txid559292[Organism] - GEO DataSets

(Submitter supplied) The disruption of chromatin structure can result in transcription initiation from cryptic promoters within gene bodies. While the passage of RNA polymerase II is a well-characterized chromatin-disrupting force, numerous factors, including histone chaperones, normally stabilize chromatin on transcribed genes, thereby repressing cryptic transcription. DNA replication, which requires a partially overlapping set of histone chaperones, is also inherently disruptive to chromatin, but a role for DNA replication in cryptic transcription has never been examined. more...

Organism:: Saccharomyces cerevisiae S288C

Type:: Expression profiling by high throughput sequencing

Platform:: GPL33992
6 Samples

Download data: FA, WIG

Series

Accession:: GSE249580

ID:: 200249580

PubMed Similar studies

Select item 2002080953.

Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Set1 S228A S228E mutant Transcriptomes

(Submitter supplied) Cells need to coordinate gene expression with their metabolic states to maintain cell homeostasis and growth. However, how cells transduce nutrient availability to appropriate gene expression response via histone modifications remains poorly understood. Here,we reported cla4 catalyzed Set1 phosphorylaton regulates cell cycle and histone gene transcription.

Organism:: Saccharomyces cerevisiae S288C

Type:: Expression profiling by high throughput sequencing

Platform:: GPL23380
9 Samples

Download data: TXT

Series

Accession:: GSE208095

ID:: 200208095

PubMed Full text in PMC Similar studies

Select item 2001606424.

RNAs associated with Upf1, Pab1, Rpl16a, Lsm1 proteins in yeast

(Submitter supplied) Nonsense mediated mRNA decay (NMD) is a translation-dependent surveillance pathway that eliminates RNAs with short open reading frames (ORFs) and long 3' untranslated regions (UTRs). Upf1 is the key protein of this degradation pathway and we were interested to purify the associated RNAs. Moreover we have done purifications of two proteins from the general mRNA turnover in yeast : Pab1 and Lsm1 that both bind RNAs poly(A) tails. more...

Organism:: Saccharomyces cerevisiae S288C

Type:: Expression profiling by high throughput sequencing

Platform:: GPL23380
18 Samples

Download data: FA, TXT

Series

Accession:: GSE160642

ID:: 200160642

SRA Run Selector

Select item 2001625135.

Scaling of cellular gene expression with ploidy

(Submitter supplied) Whereas most eukaryotic cells are diploid, carrying two chromosome sets, variances in ploidy are common. Despite the relative prevalence of ploidy changes and their relevance for pathology and evolution, the consequences of altered ploidy for cellular gene expression remain poorly understood. We quantified changes in the transcriptome and proteome of the yeast Saccharomyces cerevisiae with different ploidy, from the haploid to the tetraploid state. more...

Organism:: Schizosaccharomyces pombe; Saccharomyces cerevisiae; Saccharomyces cerevisiae S288C

Type:: Expression profiling by array

Platform:: GPL2529
24 Samples

Download data: CEL, XLSX

Series

Accession:: GSE162513

ID:: 200162513

PubMed Full text in PMC Similar studies

Select item 2001659846.

Localization of wildtype Ioc4 in wildtype and set2 yeast strains. Localization of Ioc4 mutants (dPWWP, 2KE, dINS) in wildtype yeast strains.

(Submitter supplied) ChIP-chip assays to assess the localization of FLAG-tagged, wildtype and mutant Ioc4 in yeast.

Organism:: Saccharomyces cerevisiae; Saccharomyces cerevisiae S288C

Type:: Genome variation profiling by genome tiling array

Platform:: GPL29687
15 Samples

Download data: TXT

Series

Accession:: GSE165984

ID:: 200165984

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 2001757947.

Tryptophan plays a central role in yeast’s tolerance to isobutanol

(Submitter supplied) Isobutanol is considered a potential biofuel and can be produced by genetically modified microorganisms. Saccharomyces cerevisiae inherently produces isobutanol through valine intermediate(s), so it serves as a good host. However, isobutanol's toxicity remains a key obstacle for bioproduction. In our study, we first used image recognition to screen the colony growth of a yeast gene deletion library and inferred that genes involved in tryptophan biosynthesis, ubiquitination, and the pentose phosphate pathway (PPP) contribute to isobutanol tolerance. more...

