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

Yeast Genomic Expression Patterns in Response to Zymolyase Treatment

ABSTRACT: We used microarray to investigate the influence of zymolyase treatment which is used for degradation of yeast cell wall. Two types of RNA extraction methods were used, and zymolyase preprocessing was applied to one among them. The qualities of total RNA extracted by two extraction methods were checked, and then RNAs were used for generating cloned DNA and RNA. Finally, two types of cRNA were hybridized to Affymetrix yeast genome 2.0_array. Keywords: comparison of RNA extraction process Yeast BY4743 was grown in YPD media containing 0.01% SDS, and was applied for two types of RNA extraction method.

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Tadahiro Suzuki

PROVIDER: E-GEOD-18456 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Yeast Genomic Expression Patterns in Response to glucosylated mycotoxin

Project description:The evaluation of mycotoxicity about glucosylated mycotoxin using yeast gene expression comparison analysis. Yeast BY4743 derivative PDR5 mutant was used for this study. Samples were normalized with the three replicates per condition. Yeast strain was grown in YPD medium with 80 Î¼M of deoxynivalenol-3-glucoside. The same volume of DMSO was added into control samples.

2015-04-01 | E-GEOD-63663 | biostudies-arrayexpress

Yeast Genomic Expression Patterns of Wild-type and PTC1 null mutant in Response to Aflatoxin B1 (AFB1)

Project description:The evaluation of the toxicity of Aflatoxin B1 using yeast gene expressions. Two yeast strains; parental BY4743 and PTC1 mutant, were used for this study. SDS was used to raise the penetration of the yeast cell membrane. Two conditions are compared with three replicates each. Both strains were grown in 0.01% SDS containing YPD media or 0.01% SDS, 25 ppm ABF1 containing YPD media. Publication can be found at http://www.cbi.or.jp/cbi/CBIj/vol9/9_94-E.pdf.

2010-04-12 | E-GEOD-17367 | biostudies-arrayexpress

Selective inhibition of yeast regulons by daunorubicin

Project description:The antitumor drug daunorubicin exerts some of its cytotoxic effects by binding to DNA and inhibiting the transcription of different genes. We analysed this effect in vivo transcriptome level using the budding yeast Saccharomyces cerevisiae as a model and sublethal concentrations of the drug to minimise general toxic effects. The effects of daunorubicin treatment on the yeast transcriptome are consistent with a model in which this drug impairs binding of different transcription factors by competing for their DNA binding sequences, therefore limiting their effectiveness and affecting the corresponding regulatory networks. This proposed mechanism might have broad therapeutic implications against cancer cells growing under hypoxic conditions. Keywords: Time course experiment (treated versus non-treated) Treatment with a single concentration of daunorubicin (DNR, 12 mM, IC40) for 1 or 4 hours. Three biological replicates for each sampling time (0, 1 and 4h). Untreated cultures were used as controls.

2010-05-18 | E-GEOD-19351 | biostudies-arrayexpress

Yeast Genomic Expression Patterns in Response to Zymolyase Treatment

Project description:We used microarray to investigate the influence of zymolyase treatment which is used for degradation of yeast cell wall. Two types of RNA extraction methods were used, and zymolyase preprocessing was applied to one among them. The qualities of total RNA extracted by two extraction methods were checked, and then RNAs were used for generating cloned DNA and RNA. Finally, two types of cRNA were hybridized to Affymetrix yeast genome 2.0_array. Keywords: comparison of RNA extraction process

2010-03-31 | GSE18456 | GEO

Dynamic transcriptome analysis reveals mRNA synthesis and decay in yeast

Project description:To obtain rates of mRNA synthesis and decay in yeast, we established dynamic transcriptome analysis (DTA). DTA combines non-perturbing metabolic RNA labeling with dynamic kinetic modeling. DTA was used to monitor the cellular response to osmotic stress in comparison to the wild type. Genomic occupancy profiling of RNA polymerase (Pol) II was used to predict changes in mRNA synthesis rates.

