GEO DataSets

(Submitter supplied) Ribosome biogenesis is a complex and energy-demanding process requiring tight coordination of ribosomal RNA (rRNA) and ribosomal protein (RP) production. Alteration of any step in this process may impact growth by leading to proteotoxic stress. Although the transcription factor Hsf1 has emerged as a central regulator of proteostasis, how its activity is coordinated with ribosome biogenesis is unknown. more...

Organism:

Saccharomyces cerevisiae W303

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL25517

63 Samples

Download data: BW

(Submitter supplied) To achieve maximal growth, cells must manage a massive economy of ribosomal proteins (r-proteins) and RNAs (rRNAs) to produce thousands of ribosomes every minute. Although ribosomes are essential in all cells, natural disruptions to ribosome biogenesis lead to heterogeneous phenotypes. Here, we model these perturbations in Saccharomyces cerevisiae and show that challenges to ribosome biogenesis result in acute loss of proteostasis. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19756

30 Samples

Download data: CSV, TXT

(Submitter supplied) Fhl1-9myc ChIP-chip, YPD, OD600=0.8, 2 arrays with duplicate spotting of yeast intergenic regions. AND Ifh1-9myc ChIP-chip, cells grown in YPD, OD600=0.8, 2 arrays with duplicate spotting of yeast intergenic regions. Keywords = Fhl1 Keywords: other

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by array

Platform:

GPL1689

8 Samples

Download data

(Submitter supplied) Array design -Platform: amino-silane coated glass slides (GAPS II, Corning) -S. cerevisiae intergenic regions amplified from S288C genomic DNA (ResGen) using the intergenic region primer oligonucleotides (ResGen) (Harismendy et al. EMBO J. 22(18): 4738-4747, 2003). The primers allow the amplification of the sequence located on either side of elements such as open reading frames, tRNAs, small nuclear RNAs, Ty elements, solo δ, etc. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL1695

15 Samples

Download data: TIFF

(Submitter supplied) Cells maintain proteostasis by selectively recognizing and targeting misfolded proteins for degradation. In Saccharomyces cerevisiae, the Hsp70 nucleotide exchange factor Fes1 is essential for the degradation of chaperone-associated misfolded proteins by the ubiquitin-proteasome system. Here we show that the FES1 transcript undergoes unique 3' alternative splicing that results in two equally active isoforms with alternative C-termini, Fes1L and Fes1S. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17342

18 Samples

Download data: TXT

(Submitter supplied) Transcription of eukaryotic genes involves dynamic interactions between RNA polymerases and chromatin that are facilitated by auxiliary factors. One of these chromatin factors is Spt6, encoded by an essential gene that plays regulatory functions throughout all eukaryotes, from yeast to human. We have performed a genetic analysis of Spt6 function by isolating yeast mutations that confer synthetic-lethality to a conditional spt6 allele under permissive conditions. more...

Organism:

Saccharomyces cerevisiae

Type:

Other; Genome binding/occupancy profiling by array

Platform:

GPL8568

32 Samples

Download data: TXT

(Submitter supplied) We found ribosomal transcription factor Ifh1p is dynamically acetylated and phosphorylated in response to nutrient cues. ChIP-seq data revealed dynamic binding to ribosomal genes (RP) during the OX growth phase of the yeast metabolic cycle (YMC) when RP genes are highly induced, and weaker binding in the RC quiescent-like phase. Besides RP genes, our ChIP-seq data also reveals binding of Ifh1p to non-RP genes such as translation factors and metabolic genes.

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13272

4 Samples

Download data: WIG

(Submitter supplied) Life is resilient because living systems are able to respond to elevated temperatures with an ancient gene expression program called the heat shock response (HSR). Our global analysis revealed a modular HSR dependent on the severity of the stress in yeast. Interestingly, at all temperatures analyzed, the transcription of hundreds of genes is upregulated among them the molecular chaperones, which protect proteins from aggregation. more...

