Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

41 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Expression data from Saccharomyces cerevisiae treated with Small Molecule Enhancers of Rapamycin (SMERs)

ABSTRACT: The target of rapamycin (TOR) plays a central role in eukaryotic cell growth control. With prevalent hyper-activation of the mTOR pathway in human cancers, novel strategies to enhance TOR pathway inhibition are highly desirable. We used a yeast-based high-throughput chemical genetic screen to identify small-molecule enhancers of rapamycin (SMERs) and used whole genome expression analysis to identify their mechanisms of action. We treated yeast individually with SMERs 1-5, rapamycin, or DMSO (solvent control) for 30 minutes prior to RNA extraction and hybridization on Affymetrix microarrays. Expression profiles of SMER-treated samples were compared to that of DMSO (solvent control) and rapamycin-treated samples to identify gene expression signatures unique to SMER-treated samples.

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Nao Jonai

PROVIDER: E-GEOD-22269 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Expression data from Saccharomyces cerevisiae Met30 temperature-sensitive strain

Project description:The target of rapamycin (TOR) plays a central role in eukaryotic cell growth control. With prevalent hyper-activation of the mTOR pathway in human cancers, novel strategies to enhance TOR pathway inhibition are highly desirable. We used a yeast-based high-throughput chemical genetic screen to identify small-molecule enhancers of rapamycin (SMERs) and used whole genome expression analysis to identify their mechanisms of action. We incubated Met30 temperature-sensitive yeast strain at either the permissive (room temperature) or non-permissive (35°C) temperature for 1 hour prior to RNA extraction and hybridization on Affymetrix microarrays. Comparison of expression profiles enabled identification of gene-signature characteristic of Met30 inhibition.

2011-06-30 | E-GEOD-22270 | biostudies-arrayexpress

Chemical Genetics of TOR Identifies an SCF Family E3 Ubiquitin Ligase Inhibitor

Project description:The target of rapamycin (TOR) plays a central role in eukaryotic cell growth control. With prevalent hyper-activation of the mTOR pathway in human cancers, novel strategies to enhance TOR pathway inhibition are highly desirable. We used a yeast-based high-throughput chemical genetic screen to identify small-molecule enhancers of rapamycin (SMERs) and used whole genome expression analysis to identify their mechanisms of action. This SuperSeries is composed of the following subset Series: GSE22270: Expression data from Saccharomyces cerevisiae Met30 temperature-sensitive strain GSE22271: Expression data from Saccharomyces cerevisiae temperature-sensitive strains specific for SCF core components (Skp1, Cullin (Cdc53), E2 enzyme (Cdc34)) and the F-box protein Cdc4. Refer to individual Series

2011-06-30 | E-GEOD-22272 | biostudies-arrayexpress

Expression data from Saccharomyces cerevisiae temperature-sensitive strains specific for SCF core components (Skp1, Cullin (Cdc53), E2 enzyme (Cdc34)) and the F-box protein Cdc4.

Project description:The target of rapamycin (TOR) plays a central role in eukaryotic cell growth control. With prevalent hyper-activation of the mTOR pathway in human cancers, novel strategies to enhance TOR pathway inhibition are highly desirable. We used a yeast-based high-throughput chemical genetic screen to identify small-molecule enhancers of rapamycin (SMERs) and used whole genome expression analysis to identify their mechanisms of action. We incubated various temperature-sensitive yeast strains at either the permissive (room temperature) or non-permissive (35°C) temperature for 1 hour prior to RNA extraction and hybridization on Affymetrix microarrays. Comparison of expression profiles enabled identification of gene-signatures specific to inhibition of each gene product.

2011-06-30 | E-GEOD-22271 | biostudies-arrayexpress

Rice cell culture: Control vs. Rapamycin treatment

Project description:To shed light on the TOR signaling network in crop plants, we investigated the global transcriptome changes in rice suspension cells (cultivar Kitaake) treated with the TOR-specific inhibitor rapamycin.

2017-07-15 | GSE93872 | GEO

Multilayered control of protein turnover by TORC1 and ATG1

Project description:To study TORC1-Atg1 signaling comprehensively and to identify potential additional foci of crosstalk, we chose a mass spectrometry (MS)-based phosphoproteomics strategy combing global proteomics screens in vivo with targeted analyses using in vitro kinase reactions. We present the currently largest compendium of rapamycin-sensitive phosphorylation events in the yeast Saccharomyces cerevisiae, identify numerous unknown TORC1 and Atg1 downstream phosphorylation events, and characterize hitherto unknown, functionally relevant TORC1 target sites on defined Atg proteins.

2019-09-30 | PXD013271 | Pride

Analysis of Colletotrichum orbiculare whi2Δ mutant infection of Cucumis sativus at 4hpi

Project description:Colletotrichum orbiculare Whi2, yeast stress response Whi2 homolog, is involved in switch from biotrophic to necrotrophic stage. To elucidate downstream genes regulated by Co Whi2, we have conducted DNA microarray. About 3100 genes were up or down regulated in the Co whi2Δ mutant compared with the wild-type. In particularly, 44 genes among up-regulated 58 genes in the Co whi2Δ mutant are ribosomal protein related gene. Eukaryote is widely conserved TOR (Target Of Rapamycin) which is known to regulator of ribosomal gene expression. To elucidate whether up-regulated ribosomal genes in the Co whi2Δ mutant are regulated by TOR activity, we have conducted DNA microarray in the Co whi2Δ mutant treated with rapamycin inhibiting TOR activity. The enormous ribosomal gene expression in the Co whi2Δ mutant treated with the rapamycin is lower than that without rapamycin treatment.

