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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Expression data from aged wild-type, met15Δ and rtg3Δ met15Δ yeast

ABSTRACT: To explore putative connections between genetic methionine restriction and the retrograde response, we asked whether the altered transcriptional program of methionine-restricted cells required RTG3 (which is indispensible for retrograde signaling in yeast). Towards this end, we used Affymetrix GeneChip Yeast Genome 2.0 arrays to perform expression profiling of aged (Day 3) wild-type, met15Δ and rtg3Δ met15Δ yeast.

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Jay Johnson

PROVIDER: E-GEOD-56641 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Expression data from aged wild-type, met15Δ and rtg3Δ met15Δ yeast

Project description:To explore putative connections between genetic methionine restriction and the retrograde response, we asked whether the altered transcriptional program of methionine-restricted cells required RTG3 (which is indispensible for retrograde signaling in yeast).

2014-04-10 | GSE56641 | GEO

DNA replication profiling by BrdU Immunoprecipitation of S.cerevisiae wild-type versus H3K37R mutant

Project description:Wild-type and isogenic H3K37R yeast cultures were sinchronized in G1 with alpha factor. Cell were released into the cycle in the presence of 200mM Hydroxyurea and 0.5mg/ml BrdU. After 1h 15 minutes at 30C, replication was stopped by addition of NaN3 and cells were processed for DNA immunoprecipitation with anti BrdU antibody.

2021-04-14 | E-MTAB-9097 | biostudies-arrayexpress

Expression-profiling of the Mediator transcription complex

Project description:Proteins from within the Saccharomyces cerevisiae Mediator transcription complex were knocked out and compared against wild type yeast using two-color oligo arrays.

2005-08-15 | E-UMCU-20 | biostudies-arrayexpress

A role for the nucleoporin Nup170p in chromatin structure and gene silencing [Agilent microarrays]

Project description:Embedded in the nuclear envelope, nuclear pore complexes (NPCs) not only regulate nuclear transport, but also interface with both transcriptionally active euchromatin and largely silenced heterochromatin, as well as the boundaries between these regions. It is unclear what functional role NPCs play in establishing or maintaining these distinct chromatin domains. Here we report that the yeast NPC protein Nup170p interacts with specific regions of the genome containing ribosomal protein and subtelomeric genes. At these locations, Nup170p functions to establish normal nucleosome positioning and as a repressor of transcription. We show that the function of Nup170p in subtelomeric gene silencing is linked to its association with the RSC chromatin-remodeling complex and the silencing factor Sir4p, and that the binding of Nup170p and Sir4p to subtelomeric chromatin is cooperative and necessary for the association of telomeres with the nuclear envelope. Our results establish the NPC as an active participant in the formation of peripheral heterochromatin. Two-color microarrays were performed using Agilent whole-genome Saccharomyces cerevisiae arrays (Agilent) to determine gene expression profiles in the nucleoporin mutant strains nup157M-bM-^HM-^F, nup170M-bM-^HM-^F, and nup188M-bM-^HM-^F. Similar analyses were performed on PMET3-HA3-STH1 cells depleted of Sth1p for either 2 hrs (sth1-deplete 2hrs) or depleted of Sth1p for 8 hrs followed by reinduction of Sth1p for an additional 4 hrs (sth1-reinduction 4hr), as well as WT cells grown in the presence or absence of methionine. All experiments were performed with duplicate experimental and duplicate technical replicates of each condition as previously described (Wan et al., 2009).