Organism:

Schizosaccharomyces pombe; Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL2529

45 Samples

Download data: CEL

(Submitter supplied) The protein homeostasis (proteostasis) network maintains balanced protein synthesis, folding, transport and degradation within a cell. Because failure to maintain proteostasis is associated with aging and disease, a concerted effort has been placed on studying how the proteostasis network responds to various stresses. Typically, this is accomplished using ectopic overexpression of well-characterized, model misfolded protein substrates; however, how cells tolerate large-scale, diverse burden to the proteostasis network is not understood. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13821

24 Samples

Download data: TXT

(Submitter supplied) Comparison of the average normalised ChIP-seq signal over protein-coding genes in bud27∆ mutants strain and wild-type.

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13821

8 Samples

Download data: BW

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

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:

GPL13821

18 Samples

Download data: BW

(Submitter supplied) RNA extraction for global analyisis and sequencing, to study the bud27∆ mutant and WT treated with rapamycin regarding to WT.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13821

6 Samples

Download data: TXT

(Submitter supplied) The goal of this study is to analyse genome-wide the binding profile of Bud27 prefoldin-like to the genes or other genomic regions in order to know which genes could be transcriptionally regulated by this protein and to elucidate the contribution of Bud27 to the transcription. Average normalised ChIP-seq signal for Bud27 prefoldin-like binding in a S.cerevisiae wild-type strain.

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13821

4 Samples

Download data: BW

(Submitter supplied) Cells must adjust their gene expression in order to compete in a constantly changing environment. Two alternative strategies could in principle ensure optimal coordination of gene expression with physiological requirement. First, the internal physiological state itself could feedback to regulated gene expression. Second, the expected physiological state could be inferred from the external environment, using evolutionary-tuned signaling pathways. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL4567

95 Samples

Download data: XLS

(Submitter supplied) Abf1 and Reb1, two general regulatory factors playing roles at promoters and other genome functional sites in budding yeast, were mapped genome-wide by ChIP-sequencing using strains expressing TAP-tagged versions of the proteins. As expected on the basis of previous in silico analysis of promoter regions, we found that these factors are enriched at the promoters of ribosome biogenesis (Ribi) genes, a large regulon of more than 200 genes required for ribosome biosynthesis and assembly, and known to be coordinately regulated in response to nutrient availability and cellular growth rate.

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17342

4 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; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13272

25 Samples

Download data: BAM, BIGWIG

(Submitter supplied) TORC1 is a structurally and functionally conserved multiprotein complex that regulates many aspects of eukaryote growth including the synthesis and assembly of ribosomes. The protein kinase activity of this complex is responsive to environmental cues and is potently inhibited by the natural product macrolide rapamycin. Insights into how TORC1 regulates growth have been provided with the recent identification of the rapamycin-sensitive phosphoproteome in yeast. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13272

9 Samples

Download data: BAM, BIGWIG

(Submitter supplied) TORC1 is a structurally and functionally conserved multiprotein complex that regulates many aspects of eukaryote growth including the synthesis and assembly of ribosomes. The protein kinase activity of this complex is responsive to environmental cues and is potently inhibited by the natural product macrolide rapamycin. Insights into how TORC1 regulates growth have been provided with the recent identification of the rapamycin-sensitive phosphoproteome in yeast. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13272

16 Samples

Download data: BAM

(Submitter supplied) Affymetrix experiment performed on RNA isolated from Wild type, FHL1 deleted and FHL1,IFH1 double deleted strains. Data aquired in duplicate. In S. cerevisiae the mRNAs from the 138 ribosomal protein (RP) genes are amongst the most abundant in the cell, and their transcription is regulated tightly so that they are the most prominent cluster in most transcriptome experiments. It has recently been observed that the proteins Fhl1p and Ifh1p are found almost exclusively at RP genes (Lee et al., Science, 298, 799-804, 2002;Jorgensen et al., Genes Dev, 18, 2491-2505 2004; Schawalder et al Nature in press; Rudra et al , EMBO J. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Dataset:

GDS1033

Platform:

GPL90

6 Samples

Download data

Expression profiling of fhl1 single deletion mutant and ifh1 fhl1 double deletion mutant. Mutants generated from W303 strain. Results indicate that Ifh1p and Fhl1p function together to regulate the transcription of ribosomal protein genes.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array, transformed count, 3 genotype/variation sets

Platform:

GPL90

Series:

GSE2096

6 Samples

Download data