2011-11-01 | E-MTAB-439 | biostudies-arrayexpress

Yeast genomic expression patterns in response to zymolyase treatment

Project description:The evaluation of zymolyase treatment using yeast gene expression comparison analysis. The yeast BY4743 strain was used for this study. Yeast cells were treated with Zymolyase (final conc. 300 U/ml), and incubated at 37 degree for ten minutes. Digestion process was not provided for control sample. Total RNA was isolated with commercial kit (FastRNA Pro Red kit, Q-Biogene), and amplified RNA (aRNA) was synthesized with 3'IVT Express kit (Affymetrix). All samples were hybridized with Gene Chip (Yeast Genome 2.0 Array, Affymetrix), then each array chip was scanned by GeneChip Sanner 3000 (Affymetrix). Yeast were treated with zymolyase or left untreated. The only difference in conditions between the treated and untreated samples was the enzymatic digestion process. The conditioned samples were normalized with three replicates.

2013-03-21 | E-GEOD-36955 | biostudies-arrayexpress

wild type two hours exposure to zymolyase

Project description:S. cerevisiae was grown on YEPD. For Zymolyase experiments, yeast cells were grown overnight at 24 °C to an optical density 0.8 - 1 (A600). The culture was refreshed to 0.2 O.D and grown at 24 °C for 2h 30min. Next, culture was divided into two parts. One continues growing under same conditions (non-treated culture) while the other was supplemented with 5units/ml Zymolyase 100T . Cells were collected at 2 hours of growth, frozen at -80 °C and processed for RNA extraction. Keywords: repeat sample

2004-02-16 | GSE966 | GEO

Transcription profiling of S. cerevisiae unfolding response

Project description:The accumulation of unfolded proteins in the lumen of the endoplasmic reticulum (ER) causes stress and induces the unfolded protein response (UPR) which is characterised in part by the transcriptional induction of genes involved in assisting protein folding. Translational responses to ER stress have been less well described and here we report on a genome-wide analysis of translational regulation in the response to the ER stress-inducing agent dithiothreitol (DTT) in Saccharomyces cerevisiae. Although the observed polysome profiles were similar under control and ER stress conditions microarray analysis identified transcipt-specific translational regulation. Genes with functions in ribosomal biogenesis and assembly were translationally repressed under ER stress. In contrast mRNAs for known UPR genes, including the UPR transcription factor HAC1, the ER-oxidoreductase ERO1 and the ER-associated protein degradation (ERAD) gene DER1 were enriched in polysomal fractions under ER stress conditions. In addition, we show that splicing of HAC1 mRNA is required for efficient ribosomal loading and that Gcn2p is required for normal HAC1 splicing, so shedding light on the role of this protein kinase in the UPR pathway. Experiment Overall Design: Polyribosomes were extracted from S. cerevisiae cells treated with 2 mM DTT or water (control), and fractionated according to ribosome loading. Following RNA purification from these fractions, for each sub-polysomal and polysomal RNA sample, fractions from three independent extracts per treatment (DTT/control) were pooled.

2008-06-11 | E-GEOD-10091 | biostudies-arrayexpress

Wild type 3 hour exposure to zymolyase

Project description:We did transcription profiling on the effect of Zymolyase in Saccharomyces cerevisiae using strains BY4741 (wild type). Yeast cells exposed to Zymolyase in YPD growth medium show a significant induction of cell wall compensatory mechanism. Keywords: cell wall stress response

2008-09-06 | GSE9930 | GEO

hog1, slt2, rlm1, and msn2/4 mutants exposed to zymolyase

Project description:This SuperSeries is composed of the following subset Series: GSE9930: Wild type 3 hour exposure to zymolyase GSE9931: hog1 mutant 3 hour exposure to zymolyase GSE9932: slt2 mutant 3 hour exposure to zymolyase GSE9933: rlm1 mutant 3 hour exposure to zymolyase GSE9934: msn2/4 mutant 3 hour exposure to zymolyase S. cerevisiae wild type (BY4741) and mutants were grown on YEPD. For Zymolyase experiments, yeast cells were grown overnight at 24 Â°C to an optical density 0.8 - 1 (A600). The culture was refreshed to 0.2 O.D and grown at 24 Â°C for 2h 30min. Next, culture was divided into two parts. One continues growing under same conditions (non-treated culture) while the other was supplemented with 5units/ml Zymolyase 100T. Cells were collected at 3 hours of growth, frozen at -80 Â°C and processed for RNA extraction. The total RNA from one culture was analyzed, and, in addition, for this sample two different hybridizations were performed, including fluorochrome swapping in order to minimize transcriptional changes due to technical variability. This therefore corresponded to two DNA microarrays analyzed.

2010-06-19 | E-GEOD-12684 | 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