2016-04-01 | GSE73096 | GEO

Parallels between oncogene-induced cardiac neoplasia and heart regeneration in zebrafish

Project description:We used a cardiac-specific tamoxifen-dependent Gal4-ERT2/UAS model to achieve uniform but conditionally regulated expression of the oncogene HRASG12V in zebrafish cardiomyocytes. We found that the inhibition of TOR signaling using rapamycin treatment counteracts neoplasic growth. We analyse the transcriptome of neoplasic ventricles after exposure to DMSO and rapamycin and we applied bioinformatic analysis to determine common and distinctive molecular signatures of neoplasia versus regeneration of the heart.

2022-09-05 | GSE191324 | GEO

Differentially regulated genes in TOR knockdown Arabidopsis lines

Project description:Rapamycin-sensitive transgenic Arabidopsis lines (BP12) expressing yeast FK506 Binding Protein12 (FKBP12) were developed. Inhibition of TOR in BP12 plants by rapamycin resulted in slower overall root, leaf and shoot growth and development leading to poor nutrient uptake and light energy utilization. Genetic and physiological studies together with RNA-Seq and metabolite analysis of TOR-suppressed lines revealed that TOR regulates development and lifespan in Arabidopsis by restructuring cell growth, carbon and nitrogen metabolism, gene expression, ribosomal RNA and protein synthesis. Arabidopsis WT (Col)and BP12-2 (TOR knockdown line) seedlings at 15 DAG were treated with rapamycin for 3 days by transferring from 0.5 MS medium to 0.5 MS+10 ug/ml rapamycin. Triplicate samples of rapamycin treated WT and BP12-2 seedlings were used for RNA-Seq analysis (Illumina Hiseq 2000). Paired-end alignments were obtained through aligning short reads onto the reference Arabidopsis Genome (TAIR9) using Bowtie. More than 80% of the reads mapped onto the genome. Htseq-count was used to count the reads from the Bowtie derived output files. Differential expressed genes were identified using edgeR. The FDR-corrected P value for differential expression was set to be <=0.05.

2012-12-18 | E-GEOD-42968 | biostudies-arrayexpress

Biological chromodynamics: a general method for measuring protein occupancy across the genome by calibrating ChIP-seq

Project description:Sequencing DNA fragments associated with proteins following in vivo cross-linking with formaldehyde (known as ChIP-seq) has been used extensively to describe the distribution of proteins across genomes. It is not widely appreciated that this method merely estimates a protein’s distribution and cannot reveal changes in occupancy between samples. To do this, we tagged with the same epitope orthologous proteins in Saccharomyces cerevisiae and Candida glabrata, whose sequences have diverged to a degree that most DNA fragments longer than 50 bp are unique to just one species. By mixing defined numbers of C.glabrata cells (the calibration genome) with S.cerevisiae samples (the experimental genomes) prior to chromatin fragmentation and immunoprecipitation, it is possible to derive a quantitative measure of occupancy (the occupancy ratio – OR) that enables a comparison of occupancies not only within but also between genomes. We demonstrate for the first time that this “internal standard” calibration method satisfies the sine qua non for quantifying ChIP-seq profiles, namely linearity over a wide range. Crucially, by employing functional tagged proteins, our calibration process describes a method that distinguishes genuine association within ChIP-seq profiles from background noise. Our method is applicable to any protein, not merely highly conserved ones, and obviates the need for the time consuming, expensive, and technically demanding quantification of ChIP using PCR, which can only be performed on individual loci. As we demonstrate for the first time in this paper, calibrated ChIP-seq represents a major step towards documenting the quantitative distributions of proteins along chromosomes in different cell states, which we term biological chromodynamics. Develop a method for quantitative ChIP-seq

2015-07-10 | E-GEOD-69907 | biostudies-arrayexpress

Releasing activity disengages cohesinâs Smc3/Scc1 interface in a process blocked by acetylation

Project description:Sister chromatid cohesion conferred by entrapment of sister DNAs within a tripartite ring formed between cohesinâs Scc1, Smc1, and Smc3 subunits is generated during S and eventually destroyed at anaphase through cleavage of Scc1 by separase. Throughout the cell cycle, cohesinâs association with chromosomes is controlled by opposing activities: loading by the Scc2/4 complex and release by a separase independent releasing activity. Co-entrapment of sister DNAs during replication is accompanied by acetylation of Smc3 by Eco1, which blocks releasing activity and ensures that sisters remain stably connected. Because fusion of Smc3 to Scc1 prevents release and bypasses the requirement for Eco1, we suggested that release is mediated by disengagement of the Smc3/Scc1 interface. We now show that all mutations capable of bypassing Eco1, be they in cohesinâs Smc1, Smc3, Scc1,Wapl, Pds5, or Scc3 subunits, greatly reduce dissociation of N-terminal cleavage fragments of Scc1 (NScc1) from Smc3. We show that this process involves interaction between Smc ATPase heads and is inhibited by Smc3 acetylation Effect of mutations QQ and EQ in Smc3 on cohesin loading onto chromosomes

2016-02-18 | E-GEOD-76890 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data