2013-02-28 | E-GEOD-36793 | biostudies-arrayexpress

Genome-wide Ste12-binding site mapping in MATa segregants of YJM789 x S96 cross

Project description:In this study, we mapped for the first time differences in transcription binding among individuals and elucidated the genetic basis of such variation. Whole-genome Ste12 binding profiles were determined using ChIP-Seq in pheromone-treated cells of 43 segregants of a cross between two highly diverged yeast strains, YJM789 and S288c as well as the parental lines. We identified extensive Ste12 binding variation among individuals and mapped underlying cis- and trans- acting loci responsible for such variation. We showed that the majority of TF binding variation is cis-linked and that many variations are associated with polymorphisms residing in the binding motifs of Ste12 as well as those of several known and proposed Ste12 cofactors. We also identified two trans factors, AMN1 and FLO8, that modulate Ste12 binding to promoters of more than 10 genes under Î±-factor treatment. Neither of these two genes was known to regulate Ste12 previously, and we suggest that they may be key mediators of gene activity and phenotypic diversity. Ste12 binding strongly correlates with gene expression for more than 200 genes indicating that binding variation is functional. Many of the variable bound genes are involved in cell wall organization and biogenesis. Overall, we identified key regulators of molecular diversity among individuals and provide novel insights into mechanisms of gene regulation. Two ChIP-Seq experiments and one Input DNA-Seq experiment for the yeast strains S96, HS959 and 43 MATa segregants were performed under alpha factor treatment conditions; an additional replicate was also performed for some of the strains. One ChIP-Seq experiment for each parental strain was performed without alpha factor treatment, and one ChIP-Seq experiment for each of the 24 deletion strains was performed under alpha factor treatment.

2010-02-18 | E-GEOD-19635 | biostudies-arrayexpress

Ribosome profiling of budding yeast Saccharomyces cerevisiae in eEF3 depleted conditions

Project description:Ribosome profiling (Ribo-Seq) and RNA-Seq analysis of eEF3 depletion in yeast (Saccharomyces cerevisiae). eEF3 depletion was induced by methionine in a modified strain where the native promoter was replaced by methionine repressible MET25 promoter. Conditional depletion enables us to study global effects of an essential gene.

2018-06-30 | E-MTAB-6938 | biostudies-arrayexpress

CGH of common Candida albicans strains

Project description:The purpose of this review is to describe the tools used to detect genome changes, to highlight recent advances in our understanding of large scale chromosome changes that arise in C. albicans and to discuss the role of specific stresses in eliciting these genome changes. The types of genomic diversity that have been characterized suggest C. albicans can undergo extreme genomic changes in order to survive stresses in the human host. We propose that C. albicans and other pathogens may have evolved mechanisms not only to tolerate, but also to generate, large-scale genetic variation as a means of adaptation. Strains included in this series are described in a Eukaryotic Cell review of genomic plasticity of Candida albicans. These strains are well-characterized and some of them are frequently utilized by the Candida community to generate mutant strains. Each strain was analyzed once and all strains were competed against the same reference strain, SC5314 (the first sequenced C. albicans strain).

2010-06-01 | E-GEOD-21643 | biostudies-arrayexpress

wt expression changes in deletion strain-conditioned media

Project description:To rule out expression changes caused by depletion from, or excretion into the media, wild-type yeast was transferred to filtered media in which slow-growing deletion strains were grown previously

2014-05-14 | E-MTAB-2218 | biostudies-arrayexpress

NeuCode metabolic labeling reveals a high correlation between mRNA and protein abundance during salt adaptation in S. cerevisiae.

Project description:Transcriptome profiling of yeast strains responding to 0.7M NaCl treatment for 30 or 60 minutes. This study identified affected genes under both conditions tested. Transcript and protein changes were compared to determine mRNAs contribution to protein levels during salt acclimation. Two-color fluorescence arrays reporting on mRNA abunance in strains before and at 30 min or 60 min after a shock with 0.7M NaCl, hybridized to yeast tile-genome Nimblegen arrays

2013-12-21 | E-GEOD-53549 | biostudies-arrayexpress

A role for Snf2 related nucleosome spacing enzymes in genome-wide nucleosome organization

Project description:The positioning of nucleosomes within the coding regions of eukaryotic genes is aligned with respect to transcriptional start sites. This organization is likely to influence many genetic processes, requiring access to the underlying DNA. Here we show that the combined action of Isw1 and Chd1 nucleosome spacing enzymes is required to maintain this organization. In the absence of these enzymes regular positioning of the majority of nucleosomes is lost. Exceptions include the region upstream of the promoter, the +1 nucleosome and a subset of locations distributed throughout coding regions where other factors are likely to be involved. These observations indicated that ATP-dependent remodeling enzymes are responsible for directing the positioning of the majority of nucleosomes within the Saccharomyces cerevisiae genome. Examination of nucleosome positioning in mutants of snf2-related enzymes Other data used in this study are provided in GEO Series GSE31301 and GSE31833.

2011-09-16 | E-GEOD-31015 | biostudies-arrayexpress

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