Organism:: Saccharomyces cerevisiae S288C

Type:: Expression profiling by high throughput sequencing

Platform:: GPL23380
24 Samples

Download data: XLSX

Series

Accession:: GSE175794

ID:: 200175794

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2001480688.

Dbf4-Dependent Kinase (DDK)-Mediated Proteolysis of CENP-A Prevents Mislocalization of CENP-A in Saccharomyces cerevisiae

(Submitter supplied) Restricting the localization of the centromeric histone H3 variant CENP-A to centromeres is essential to prevent chromosomal instability (CIN). Mislocalization of overexpressed CENP-A contributes to CIN in yeast, fly, and human cells. CENP-A is overexpressed in many cancers. Therefore, defining mechanisms that prevent CENP-A mislocalization will help us understand how CENP-A overexpression contributes to CIN in cancer. more...

Organism:: Saccharomyces cerevisiae S288C

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL23380
8 Samples

Download data: BEDGRAPH, NARROWPEAK

Series

Accession:: GSE148068

ID:: 200148068

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2001456029.

Deposition of centromeric histone H3 variant CENP-A/Cse4 into chromatin is facilitated by its C-terminal sumoylation

(Submitter supplied) Centromeric localization of CENP-A (Cse4 in S. cerevisiae, CID in flies, CENP-A in humans) is essential for faithful chromosome segregation. Overexpression of CENP-A leads to its mislocalization and contributes to aneuploidy in yeast, flies, humans and is proposed to promote tumorigenesis in human cancers. Hence, defining molecular mechanisms that promote or prevent mislocalization of CENP-A is an area of active investigation. more...

Organism:: Saccharomyces cerevisiae S288C

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL28175
12 Samples

Download data: BED, NARROWPEAK

Series

Accession:: GSE145602

ID:: 200145602

SRA Run Selector

Select item 20012535310.

Saccharomyces cerevisiae deletion collections chemogenomic screen with Triclosan, Methylparaben and Ethylzingerone

(Submitter supplied) Growth assay in the presence of a toxic chemical that uses the barcoded collections of yeast gene deletions (haploid, diploid, DamP) to identify deletion strains that are hypersensitive to the drug.

Organism:: Saccharomyces cerevisiae; Saccharomyces cerevisiae S288C

Type:: Expression profiling by array

Platform:: GPL18088
6 Samples

Download data: GPR

Series

Accession:: GSE125353

ID:: 200125353

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20011917411.

Genetic interaction mapping (GIM) for factors involved in RNA and protein synthesis and degradation

(Submitter supplied) A S. cerevisiae strain a gene of interest mutated or deleted was combined with two collections of yeast mutants: one in which non-essential genes were deleted and one in which an long 3' UTR extension has been added to the mRNA of essential genes (GIM method, Decourty et al., 2008). Combined double-mutant deletion cells growth was quantified using barcodes that are specific for each gene mutation. A reference population was obtained by mixing the results of 15 GIM screens DNA prior to barcode amplification and labeling (Decourty et al., in preparation). more...

Organism:: Saccharomyces cerevisiae; Saccharomyces cerevisiae S288C

Type:: Genome variation profiling by array

Platform:: GPL18088
312 Samples

Download data: GPR

Series

Accession:: GSE119174

ID:: 200119174

Analyze with GEO2R

Select item 20014035412.

Loss of major nutrient sensing and signaling pathways suppresses starvation lethality in electron transport chain mutants

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

Organism:: Saccharomyces cerevisiae S288C

Type:: Expression profiling by high throughput sequencing

Platform:: GPL27752
143 Samples

Download data

Series

Accession:: GSE140354

ID:: 200140354

Select item 20014035313.

Loss of major nutrient sensing and signaling pathways suppresses starvation lethality in electron transport chain mutants (DenseTimeCourse)

(Submitter supplied) Here we sought to comprehensively characterize the role of the electron transport chain in yeast models of aging. Using a panel of ETC mutants, we observed that ETC mutants fail to survive starvation when grown to saturation in standard SD growth medium. This starvation lethality is associated with a significantly lower cytosolic pH and dysregulated gene expression compared to wild type cells. In an unbiased genetic suppressor screen, we found that loss of function mutations in major cellular nutrient sensing/signaling pathways (Ras/PKA, Tor, PP2A) along with a number of gene expression regulators can prevent starvation lethality in these mutants. more...

