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Expression data from yeast (wild type, rlm1 and swi3 mutants) exposed to Congo Red

ABSTRACT: We did transcription profiling on the effect of rlm1 (MAPK Slt2 transcription factor) deletion and swi3 (component of SWI/SNF complex involved in chromatin remodeling) deletion in genes involved in cell wall stress (Congo Red) response. Three biological samples were analyzed for each condition, and a microarray experiment were carried out for each sample 1. absence of the drug 2. presence of 30 µg/ml of Congo Red

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Javier Arroyo

PROVIDER: E-GEOD-31176 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Chromatin remodeling by the SWI/SNF complex is essential for transcription mediated by the yeast cell wall integrity MAPK pathway.

Sanz A Belén AB Sanz A Belén AB García Raúl R Rodríguez-Peña Jose Manuel JM Díez-Muñiz Sonia S Nombela César C Peterson Craig L CL Arroyo Javier J

Molecular biology of the cell 20120523 14

In Saccharomyces cerevisiae, the transcriptional program triggered by cell wall stress is coordinated by Slt2/Mpk1, the mitogen-activated protein kinase (MAPK) of the cell wall integrity (CWI) pathway, and is mostly mediated by the transcription factor Rlm1. Here we show that the SWI/SNF chromatin-remodeling complex plays a critical role in orchestrating the transcriptional response regulated by Rlm1. swi/snf mutants show drastically reduced expression of cell wall stress-responsive genes and hy ...[more]

PMID: 22621902

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Expression data from yeast (wild type, rlm1 and swi3 mutants) exposed to Congo Red

Project description:We did transcription profiling on the effect of rlm1 (MAPK Slt2 transcription factor) deletion and swi3 (component of SWI/SNF complex involved in chromatin remodeling) deletion in genes involved in cell wall stress (Congo Red) response.

2012-05-25 | GSE31176 | GEO

Transcriptional profile of pmt1 pmt2 mutants

Project description:We did transcription profiling on the effect of pmt1 pmt2 deletion. These genes are involved in the O-glycosylation process. These mutants cells show inhibition of mating, filamentation and induction of cell wall compensatory mechanism. Two biological samples were analyzed for each condition, and a microarray experiment were carried out for each sample 1. wild type cells SEY6210 2. pmt1 pmt2 cells from SEY6210 background

2010-09-29 | E-GEOD-12181 | biostudies-arrayexpress

Transcriptional profile of pmt1 pmt4 mutants

Project description:We did transcription profiling on the effect of pmt1 pmt4 deletion, genes involved in the O-glycosylation process. These mutants cells show inhibition of mating, filamentation and induction of cell wall compensatory mechanism. Two biological samples were analyzed for each condition, and a microarray experiment were carried out for each sample 1. wild type cells SEY6210 2. pmt1 pmt2 cells from SEY6210 background

2010-09-29 | E-GEOD-12182 | biostudies-arrayexpress

O-glycosylation inhibition and O-glycosylation mutants

Project description:This SuperSeries is composed of the following subset Series: GSE12180: Wild type 3 hours exposure to 1 microM OGT2468 GSE12181: Transcriptional profile of pmt1 pmt2 mutants GSE12182: Transcriptional profile of pmt1 pmt4 mutants GSE12193: Wild type 3 hours exposure to 0.1 microM OGT2468 Refer to individual Series

2010-09-29 | E-GEOD-12197 | biostudies-arrayexpress

Sodium arsenate response of wild type and slt2 deficient cells

Project description:Wild type (BY4741) Saccharomyces cerevisiae strains and their isogenic slt2 deficient counterparts, were treated for 2 hours with sodium arsenate 100 micromolar. Control (untreated) cells were also collected. Total RNA was extracted and analyzed by microarray hybridization. The data obtained from these experiments allows to determine those genes that are regulated by Slt2 activity after arsenate treatment. The experiments was designed as follows: Four types of samples were used: untreated wild type cells, treated wild type cells, untreated slt2- cells and treated slt2- cells. 3 independent replicates were performed for each experiment.

2010-07-25 | E-GEOD-17364 | biostudies-arrayexpress

Transcriptional data from yeast expressing mammalian PIK3CA

Project description:We studied the transcriptional profile in response to acute PtdIns-4,5P2 depletion induced by heterologous expression of a plasma membrane-directed version of mammalian PI3K catalytic subunit (p110M-NM-1-CAAX). Three biological samples were analyzed for samples expressing for 4 hours p110M-NM-1-CAAX (PI3K) versus the kinase dead mutant p110M-NM-1-CAAX K802R (KD), and one microarray experiment was carried out for each sample.

2014-07-19 | E-GEOD-59596 | biostudies-arrayexpress

Global transcriptional response to transient cell wall damage

Project description:Data processing included: 1. Filtering of those bad quality image spots (these includes alterations on the shape or hybridization) 2. Filtering of low intensity which was done flagging with -50 those spots whose feature intensity was lower in any of both channels than the average of the local background in the corresponding channel for all spots. However, those genes whose feature intensity in one channel was under the limit but in the other channel was 5 times over limit were considered as on-off genes and were not filtered. 3. Filtering of low reproducibility intrachip replicated spots. Normal distribution was created with the value obtained from the formula: log2(Rax1/Rb) which means logarithm (two-based) of one ratio multiplied by the inverse of its replicate. This value for each gene shoud keep between the range of average Â± 3SD. Those genes out of these range are flagged as -25 4. Normalization of ratios was done by Lowess mathematical method. Correction factor was 0.33 This SuperSeries is composed of the following subset Series: GSE960: wild type 0 hours exposure to congo red GSE961: wild type 2 hours exposure to congo red GSE962: wild type 4 hours exposure to congo red GSE963: wild type 6 hours exposure to congo red GSE964: slt2 mutant 4 hours exposure to congo red GSE965: rlm1 mutant 4 hours exposure to congo red GSE966: wild type two hours exposure to zymolyase Keywords: SuperSeries Refer to individual Series

2010-06-09 | E-GEOD-959 | biostudies-arrayexpress

Plasticity of Mitochondrial DNA Inheritance and its Impact on Nuclear Gene Transcription in Yeast Hybrids grown on YP Glycerol 28C

Project description:Mitochondrial DNA (mtDNA) in budding yeast is biparentally inherited, but colonies rapidly lose one type of parental mtDNA, becoming homoplasmic. Therefore, hybrids between different yeast species possess two homologous nuclear genomes, but only one type of mitochondrial DNA. We hypothesise that the choice of mtDNA retention is influenced by its contribution to hybrid fitness in different environments, and that the allelic expression of the two nuclear sub-genomes is affected by the presence of different mtDNAs in hybrids. Here, we crossed Saccharomyces cerevisiae with S. uvarum under different environmental conditions and examined the plasticity of the retention of mtDNA in each hybrid.

2020-04-16 | E-MTAB-7922 | biostudies-arrayexpress

Plasticity of Mitochondrial DNA Inheritance and its Impact on Nuclear Gene Transcription in Yeast Hybrids Compared to parents strains

2020-10-26 | E-MTAB-8900 | biostudies-arrayexpress

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

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