Expression profiling by high throughput sequencing

Platforms:

GPL9825 GPL13821 GPL17846

16 Samples

Download data: TXT

(Submitter supplied) Measurement of the change in steady state mRNA level in cells with whi3 deletion or WHI3 overexpression relative to wildtype cells. In the overexpression experiment, WHI3 is moderately overexpressed by integrating four copies of WHI3 at its endogenous locus. This was performed in YEP glucose medium and YEP ethanol medium. Goal was to measure the effects of WHI3 on global gene expression at RNA level.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL9825

8 Samples

Download data: TXT

(Submitter supplied) In general, RNA-binding proteins act to modulate gene expression at transcript level through degradation or at protein level through translation. To elucidate the effect of Whi3, a yeast RNA binding protein, on gene expression, we performed ribosome profiling experiment on whi3 mutant and wildtype cells.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL13821

4 Samples

Download data: TXT

(Submitter supplied) Transcript dynamics in the S. cerevisiae BF264-15D strains with genetically perturbed TFN or CDK-APC/C components. We compared the extents to which the programs of cell-cycle transcription were initiated during various cell-cycle arrests.

Organism:

Schizosaccharomyces pombe; Saccharomyces cerevisiae

Type:

Expression profiling by array; Third-party reanalysis

Platform:

GPL2529

270 Samples

Download data: CEL, TXT