Organism:: Saccharomyces cerevisiae S288C

Type:: Expression profiling by high throughput sequencing

Platform:: GPL27752
72 Samples

Download data: TXT

Series

Accession:: GSE140353

ID:: 200140353

SRA Run Selector

Select item 20014035214.

Loss of major nutrient sensing and signaling pathways suppresses starvation lethality in electron transport chain mutants (ETC_Mutants)

Organism:: Saccharomyces cerevisiae S288C

Type:: Expression profiling by high throughput sequencing

Platform:: GPL27752
71 Samples

Download data: TXT

Series

Accession:: GSE140352

ID:: 200140352

SRA Run Selector

Select item 20011855015.

Genetic interaction analysis of RSA1 deletion strains (GIM screen)

(Submitter supplied) A S. cerevisiae strain with deletion of RSA1 gene was combined with two collections of yeast mutants: one in which non-essential genes were deleted and one in which an long 3' UTR extension has been added to the mRNA of essential genes (GIM method, Decourty et al., 2008). Combined double-mutant deletion cells growth was quantified using barcodes that are specific for each gene mutation. A reference population was obtained by mixing the results of 15 GIM screens DNA prior to barcode amplification and labeling (Decourty et al., in preparation). more...

Organism:: Saccharomyces cerevisiae S288C; Saccharomyces cerevisiae

Type:: Other

Platform:: GPL18088
2 Samples

Download data: GPR

Series

Accession:: GSE118550

ID:: 200118550

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 20009826016.

Promoter DNA sequence guides factors that position the +1 nucleosome and facilitate TBP binding

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

Organism:: Saccharomyces cerevisiae S288C; Saccharomyces cerevisiae W303; Saccharomyces cerevisiae

Type:: Expression profiling by array; Genome binding/occupancy profiling by high throughput sequencing

Platforms:: GPL17342 GPL11232
64 Samples

Download data: BW, TXT

Series

Accession:: GSE98260

ID:: 200098260

Select item 20009820517.

Promoter DNA sequence guides factors that position the +1 nucleosome and facilitate TBP binding [array]

(Submitter supplied) Here we present evidence that precise positioning of the +1 promoter nucleosome in yeast is critical for efficient TBP binding and pre-initiation complex assembly, and is determined, at least in part, by the action of two key factors, the essential chromatin remodeler RSC and one (or more) of a small set of ubiquitous pioneer transcription factors (PTFs). Despite their widespread co-localization, we show that RSC and PTFs often act independently to generate accessible chromatin. more...

Organism:: Saccharomyces cerevisiae W303; Saccharomyces cerevisiae; Saccharomyces cerevisiae S288C

Type:: Expression profiling by array

Platform:: GPL11232
12 Samples

Download data: TXT

Series

Accession:: GSE98205

ID:: 200098205

Select item 20009828218.

ChIP Seq analysis of H3K4me3 and H3K79me3 in euploid and aneuploid Saccharomyces cerevisiae

(Submitter supplied) Aneuploidy and epigenetic alterations have long been associated with carcinogenesis, but it was unknown whether aneuploidy could disrupt the epigenetic states required for cellular differentiation. In this study, we found that ~3% of random aneuploid karyotypes in yeast disrupt the stable inheritance of silenced chromatin during cell proliferation. Karyotype analysis revealed that this phenotype was significantly correlated with gains of chromosomes III and X. more...

Organism:: Saccharomyces cerevisiae S288C

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL23380
12 Samples

Download data: TXT

Series

Accession:: GSE98282

ID:: 200098282

SRA Run Selector

Select item 20008434019.

Saccharomyces cerevisiae deletion and DAmP collections chemogenomic screen with Selenomethionine

(Submitter supplied) Growth assay in the presence of Selenomethionine that uses the barcoded collections of yeast gene modification (deletion or DamP) to identify strains that are hypersensitive to the presence of the aminoacid.