Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

10 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Tadahiro Suzuki

PROVIDER: E-GEOD-17367 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

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 Yeast BY4743 was grown in YPD media containing 0.01% SDS, and was applied for two types of RNA extraction method.

2010-04-12 | E-GEOD-18456 | biostudies-arrayexpress

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 in response to deoxynivalenol

Project description:The assessment of toxicity about deoxynivalenol (DON) using yeast gene expression comparison analysis. 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. Keywords: stress response Four conditions are compared with three replicates each. Each of the two strains was grown in either 0.01% SDS-containing YPD media or 0.01% SDS-containing YPD media with 25 ppm of deoxynivalenol.

2010-06-08 | E-GEOD-14748 | 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

PTC1 mutant Yeast Genomic Expression Patterns in Response to deoxynivalenol

Project description:The evaluation of the toxicity of deoxynivalenol using yeast gene expressions. Yeast PTC1 mutant strain was used for this study. SDS was used to raise the penetration of the yeast cell membrane. Keywords: stress response Two conditions were compared by the gene expression profiles. Both samples were grown in 0.01% SDS contained YPD media, and one of them was also supplied with 50 ppm of deoxynivalenol.

2011-07-21 | E-GEOD-20378 | biostudies-arrayexpress

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

Coordinating Expression of RNA Binding Proteins with Their mRNA Targets

Project description:Post-transcriptional regulation by RNA binding proteins (RBPs) plays prominent roles in a variety of biological processes. In this study, by analyzing the global regulatory relationship between RBPs and their target mRNAs in yeast, we discovered that most RBP genes are co-regulated with their target genes, but the RBPs tend to dampen expression variation among their target mRNAs. We further examined a well-studied RBP gene, PUF3, and found that the protein decreases the variation of its target mRNAs by differentially affecting their decay. Our results provided new insights into the functional importance of RBPs in coordinating their target genes expression. Both the PUF3 deletion strain and wild type BY4742 (MATa, his3Δ1, leu2Δ0, met15Δ0, ura3Δ0) strain were cultured overnight in YPD media. 0.01 OD cells were transferred into fresh YPEG media until 1.0 OD. Total RNA was extracted by the standard Trizol protocol. mRNA was then purified using oligo-dT DynaBeads. cDNA sequencing library was constructed according to the protocol described by Wang et al. After sequencing, the reads were also mapped into S. cerevisiae genome by SOAP2 with no more than two mismatches. RPKM was used to represent the expression level of each gene.

2014-06-01 | E-GEOD-55419 | biostudies-arrayexpress

RNA-Seq of Saccharomyces cerevisiae cells carrying different YRR1 alleles in response to 4-nitroquinoline-N-oxide (4NQO) and to glycerol as the sole carbon source

Project description:In this study, we constructed three isogenic strains of S96 yrr1Î? background (its native YRR1 gene was knocked out) carrying three different YRR1 alleles, YRR1_S96, YRR1_YJM789 and YRR1_S96-I775E, respectively. We then conducted RNA deep sequencing (RNA-Seq) on the three strains grown in Yeast Peptone Dextrose medium (YPD), YPD + 4NQO and Yeast Peptone glycerol medium (YPglycerol). RNA-Seq was performed in biological duplicates on S96 cells carrying three different YRR1 alleles grown in YPD, YPD + 4NQO, YPglycerol

2016-03-01 | E-GEOD-74642 | biostudies-arrayexpress

Transcription profiling by array of Yeast strain BY4741 treated with alpha -factor mating pheromone to investigate nucleosome plasticity during cell cycle

Project description:Yeast strain BY4741 was grown overnight at 30C in YPD rich media. The yeast culture was diluted to an OD600 of 0.1 using fresh YPD media and further grown until an OD600 of 0.2. Then, alpha -factor mating pheromone (GenScript) was added to a final concentration of 10 uM to allow cell synchronization at G1 phase. After 2.5 h, the alpha-factor was removed by harvesting the cells for 10 min at 6000 rpm and decanting supernatant. The arrested cells were inoculated in fresh YPD rich medium to be released from G1-arrest. Samples were collected at 0, 30, 40, 50, and 70 mins, 7.5 ml samples were collected for RNA extraction while 40 ml samples were taken for nucleosomal DNA preparation and for flow cytometry (FACS). Samples for RNA isolation were collected by pipetting the culture directly into 15-ml Falcon tubes containing 7.5 ml of icy-water to quickly chill the cells. Cells were harvested by spinning for 3-4 min at 6000 rpm, frozen in liquid N2 and stored at - 80C. Total cellular RNA was extracted using the RNeasy kit (Qiagen), following the manufacturerM-^Rs instructions with the spheroplasting protocol. Purified RNA samples were quantified by Qubit fluorometer (Invitrogen, Inc.) and Nanodrop spectrophotometer (Thermo Scientific, Inc.). The total RNA was hybridized to Affymetrix GeneChip Yeast Genome 2.0 arrays for gene expression analysis.

2012-09-01 | E-MEXP-3702 | biostudies-arrayexpress

Whole genome sequencing of sodium dodecyl sulfate (SDS) adaptors in Candida auris

Project description:Candida auris clade III isolate B12039 was spread on YPD plate supplemented with 0.5% SDS. Randomly 30 adaptors were chosen for further analysis. We did sequencing of these 30 adaptors as well as the parent.

2021-06-24 | E-MTAB-10542 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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