GEO DataSets

(Submitter supplied) The proper maintenance of genetic material is essential for the survival of living organisms. One of the main safeguards of genome stability is homologous recombination involved in the faithful repair of DNA double-strand breaks, the restoration of collapsed replication forks, and the bypass of replication barriers. Homologous recombination relies on the formation of Rad51 nucleofilaments which are responsible for the homology-based interactions between DNA strands. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL22715

12 Samples

Download data: BIGWIG

(Submitter supplied) To reach an economically feasible bioethanol process from lignocellulose, efficient fermentation by yeast of all sugars present in the hydrolysate has to be achieved. However, when exposed to lignocellulosic hydrolysate, Saccharomyces cerevisiae is challenged with a variety of inhibitors that reduce yeast viability, growth and fermentation rate, and in addition damage cellular structures. In order to evaluate the yeast capability to adapt to lignocellulosic hydrolysates and to investigate the yeast molecular response to inhibitors, fed-batch cultivation of an industrial S. more...

Organism:

Schizosaccharomyces pombe; Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL2529

10 Samples

Download data: CEL, XLSX

(Submitter supplied) One of the essential or beneficial micronutrient for plants and animals is boron that is an ultra-trace element. Although boron can inhibit the growth of Saccharomyces cerevisiae around 80 mM, it is also a growth supplement. However, little information is currently available regarding the molecular mechanisms and essentiality of boron. In this paper, the approach was to generate S. cerevisiae mutants with high boron resistance by using evolutionary engineering strategy that was previously applied successfully. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by array

Platform:

GPL16244

6 Samples

Download data: TXT

(Submitter supplied) The fungal cell wall provides protection and structure to cells, and serves as an important target for antifungal compounds. The cell wall integrity (CWI) signaling pathway regulates the transcriptional response to various cell wall stresses, but emerging evidence suggests posttranscriptional pathways play an important complementary role. Here, we show that the RNA-binding proteins (RBPs) Mrn1 and Nab6 specifically target the 3′ UTRs of a largely overlapping set of cell wall-associated mRNAs. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL19756

54 Samples

Download data: BEDGRAPH, BW, FASTA, GTF, TXT

(Submitter supplied) We investigated the effect of the absence of the eisosome on the overall yeast transcriptome by gene expression profiling analysis. We used data obtained from RNA-seq (polyA enrichment of total RNA isolates) of 3 different strains, specifically wild type (BY4742), a strain missing PIL1 gene that forms eisosome remanants instead of eisosome and our newly described seg1Δnce102Δpil1Δ strain, which forms neither eisosomes, nor eisosome remnants, even in the response to stress.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19756

9 Samples

Download data: TSV

(Submitter supplied) To study the role of the exonuclease Xrn1 in gene expression dynamics under osmotic stress conditions, we performed RNA-seq in Xrn1-depleted cells. By using an auxin-inducible degron, we were able to study immediate effects of Xrn1 depletion in gene expression dynamics. Therefore, we could overcome experimental limitations associated to stable deletion mutants.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17342

17 Samples

Download data: TSV

(Submitter supplied) To investigate translation events in the absence of eIF4E in Saccharomyces cerevisiae, we used a strain with a temperature-sensitive allele of eIF4E (cdc33-ts4-2). At 25°C, the factor is stable, but at 37°C it degrades. Here we conducted ribosome profiling and RNA-seq of both wild-type and temperature-sensitive strains subjected to 25°C and 37°C.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17342

20 Samples

Download data: XLSX

(Submitter supplied) To better understand how yeast adapt and respond to sequential stressors, an industrial yeast strain, URM 6670 (also known as BT0510), which is highly flocculent, tolerant to ethanol, osmotic and heat shock stresses, was subjected to three different treatments: 1. osmotic stress followed by ethanol stress, 2. oxidative stress followed by ethanol stress, 3. glucose withdrawal followed by ethanol stress. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27812

27 Samples

Download data: DIFF

(Submitter supplied) Histone chaperones are an important class of factors that regulate chromatin accessibility for DNA-templated processes. Spt6 is a conserved histone chaperone and key regulator of transcription and chromatin structure. However, its functions outside of these roles have been little explored. In this work, we demonstrate a role for Spt6 in DNA replication and more broadly as a regulator of genome stability. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19756

22 Samples

Download data: BW

(Submitter supplied) Industrial bioethanol production may involve a low pH environment,improving the tolerance of S. cerevisiae to a low pH environment caused by inorganic acids may be of industrial importance to control bacterial contamination, increase ethanol yield and reduce production cost. Through analysis the transcriptomic data of Saccharomyces cerevisiae with different ploidy under low pH stress, we hope to find the tolerance mechanism of Saccharomyces cerevisiae to low pH.

