Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcription profiling of S. cerevisiae acs2Ts1 mutant

ABSTRACT: Wild-type and the acs2Ts1 mutant yeasts were shifted from 25deg to 37deg. After 60 minutes, Yeasts were harvested and divided into 2 x 2 cell samples. Total RNAs were purified from 4 populations. Experiment Overall Design: microarray data of 2 x 2 = 4 samples were background-corrected with RMA. Because of a global change in expression, the data were taken as 1 x 2 = 2 means and normalized with controls using lowess curve.

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Hidekazu Takahashi

PROVIDER: E-GEOD-2806 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Nucleocytosolic acetyl-coenzyme a synthetase is required for histone acetylation and global transcription.

Takahashi Hidekazu H McCaffery J Michael JM Irizarry Rafael A RA Boeke Jef D JD

Molecular cell 20060701 2

Metabolic enzymes rarely regulate informational processes like gene expression. Yeast acetyl-CoA synthetases (Acs1p and 2p) are exceptional, as they are important not only for carbon metabolism but also are shown here to supply the acetyl-CoA for histone acetylation by histone acetyltransferases (HATs). acs2-Ts mutants exhibit global histone deacetylation, transcriptional defects, and synthetic growth defects with HAT mutants at high temperatures. In glycerol with ethanol, Acs1p is an alternate ...[more]

PMID: 16857587

Similar Datasets

Comparison of gene regulation by Gcn5 under KCl stress in S. cerevisiae and S. pombe

Project description:This is parallel comparison of gene regulation by Gcn5 in evolutionarily divergent yeasts S. pombe and S. cerevisiae. Our study showed Gcn5 is required for a similar spectrum of stress responses in both organisms, including the response to KCl. This DNA microarray studies is to find conserved or diverged gene regulation pattern under KCl stress condition in the two yeasts. There are 6 subsets in total, 3 subsets in each evolutionarily divergent yeasts including the following: 1 gcn5 mutant compared to wt under rich medium without treatment, 2 gcn5 mutant compared to wild type both under KCl treatment, 3 wild type strains under KCl treatment compared to wild type without treatment. Keywords: stress response, Gcn5, Comparative genomics, Transcriptional co-activator Gene expression profiling experiment in which gene expression in logarithmically growing cultures of test groups was compared to that of the control groups in rich medium at 25C. There are 6 subsets in total, 3 subsets in each yeast including the following: 1 gcn5 mutant compared to wt under rich medium without treatment, 2 gcn5 mutant compared to wild type both under KCl treatment, 3 wild type strains under KCl treatment compared to wild type without treatment. RNA was extracted and subjected to cDNA expression profiling analysis using the established protocols (Xue et al, 2004). Independent RNA preparations were used to hybridize to microarray slides with dye swap. Data normalized with 'Lowess' per chip per spot normalization.

2010-06-24 | E-GEOD-5218 | biostudies-arrayexpress

Evolutionary principles of modular gene regulation in Yeasts

Project description:Comparative time-series expression analysis of growth curves through carbon depletion in the ascomycete yeasts. Each of the following species-specific, growth curve derived samples competitively hybed to their own mid-log samples: lag phase, late log, diauxic shift, post-shift, plateau.

2013-04-25 | E-GEOD-38478 | biostudies-arrayexpress

Transcriptional profile of an acs2Ts1 mutant yeast

Project description:Wild-type and the acs2Ts1 mutant yeasts were shifted from 25deg to 37deg. After 60 minutes, Yeasts were harvested and divided into 2 x 2 cell samples. Total RNAs were purified from 4 populations. Keywords: WT vs mutant

2006-10-01 | GSE2806 | GEO

Measurement of Isoform Specific Turnover using sequencing (MIST-Seq) after transcriptional arrest in rpb1-1 strain of budding yeast

Project description:Transcriptional arrest is performed in the rpb1-1 strain grown at 24C in two independent biological replicates by raising the temperature instantly to 37C. Total RNA was collected at fixed time points after the arrest and sequenced using the 3' T-filling protocol as described by Wilkening et al 2013 to obtain accurate quantification of 3' isoforms. The decaying library size is corrected for the by reads mapping to the S.pombe spike-in control RNA. The decay rates are estimated on fitting a single parameter exponential decay curve after taking the technical reproducibility of low counts for every time point into account.

