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ABSTRACT:
PROVIDER: PRJNA386475 | ENA |
REPOSITORIES: ENA
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Project description:Hydrostatic pressure is one of the physical factors affecting cellular physiology. Hydrostatic pressure of a few hundred MPa decreases the viability of yeast cells, and pressure of a few tens MPa decreases the growth rate. To understand the effect of hydrostatic pressure, we employed yeast, Saccharomyces cerevisiae, DNA microarrays and analyzed genome-wide mRNA expression profiles under hydrostatic pressures. In this experiment, we selected a hydrostatic pressure of 30 MPa at 25 degrees C because yeast cells are able to grow with this condition. Keywords: stress response
2007-11-01 | GSE9403 | GEO
Project description:Hydrostatic pressure is one of the physical factors affecting cellular physiology. Hydrostatic pressure of a few hundred MPa decreases the viability of yeast cells, and pressure of a few tens MPa decreases the growth rate. To understand the effect of hydrostatic pressure, we employed yeast, Saccharomyces cerevisiae, DNA microarrays and analyzed genome-wide mRNA expression profiles under hydrostatic pressures. In this experiment, we selected a hydrostatic pressure of 40 MPa at 25 degrees C because the condition is not lethal for yeast cells but the growth was suppressed. Keywords: stress response
2007-11-01 | GSE9406 | GEO
Project description:The hormonal contraceptive medroxyprogesterone acetate (MPA) is associated with increased risk of human immunodeficiency virus (HIV), via incompletely understood mechanisms. Increased diversity in the vaginal microbiota modulates genital inflammation and is associated with increased HIV-1 acquisition. However, the effect of MPA on diversity of the vaginal microbiota is relatively unknown. In a cohort of female Kenyan sex workers, negative for sexually transmitted infections (STIs), with Nugent scores <7 (N=58 of 370 screened), MPA correlated with significantly increased diversity of the vaginal microbiota as assessed by 16S rRNA gene sequencing. MPA was also significantly associated with decreased levels of estrogen in the plasma, and low vaginal glycogen and α-amylase, factors implicated in vaginal colonization by lactobacilli, bacteria that are believed to protect against STIs. In a humanized mouse model, MPA treatment was associated with low serum estrogen, low glycogen and enhanced HIV-1 susceptibility. The mechanism by which the MPA mediated changes in the vaginal microbiota may contribute to HIV-1 susceptibility in humans appears to be independent of inflammatory cytokines and/or activated T cells. Altogether, these results suggest MPA-induced hypo-estrogenism may alter key metabolic components that are necessary for vaginal colonization by certain bacterial species including lactobacilli, and allow for greater bacterial diversity in the vaginal microbiota.
2019-10-17 | GSE138971 | GEO
Project description:Piezophysiology of genome wide gene expression levels in the yeast Saccharomyces cerevisiae: Hydrostatic pressure is one of the physical factors affecting cellular physiology. Hydrostatic pressure of a few hundred MPa decreases the viability of yeast cells, and pressure of a few tens MPa decreases the growth rate. To understand the effect of hydrostatic pressure, we employed yeast DNA microarrays and analyzed genome-wide gene-expression levels after the pressure treatment with 180 MPa (immediate) at 4 degrees C and recovery incubation for 1 h and 40 MPa (16 h) at 4 degrees C and recovery incubation for 1 h. The transcription of genes involved in energy metabolism, cell defense, and protein metabolism was significantly induced by the pressure treatment. Genome-wide expression profiles suggested that high pressure caused damage to cellular organelles, since the induced gene products were localized in the membrane structure and/or cellular organelles. Hierarchical clustering analysis suggested that the damage caused by the pressure was similar to that caused by detergents, oils, and freezing/thawing. We also estimated the contribution of induced genes to barotolerance using some strains that have the deletion in the corresponding genes. Keywords: stress response
2007-11-01 | GSE9407 | GEO
Project description:The ability to measure the number of gene-specific mRNA molecules in individual mammalian cells has transformed the transcriptomics field. Among the key technologies enabling single-cell mRNA sequencing has been Droplet Sequencing (Drop-Seq). While this method works efficiently for mammalian cells, its direct application to yeast cells has been problematic due to cell-type specific differences such as size, doublet formation rate, and cell wall. Here we introduce YeastDropSeq, a single-cell RNA sequencing method for the study of transcriptomics in yeast. We modified and optimized the original Drop-Seq method to address the issues that emerged from smaller cell sizes and the presence of a cell wall in yeast. We also quantified the rate of doublet formation through a species-mixing experiment. As proof-of-principle application of the YeastDropSeq, we investigated the transcriptomic effects of mycophenolic acid (MPA), a lifespan-extending compound that decreases de novo GMP synthesis. We compared transcript levels between cells treated with MPA and cells treated with DMSO and/or guanine, MPA’s epistatic agent. We discovered that isogenic populations of yeast cells contain transcriptionally distinct subpopulations and that the subpopulation structures were maintained despite the different treatment conditions. We found that cells treated with MPA experience an upregulation of genes coding for proteins involved in DNA replication stress-response, antioxidation, pre-RNA processing, and translation initiation. Conversely, a downregulation of mRNA expression was observed for genes encoding translation initiation and elongation factors, the 40S and 60S ribosomal subunits, and for genes involved in metal transport and mitochondrial function. Additionally, we elucidated that expression levels of several genes of unknown function were affected by the MPA treatment. YeastDropSeq will accelerate biological discovery by facilitating droplet-based transcriptomics of yeast cells.
