Transcriptomic analysis of two ethanol-tolerant Saccharomyces cerevisiae clones obtained by evolutionary engineering
Ontology highlight
ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
PROVIDER: GSE78759 | GEO | 2016/03/01
SECONDARY ACCESSION(S): PRJNA313443
REPOSITORIES: GEO
Similar Datasets
Project description:Evolutionary engineering strategy was used for selection of ethanol-tolerant Saccharomyces cerevisiae clones under gradually increasing ethanol stress levels. Clones B2 and B8 were selected based on their higher ethanol-tolerance and higher ethanol production levels. Whole genome microarray analysis was used for identifying the gene expression levels of these two evolved clones compared to the reference strain. Two evolved ethanol-tolerant strains B2 and B8, which were selected by evolutionary engineering under gradually increasing ethanol stress, were used for whole genome transcriptomic analysis in comparison with the reference strain. Cells were grown in yeast minimal media until they reach a final OD600 of 1. Following total RNA isolation, gene expression levels were analyzed using One-color microarray-based gene expression analysis (Agilent Technologies). Experiments were done in triplicates.
2016-03-01 | E-GEOD-78759 | biostudies-arrayexpress
Project description:It remains controversial whether human induced pluripotent stem cells (hiPSCs) are distinct from human embryonic stem cells (hESCs) in their molecular signatures and differentiation properties. We examined the gene expression and DNA methylation of 49 hiPSC and 10 hESC lines and identified no molecular signatures that distinguished hiPSCs from hESCs. Comparisons of the in vitro directed neural differentiation of 40 hiPSC and four hESC lines showed that most hiPSC clones were comparable to hESCs. However, in seven hiPSC clones, significant amount of undifferentiated cells persisted even after neural differentiation and resulted in teratoma formation when transplantated into mouse brains. These differentiation-defective hiPSC clones were marked by higher expression of several genes, including those expressed from long terminal repeats of human endogenous retroviruses. These data demonstrated that many hiPSC clones are indistinguishable from hESCs, while some defective hiPSC clones need to be eliminated prior to their application for regenerative medicine.
2013-12-03 | GSE42449 | GEO
Project description:It remains controversial whether human induced pluripotent stem cells (hiPSCs) are distinct from human embryonic stem cells (hESCs) in their molecular signatures and differentiation properties. We examined the gene expression and DNA methylation of 49 hiPSC and 10 hESC lines and identified no molecular signatures that distinguished hiPSCs from hESCs. Comparisons of the in vitro directed neural differentiation of 40 hiPSC and four hESC lines showed that most hiPSC clones were comparable to hESCs. However, in seven hiPSC clones, significant amount of undifferentiated cells persisted even after neural differentiation and resulted in teratoma formation when transplantated into mouse brains. These differentiation-defective hiPSC clones were marked by higher expression of several genes, including those expressed from long terminal repeats of human endogenous retroviruses. These data demonstrated that many hiPSC clones are indistinguishable from hESCs, while some defective hiPSC clones need to be eliminated prior to their application for regenerative medicine.
2013-12-03 | GSE42452 | GEO
Project description:This project is about the proteomes of wild type cells (WT) and spo0A-null strain of B. subtilis during exponential growth in mannose medium. B2 & B4 corresponds to the wild type cells (two biological replicate samples) and B6 & B8 corresponds to spo0A-null data (two biological replicate samples).
2023-05-10 | PXD039192 | Pride
Project description:For yeast cells, tolerance to high levels of ethanol is vital both in their natural environment and in industrially relevant conditions. We recently genotyped experimentally evolved yeast strains, tolerant to high levels of ethanol. In this study, we elucidate how the genotype and phenotype are related to each other on the molecular level through an integrated analysis of mutation data with protein abundance profiles from six evolved, ethanol-tolerant clones. We constructed a protein network of regulatory proteins, mutated and differentially regulated proteins. This resulted in the identification of a rewired regulatory network after adaptation to high levels of ethanol.
2020-12-03 | PXD006631 | Pride
Project description:Human adipose mesenchymal stem cells are a heterogeneous population, where cell cultures derived from single cell-expanded clones present varying degrees of differential plasticity. This work focuses on the immunomodulatory/anti-inflammatory properties of these cells. To this end, 5 single cell clones were isolated (1.X and 3.X) from 2 volunteers. Regarding the expression level of the lineage-characteristic surface antigens, clones 1.10 and 1.22 expressed the lowest amounts, while clones 3.10 and 3.5 expressed more CD105 than the rest and clone 1.7 expressed higher amounts of CD73 and CD44. Regarding cytokine secretion, all clones were capable of spontaneously releasing high levels of IL-6 and low to moderate levels of IL-8. Furthermore, clone 3.X produced the highest amounts of pro-inflammatory cytokines such as IL-1β, while clones 1.10 and 1.22 highly expressed IL-4 and IL-5. These differences can be explained in part by the distinct DNA promoter methylation profile exhibited by the clones. The results of this work indicates that this stem cell population is heterogeneous in its secretion profile, and that isolation, characterization and selection of the appropriate cell clone is a more exact method for the possible treatment of different patients or pathologies.