Organism:

Saccharomyces cerevisiae; Schizosaccharomyces pombe

Type:

Expression profiling by array

Platform:

GPL2529

16 Samples

Download data: CEL

(Submitter supplied) N6-methyladenosine (m6A) RNA modification impacts mRNA fate primarily via reader proteins, which dictate processes in development, stress, and disease. Yet little is known about m6A function in Saccharomyces cerevisiae, which occurs solely during early meiosis. Here we perform a multifaceted analysis of the m6A reader protein Pho92/Mrb1. Cross-linking immunoprecipitation analysis reveals that Pho92 associates with the 3’end of meiotic mRNAs in both an m6A-dependent and independent manner. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27812

10 Samples

Download data: TSV

(Submitter supplied) N6-methyladenosine (m6A) RNA modification impacts mRNA fate primarily via reader proteins, which dictate processes in development, stress, and disease. Yet little is known about m6A function in Saccharomyces cerevisiae, which occurs solely during early meiosis. Here we perform a multifaceted analysis of the m6A reader protein Pho92/Mrb1. Cross-linking immunoprecipitation analysis reveals that Pho92 associates with the 3’end of meiotic mRNAs in both an m6A-dependent and independent manner. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21656

18 Samples

Download data: TSV

(Submitter supplied) N6-methyladenosine (m6A) RNA modification impacts mRNA fate primarily via reader proteins, which dictate processes in development, stress, and disease. Yet little is known about m6A function in Saccharomyces cerevisiae, which occurs solely during early meiosis. Here we perform a multifaceted analysis of the m6A reader protein Pho92/Mrb1. Cross-linking immunoprecipitation analysis reveals that Pho92 associates with the 3’end of meiotic mRNAs in both an m6A-dependent and independent manner. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21656

18 Samples

Download data: TSV

(Submitter supplied) Replication forks terminate at TERs and telomeres. Forks that converge or encounter transcription generate topological stress. Combining genetic, genomic and imaging approaches we found that Rrm3hPif1 and Sen1hSenataxin helicases assist termination at TERs, Sen1 at telomeres. rrm3 and sen1 are synthetic lethal, fail to terminate replication exhibiting lagging chromosomes and fragility at TERs and telomeres. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL26302

48 Samples

Download data: BED, BEDGRAPH

(Submitter supplied) Replication forks terminate at TERs and telomeres. Forks that converge or encounter transcription generate topological stress. Combining genetic, genomic and imaging approaches we found that Rrm3hPif1 and Sen1hSenataxin helicases assist termination at TERs, Sen1 at telomeres. rrm3 and sen1 are synthetic lethal, fail to terminate replication exhibiting lagging chromosomes and fragility at TERs and telomeres. more...

Organism:

Saccharomyces cerevisiae

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL7250

16 Samples

Download data: BED, BEDGRAPH, CEL

(Submitter supplied) QuantSeq analysis to screen Yap1-dependent target genes for caffeine resistance.

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19756

13 Samples

Download data: TXT

(Submitter supplied) We obtained RNA polymerase II occupancy profile across the genome of WT and isw1Δ Saccharomyces cerevisiae strains grown under normal conditions or after ER stress induction for 2H with1 µg/mL tunicamycin (Tm).

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13821

4 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:

GPL17342

256 Samples

Download data: CSV, WIG

(Submitter supplied) Mediator (MED) is a conserved factor with important roles in basal and activated transcription. Here, we investigate the genome-wide roles of yeast MED by rapid depletion of its activator-binding domain (Tail) and monitoring changes in nascent transcription. Rapid Tail depletion surprisingly reduces transcription from only a small subset of genes. At most of these Tail-dependent genes, in unperturbed conditions, MED is detected at both the UASs and promoters. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17342

177 Samples

Download data: CSV

(Submitter supplied) Ribosomes are often seen as monolithic machines produced from uniformly regulated genes. However, in yeast most ribosomal proteins come from duplicated genes. Here, we demonstrate that gene duplication may serve as an adaption mechanism modulating the global proteome through the differential expression of ribosomal proteins paralogs after exposure to stress. Our data indicate that the yeast paralog pair of the ribosomal protein L7/uL30 produces two differentially acetylated proteins. more...

Organism:

Saccharomyces cerevisiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19756

18 Samples

Download data: TSV