GEO DataSets

(Submitter supplied) Activation domains (ADs) within transcription factors (TFs) induce gene expression by recruiting coactivators to specific regulatory regions. Within the prevailing model, TF-coactivator recruitment is independent of DNA binding, which is consistent with direct AD-coactivator interactions seen outside cells. However, this independence was not yet tested within the genomic context. Here, we targeted two Med15-interacting ADs to hundreds of budding yeast promoters through fusions with multiple DNA binding domains (DBDs), gradually controlling their abundances using libraries of synthetic promoters. more...

Organism:

Saccharomyces cerevisiae; Saccharomyces cerevisiae BY4741

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platforms:

GPL27812 GPL28475

345 Samples

Download data: TXT

(Submitter supplied) Peroxisomes are organelles that are crucial for cellular metabolism. However, these organelles play also important roles in non-metabolic processes, such as signalling. To uncover the consequences of peroxisome deficiency, we compared two extremes, namely Saccharomyces cerevisiae wild-type and pex3 cells, which lack functional peroxisomes, employing transcriptomics and quantitative proteomics technology. more...

Organism:

Saccharomyces cerevisiae BY4741

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28475

6 Samples

Download data: CSV

(Submitter supplied) The 18S rRNA sequence is highly conserved, particularly at its 3’-end, which is formed by the endonuclease Nob1. How Nob1 identifies its target sequence is not known, and in vitro experiments have shown Nob1 to be error-prone. Moreover, the sequence around the 3’-end is degenerate with similar sites nearby. Here we used yeast genetics, biochemistry, and next generation sequencing to investigate a role for the ATPase Rio1 in monitoring the accuracy of the 18S rRNA 3’-end. more...

Organism:

Saccharomyces cerevisiae BY4741

Type:

Other

Platform:

GPL20138

22 Samples

Download data: XLSX

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

Organism:

Saccharomyces cerevisiae; Saccharomyces cerevisiae BY4741

Type:

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

Platforms:

GPL27812 GPL28475

1242 Samples

Download data: TXT

(Submitter supplied) Activation domains (ADs) within transcription factors (TFs) induce gene expression by recruiting coactivators to specific regulatory regions. Within the prevailing model, TF-coactivator recruitment is independent of DNA binding, which is consistent with direct AD-coactivator interactions seen outside cells. However, this independence was not yet tested within the genomic context. Here, we targeted two Med15-interacting ADs to hundreds of budding yeast promoters through fusions with multiple DNA binding domains (DBDs), gradually controlling their abundances using libraries of synthetic promoters. more...

Organism:

Saccharomyces cerevisiae BY4741

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28475

897 Samples

Download data: TXT

(Submitter supplied) We describe the complete synthesis, assembly, debugging and characterization of a synthetic 404,963 bp yeast chromosome, synIX. Combined chromosome construction methods were used to synthesize the left arm of synIX (synIXL) and retrofit previously described synIXR. During synIX strain characterization, we identified and resolved a bug related to EST3, a gene involved in telomerase function, producing a synIX strain with near wild-type fitness. more...

Organism:

Saccharomyces cerevisiae BY4741

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20138

12 Samples

Download data: CSV, TSV

(Submitter supplied) We studied the transcriptional profile in yeast cells in response to treatment with 10mg/ml of neomycin sulfate for 4 h.

Organism:

Schizosaccharomyces pombe; Saccharomyces cerevisiae; Saccharomyces cerevisiae BY4741

Type:

Expression profiling by array

Platform:

GPL2529

6 Samples

Download data: CEL

(Submitter supplied) Inhibition of Kin28/CDK7, the kinase subunit of TFIIH, leads to defects in transcription of protein-coding genes. Despite a severe reduction in nascent RNA synthesis, the majority of mRNAs retain their steady-state level upon inhibition. In this study, we examined the determinants of mRNA stability in cells experiencing transcriptional crisis via irreversible chemical inhibition of Kin28. We discovered that the inhibited Kin28 transcriptome resembles the transcriptome of cells treated with an inhibitor of protein synthesis. more...

Organism:

Saccharomyces cerevisiae BY4741

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL20138 GPL18330

24 Samples

Download data: BIGWIG

(Submitter supplied) Histone H3K36 can be added up to three methyl groups to form mono-, di-, and tri-methylation states. Recent study has shown that Set2 can suppress a specific group of antisense transcripts, which largely depends on the presence of H3K36 methylation. However, whether different methylation states possess distinct regulatory mechanisms on antisense transcripts is still unclear. In this study, we identified two yeast mutants that lack H3K36 di-methylation and tri-methylation, respectively. more...