2014-03-03 | GSE44222 | GEO
Project description:It remains controversial whether human induced pluripotent stem cells (hiPSCs) are distinct from human embryonic stem cells (hESCs) in their molecular signatures and differentiation properties. We examined the gene expression and DNA methylation of 49 hiPSC and 10 hESC lines and identified no molecular signatures that distinguished hiPSCs from hESCs. Comparisons of the in vitro directed neural differentiation of 40 hiPSC and four hESC lines showed that most hiPSC clones were comparable to hESCs. However, in seven hiPSC clones, significant amount of undifferentiated cells persisted even after neural differentiation and resulted in teratoma formation when transplantated into mouse brains. These differentiation-defective hiPSC clones were marked by higher expression of several genes, including those expressed from long terminal repeats of human endogenous retroviruses. These data demonstrated that many hiPSC clones are indistinguishable from hESCs, while some defective hiPSC clones need to be eliminated prior to their application for regenerative medicine. We extracted total RNA from 3 differentiation-defective clones, 3 good clones and 2 somatic cells, and hybridized them to Affymetrix exon arrays.
2013-12-03 | E-GEOD-42449 | biostudies-arrayexpress
Project description:Saccharomyces spp. are widely used for ethanol production however fermentation productivity is negatively affected by the impact of ethanol accumulation on yeast metabolic rate and viability. This study used microarray and statistical two-way ANOVA analysis to compare and evaluate gene expression profiles of two previously generated ethanol-tolerant mutants, CM1 and SM1, with their parent, S. cerevisiae W303-1A, in the presence and absence of ethanol stress. Although sharing the same parentage, the mutants were created differently; SM1 by adaptive evolution involving long-term exposure to ethanol stress, and CM1 using chemical mutagenesis followed by adaptive evolution-based screening. Compared to the parent, differences in the expression levels of genes associated with a number of GO categories in the mutants suggest that their improved ethanol stress response is a consequence of increased mitochondrial and NADH oxidation activities, stimulating glycolysis and energy production. This leads to increased activity of energy-demanding processes associated with the production of proteins and plasma membrane components, which are necessary for acclimation to ethanol stress. It is suggested that a key function of the ethanol stress response is restoration of the NAD+/NADH redox balance, which increases glyceraldehyde-3-phosphate dehydrogenase activity, and higher glycolytic flux in the ethanol-stressed cell. Both mutants achieved this by a constitutive increase in carbon flux in the glycerol pathway as a means of increasing NADH oxidation.
2010-07-01 | GSE21120 | GEO
Project description:We have evaluated the response of M14 cells to VSV virus expressing eGFP or insect virus B2 protein. We find interferon related genes to be at higher levels when cells are infected with VSV-B2
2018-06-01 | GSE115138 | GEO
Project description:Human adipose mesenchymal stem cells are a heterogeneous population, where cell cultures derived from single cell-expanded clones present varying degrees of differential plasticity. This work focuses on the immunomodulatory/anti-inflammatory properties of these cells. To this end, 5 single cell clones were isolated (1.X and 3.X) from 2 volunteers. Regarding the expression level of the lineage-characteristic surface antigens, clones 1.10 and 1.22 expressed the lowest amounts, while clones 3.10 and 3.5 expressed more CD105 than the rest and clone 1.7 expressed higher amounts of CD73 and CD44. Regarding cytokine secretion, all clones were capable of spontaneously releasing high levels of IL-6 and low to moderate levels of IL-8. Furthermore, clone 3.X produced the highest amounts of pro-inflammatory cytokines such as IL-1β, while clones 1.10 and 1.22 highly expressed IL-4 and IL-5. These differences can be explained in part by the distinct DNA promoter methylation profile exhibited by the clones. The results of this work indicates that this stem cell population is heterogeneous in its secretion profile, and that isolation, characterization and selection of the appropriate cell clone is a more exact method for the possible treatment of different patients or pathologies. Total DNA isolated by standard procedures from different clones of human dipose mesenchymal stem cells (hMSC)
2014-03-03 | E-GEOD-44222 | biostudies-arrayexpress