2020-06-26 | GSE144636 | GEO
Project description:Series containes 4 independent experiments and high and low power scanns for each independent experiment. Genome-wide mRNA expression profiles of Saccharomyces cerevisiae growing under hydrostatic pressure were characterized. We selected a hydrostatic pressure of 30 MPa at 25°C because yeast cells were able to grow under these conditions, while cell size and complexity were increased after decompression. Functional characterization of pressure-induced genes suggests that genes involved in protein metabolism and membrane metabolism were induced. The response to 30 MPa was significantly different from that observed under lethal conditions because protein degradation was not activated under 30 MPa pressure. Strongly induced genes included those that contribute to membrane metabolism and which are also induced by detergents, oils, and membrane stabilizers. Keywords: repeat sample
2005-04-14 | GSE2526 | GEO
Project description:The ability to measure the number of gene-specific mRNA molecules in individual mammalian cells has transformed the transcriptomics field. Among the key technologies enabling single-cell mRNA sequencing has been Droplet Sequencing (Drop-Seq). While this method works efficiently for mammalian cells, its direct application to yeast cells has been problematic due to cell-type specific differences such as size, doublet formation rate, and cell wall. Here we introduce YeastDropSeq, a single-cell RNA sequencing method for the study of transcriptomics in yeast. We modified and optimized the original Drop-Seq method to address the issues that emerged from smaller cell sizes and the presence of a cell wall in yeast. As proof-of-principle application of the YeastDropSeq, we investigated the transcriptomic effects of mycophenolic acid (MPA), a lifespan-extending compound that decreases de novo GMP synthesis. We compared transcript levels between cells treated with MPA and cells treated with DMSO and/or guanine, MPA’s epistatic agent. We discovered that isogenic populations of yeast cells contain transcriptionally distinct subpopulations and that the subpopulation structures were maintained despite the different treatment conditions. We found that cells treated with MPA experience an upregulation of genes coding for proteins involved in DNA replication stress-response, antioxidation, pre-RNA processing, and translation initiation. Conversely, a downregulation of mRNA expression was observed for genes encoding translation initiation and elongation factors, the 40S and 60S ribosomal subunits, and for genes involved in metal transport and mitochondrial function. YeastDropSeq will accelerate biological discovery by facilitating droplet-based transcriptomics of yeast cells.
2021-01-29 | GSE165686 | GEO
Project description:Series containes 4 independent experiments and high and low power scanns for each independent experiment. Genome-wide mRNA expression profiles of Saccharomyces cerevisiae growing under hydrostatic pressure were characterized. We selected a hydrostatic pressure of 30 MPa at 25°C because yeast cells were able to grow under these conditions, while cell size and complexity were increased after decompression. Functional characterization of pressure-induced genes suggests that genes involved in protein metabolism and membrane metabolism were induced. The response to 30 MPa was significantly different from that observed under lethal conditions because protein degradation was not activated under 30 MPa pressure. Strongly induced genes included those that contribute to membrane metabolism and which are also induced by detergents, oils, and membrane stabilizers.
2010-06-10 | E-GEOD-2526 | biostudies-arrayexpress
Project description:To know the differences of decidualization induced by different stimuli, we compared the mRNA expression profiles of decidualized ESCs stimulated by cAMP or cAMP+MPA for 4 days, or by MPA or E2+MPA for 14 days.
2024-04-10 | GSE235151 | GEO
Project description:Mycophenolic acid (MPA), effectively promoted ES cell pancreatic differentiation with a concomitant reduction of neuronal cells. The targets of MPA were investigated by microarray analysis of cells treated on day 5 with MPA and harvested on day 6 and 8.
2016-03-02 | GSE78797 | GEO