Organism:

Saccharomyces cerevisiae BY4741

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20138

12 Samples

Download data: XLSX

(Submitter supplied) Ribonucleotides incorporated in the genome are a source of endogenous DNA damage, and also serve as signals for repair. Although recent advances of ribonucleotide detection by sequencing, the balance between incorporation and repair of ribonucleotides has not been elucidated. Here, we describe a competitive sequencing method, Ribonucleotide Scanning Quantification sequencing (RiSQ-seq), which enables absolute quantification of misincorporated ribonucleotides throughout the genome by background normalization and standard adjustment within a single sample. more...

Organism:

Saccharomyces cerevisiae BY4741; Sinsheimervirus phiX174

Type:

Other

Platforms:

GPL21372 GPL22273

58 Samples

Download data: BED, BEDGRAPH, FA, GTF, TSV

(Submitter supplied) We quantified the exact RNA binding sites of the Ssd1 protein in Saccharomyces cerevisiae, in exponential growth and heat shock conditions, using the CRAC protocol. We used a His-TEV-protein A tag (HTP) on the C-terminal of the genomic copy of Ssd1, with the 3'UTR replaced by the 3'UTR/terminator from the K. lactis Ssd1 homolog, followed by a KlURA3 selection marker.

Organism:

Saccharomyces cerevisiae BY4741

Type:

Other

Platform:

GPL29267

5 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) Effective design of combination therapies requires understanding the changes in cell physiology resulting from drug interactions. Here, we show that the genome-wide transcriptional response to combinations of two drugs, measured at a rigorously controlled growth rate, can predict higher-order antagonism with a third drug in Saccharomyces cerevisiae. Using isogrowth profiling, over 90% of the variation in cellular response can be decomposed into three principal components (PCs) that have clear biological interpretations. more...

Organism:

Saccharomyces cerevisiae BY4741

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18334

238 Samples

Download data: CSV

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

Organism:

Saccharomyces cerevisiae BY4741

Type:

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

Platforms:

GPL20138 GPL18330

50 Samples

Download data

(Submitter supplied) Despite the well-reported association between H3K4me3 and transcription, depletion of RNAPII from the nucleus has little effect on H3K4me3, while having a much larger effect on H3K36me3

Organism:

Saccharomyces cerevisiae BY4741

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20138

16 Samples

Download data: XLSX

(Submitter supplied) Despite the well-reported association between H3K4me3 and transcription, ablation of H3K4me3 by deletion of SPP1 has little effect on nascent transcription.

Organism:

Saccharomyces cerevisiae BY4741

Type:

Other

Platform:

GPL18330

6 Samples

Download data: XLSX

(Submitter supplied) Ablation of H3K4me3 by deletion of SPP1 has no strong or consistent effect on the rate of mRNA degradation following depeletion of RNAPII from the nucleus.

Organism:

Saccharomyces cerevisiae BY4741

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20138

24 Samples

Download data: XLSX

(Submitter supplied) We report a drastic genome-wide reduction of H3K4me3 levels following deletion of SPP1.

Organism:

Saccharomyces cerevisiae BY4741

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20138

4 Samples

Download data: XLSX

(Submitter supplied) Post-transcriptional modifications to messenger RNAs (mRNAs) have the potential to alter the biological function of this important class of biomolecules. The study of mRNA modifications is a rapidly emerging field, and the full complement of chemical modifications in mRNAs is not yet established. We sought to identify and quantify the modifications present in yeast mRNAs using an ultra-high performance liquid chromatography tandem mass spectrometry method to detect 40 nucleoside variations in parallel. more...

Organism:

Saccharomyces cerevisiae BY4741

Type:

Expression profiling by high throughput sequencing

Platform:

GPL22674

4 Samples

Download data: XLSX

(Submitter supplied) We compare patterns of H3K79me and H2Bub across genes in budding yeast

Organism:

Saccharomyces cerevisiae BY4741

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18330

20 Samples

Download data: BW

(Submitter supplied) Ribosome is the most abundant RNA-protein complex in a cell and many copies of the ribosomal RNA gene (rDNA) have to be maintained. However, arrays of tandemly repeated rDNA genes can lose the copies by intra-repeat recombination. Loss of the rDNA copies of Saccharomyces cerevisiae is counteracted by gene amplification whereby the number of rDNA repeats stabilizes around 150 copies, suggesting the presence of a monitoring mechanism that counts and adjusts the number. more...

Organism:

Saccharomyces cerevisiae BY4741

Type:

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

Platform:

GPL21372

25 Samples

Download data: BEDGRAPH, TSV, XLS