2014-11-17 | E-MTAB-2123 | biostudies-arrayexpress

Evolutionary principles of modular gene regulation in Yeasts

Project description:Comparative time-series expression analysis of growth curves through carbon depletion in the ascomycete yeasts Each of the following species-specific, growth curve derived samples competitively hybed to their own mid-log samples: lag phase, late log, diauxic shift, post-shift, plateau

2013-06-20 | E-GEOD-36253 | biostudies-arrayexpress

Transcription profiling of yeast grwon in high glucose medium and shifted to low glucose medium

Project description:Time series expression profile of yeast cells grown at high glucose and shifted to low glucose containing medium. Lowess normalized data in raw data files.

2008-09-01 | E-MTAB-22 | biostudies-arrayexpress

Kidney development time course

Project description:Array Design; Mouse Compugen 22K Spotted Oligo Author; Sean Grimmond Common Reference (Yes/No, ID); Yes Mouse universal Reference (Stratagene) Concentration; 100 Data processing/normalization; Lowess Normalisation GeneSpring) Developmental Stage; embryonic Diseased/Normal; normal Dye Swap; red/green Experiment Type; time course Genetic Characteristic; Wild type Image Analysis Software; Imagene5.5 (Biodiscovery) Labeling Protocol; Amino Allyl Message Amp- Ambion Organ/Organism part; kidney Organism; Mus Musculus RNA type; aRNA Message Amp-ambion Tissue Type; Pool of whole organs Organization; IMB, Uni of QLD, Brisbane Australia Sample Source; primary tissue Sampling Method; Dissection of whole organ Sex; Pool of both sexes Strain/Cell-line; CD1 Series_overall_design: To account for dye swap, the signal channel and control channel measurements for each sample were reversed. A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead. Specific samples were normalized to one another: sample(s) 1-38 were normalized against the median of the control sample(s) 1-38. Each measurement for each gene in those specific samples was divided by the median of that gene's measurements in the corresponding control samples. Keywords: time-course

2005-07-20 | GSE2282 | GEO

Transcription profiling of wild type and talA talB double knock out E. coli

Project description:Wild-type and talA talB double knockout cells were grown in 50 ml of MOPS medium supplemented with 0.2% glucose or xylose in 500 ml Erlenmeyer flasks until the OD600 reached 1. At the sampling RNA was stabilized by mixing with RNAprotect Bacteria regent (Qiagen) and total RNA were isolated, by RNeasy mini Kit (Qiagen). Duplicate experiments employing dye swapping were performed for comparison. Protocol and conditions used for hybridization and washing were as described {Oshima, 2002 #712}. Images were scanned by Affymetrix 428 in 10µm resolution using Jaguar 2.0 software and processed by Imagene 4.0 software (BioDiscovery, Segundo ,USA) by default setting.?The raw numerical data files from Imagene were further processed by GeneSpring 7.3 (Agilent) software package. A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement.

2009-06-01 | E-MEXP-1841 | biostudies-arrayexpress

Kidney development time course

2010-06-09 | E-GEOD-2282 | biostudies-arrayexpress

FT1 and FT2 network analysis in poplar

Project description:We conducted microarray experiments by comparing constitutive and inducible Flowering Locus T1 (FT1) and FT2 constructs with appropriate controls, followed by the identification of common targets of Pro35S:FT1 and ProHSP:FT1 or Pro35S:FT2 and ProHSP:FT2. Independent samples of leaf tissues were collected from 1- to 2-year-old plants. Each replication represents an individual plant from one of the treatment lines. RNA was extracted from tissues and hybridized on the Affymetrix GeneChip Poplar Genome Array.

2011-05-23 | E-GEOD-24609 | 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