The effects of Lactobacillus plantarum and E. coli on Caco2 human colonocytes genes expression
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Pinaki Panigrahi
PROVIDER: E-GEOD-5874 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Cells in glucose-limited Saccharomyces cerevisiae cultures differentiate into quiescent (Q) and non-quiescent (NQ) fractions prior to entering stationary phase. To identify genes involved in this differentiation, Q and NQ cells from 101 deletion-mutant strains were tested for viability and reproductive capacity. Twenty-one mutants were identified, including 7 that affected reproductive capacity of both cell types. Thirteen affected only Q or NQ cells, indicating significant differentiation of these cell types. doa4 strains, lacking ubiquitin hydrolase, affected viability and reproductive capacity in both cell types. More than 1300 mRNAs differentiating Q and NQ cell fractions were identified by microarray analysis. Gene-ontology analysis of Q-cell mRNAs showed significant increases in protein-encoding mRNAs involved in membrane maintenance, oxidative stress response, and signal transduction. NQ-cell mRNAs encode proteins involved in Ty-element transposition and DNA recombination, consistent with apoptosis in these cells. Consistent with preparation for rapid response to environmental stimuli, approximately 2000 protease-labile mRNAs were identified in Q cells. The differentiation of these cell types and the ability of genes to selectively affect the survival of Q or NQ cells in yeast are relevant to chronological aging, cell-cycle, genome-evolution, and stem-cell research and provides insight into complex responses that even simple organisms have to starvation. 10 replicates per cell-type. Channel 1 (Cy3) was the control of mixture of exponential and stationary phase cells. Channel 2 (Cy5) was the experimental cell-types of parental strain BY4742.
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Project description:Cells in glucose-limited Saccharomyces cerevisiae cultures differentiate into quiescent (Q) and non-quiescent (NQ) fractions prior to entering stationary phase. To identify genes involved in this differentiation, Q and NQ cells from 101 deletion-mutant strains were tested for viability and reproductive capacity. Twenty-one mutants were identified, including 7 that affected reproductive capacity of both cell types. Thirteen affected only Q or NQ cells, indicating significant differentiation of these cell types. doa4 strains, lacking ubiquitin hydrolase, affected viability and reproductive capacity in both cell types. More than 1300 mRNAs differentiating Q and NQ cell fractions were identified by microarray analysis. Gene-ontology analysis of Q-cell mRNAs showed significant increases in protein-encoding mRNAs involved in membrane maintenance, oxidative stress response, and signal transduction. NQ-cell mRNAs encode proteins involved in Ty-element transposition and DNA recombination, consistent with apoptosis in these cells. Consistent with preparation for rapid response to environmental stimuli, approximately 2000 protease-labile mRNAs were identified in Q cells. The differentiation of these cell types and the ability of genes to selectively affect the survival of Q or NQ cells in yeast are relevant to chronological aging, cell-cycle, genome-evolution, and stem-cell research and provides insight into complex responses that even simple organisms have to starvation. Yeast deletion mutants (BY4742 background) were grown to stationary-phase (7 days) and then separted into Q and NQ cells using Percoll density gradients. Microarrays were carried out on these different cell fractions.
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Project description:Cells in glucose-limited Saccharomyces cerevisiae cultures differentiate into quiescent (Q) and non-quiescent (NQ) fractions prior to entering stationary phase. To identify genes involved in this differentiation, Q and NQ cells from 101 deletion-mutant strains were tested for viability and reproductive capacity. Twenty-one mutants were identified, including 7 that affected reproductive capacity of both cell types. Thirteen affected only Q or NQ cells, indicating significant differentiation of these cell types. doa4 strains, lacking ubiquitin hydrolase, affected viability and reproductive capacity in both cell types. More than 1300 mRNAs differentiating Q and NQ cell fractions were identified by microarray analysis. Gene-ontology analysis of Q-cell mRNAs showed significant increases in protein-encoding mRNAs involved in membrane maintenance, oxidative stress response, and signal transduction. NQ-cell mRNAs encode proteins involved in Ty-element transposition and DNA recombination, consistent with apoptosis in these cells. Consistent with preparation for rapid response to environmental stimuli, approximately 2000 protease-labile mRNAs were identified in Q cells. The differentiation of these cell types and the ability of genes to selectively affect the survival of Q or NQ cells in yeast are relevant to chronological aging, cell-cycle, genome-evolution, and stem-cell research and provides insight into complex responses that even simple organisms have to starvation. Samples were separeted into Q and NQ fractions using percoll density gradients. During RNA isolation samples were treated with proteinase K or 10 mM tris. This was done to test of any differences in portease labile mRNAs in Q and NQ cells.
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Project description:Cells in glucose-limited Saccharomyces cerevisiae cultures differentiate into quiescent (Q) and non-quiescent (NQ) fractions prior to entering stationary phase. To identify genes involved in this differentiation, Q and NQ cells from 101 deletion-mutant strains were tested for viability and reproductive capacity. Twenty-one mutants were identified, including 7 that affected reproductive capacity of both cell types. Thirteen affected only Q or NQ cells, indicating significant differentiation of these cell types. doa4 strains, lacking ubiquitin hydrolase, affected viability and reproductive capacity in both cell types. More than 1300 mRNAs differentiating Q and NQ cell fractions were identified by microarray analysis. Gene-ontology analysis of Q-cell mRNAs showed significant increases in protein-encoding mRNAs involved in membrane maintenance, oxidative stress response, and signal transduction. NQ-cell mRNAs encode proteins involved in Ty-element transposition and DNA recombination, consistent with apoptosis in these cells. Consistent with preparation for rapid response to environmental stimuli, approximately 2000 protease-labile mRNAs were identified in Q cells. The differentiation of these cell types and the ability of genes to selectively affect the survival of Q or NQ cells in yeast are relevant to chronological aging, cell-cycle, genome-evolution, and stem-cell research and provides insight into complex responses that even simple organisms have to starvation. 10 replicates per cell-type. Channel 1 (Cy3) was the control of mixture of exponential and stationary phase cells. Channel 2 (Cy5) was the experimental cell-types of wild-type strain S288c.
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Project description:Cells in glucose-limited Saccharomyces cerevisiae cultures differentiate into quiescent (Q) and non-quiescent (NQ) fractions prior to entering stationary phase. To identify genes involved in this differentiation, Q and NQ cells from 101 deletion-mutant strains were tested for viability and reproductive capacity. Twenty-one mutants were identified, including 7 that affected reproductive capacity of both cell types. Thirteen affected only Q or NQ cells, indicating significant differentiation of these cell types. doa4 strains, lacking ubiquitin hydrolase, affected viability and reproductive capacity in both cell types. More than 1300 mRNAs differentiating Q and NQ cell fractions were identified by microarray analysis. Gene-ontology analysis of Q-cell mRNAs showed significant increases in protein-encoding mRNAs involved in membrane maintenance, oxidative stress response, and signal transduction. NQ-cell mRNAs encode proteins involved in Ty-element transposition and DNA recombination, consistent with apoptosis in these cells. Consistent with preparation for rapid response to environmental stimuli, approximately 2000 protease-labile mRNAs were identified in Q cells. The differentiation of these cell types and the ability of genes to selectively affect the survival of Q or NQ cells in yeast are relevant to chronological aging, cell-cycle, genome-evolution, and stem-cell research and provides insight into complex responses that even simple organisms have to starvation. Yeast deletion mutants (BY4742 background) were grown to stationary-phase (7 days) and then separted into Q and NQ cells using Percoll density gradients. Microarrays were carried out on these different cell fractions.
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