Wt expression changes in deletion strain-conditioned media
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ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
PROVIDER: GSE54539 | GEO | 2014/05/14
SECONDARY ACCESSION(S): PRJNA237312
REPOSITORIES: GEO
Similar Datasets
Project description:Alteration of growth condition or disruption of gene function are commonly used strategies to study cellular systems. Although widely appreciated that such experiments may result in indirect effects, these frequently remain uncharacterized. Here, genome-wide expression reanalysis of functionally unrelated Saccharyomyces cerevisiae deletion strains reveals a common expression signature. One property shared by these strains is slower growth, with increased presence of the signature in more slowly growing strains. The slow growth signature is highly similar to the environmental stress response, an expression response common to diverse environmental perturbations. Both environmental and genetic perturbations result in growth rate changes. These are accompanied by a change in the distribution of cells over different cell cycle phases. Rather than representing a direct expression response, the slow growth signature is a consequence of the redistribution of cells over different cell cycle phases, primarily characterized by an increase in the G1 population. The findings have implications for any study of perturbation that is accompanied by growth rate changes. Strategies to counter these effects are presented and discussed. This series shows the absence of media effects by growing wt strains in filtered medium in which slow-growing strains were grown previously. Two channel microarrays were used. RNA isolated from a large amount of wt yeast from a single culture was used as a common reference. Two independent cultures were hybridized on two separate microarrays. For the first hybridization the Cy5 (red) labeled cRNA from the deletion mutant is hybridized together with the Cy3 (green) labeled cRNA from the common reference. For the replicate hybridization, the labels are swapped.
2014-05-14 | E-GEOD-54539 | biostudies-arrayexpress
Project description:Alteration of growth condition or disruption of gene function are commonly used strategies to study cellular systems. Although widely appreciated that such experiments may result in indirect effects, these frequently remain uncharacterized. Here, genome-wide expression reanalysis of functionally unrelated Saccharyomyces cerevisiae deletion strains reveals a common expression signature. One property shared by these strains is slower growth, with increased presence of the signature in more slowly growing strains. The slow growth signature is highly similar to the environmental stress response, an expression response common to diverse environmental perturbations. Both environmental and genetic perturbations result in growth rate changes. These are accompanied by a change in the distribution of cells over different cell cycle phases. Rather than representing a direct expression response, the slow growth signature is a consequence of the redistribution of cells over different cell cycle phases, primarily characterized by an increase in the G1 population. The findings have implications for any study of perturbation that is accompanied by growth rate changes. Strategies to counter these effects are presented and discussed. In this series, the effects, over time, of heatshock (shifting cells from 30 to 37 C) or the reverse (cold 'shock') are studied.
2014-05-14 | GSE54528 | GEO
Project description:Alteration of growth condition or disruption of gene function are commonly used strategies to study cellular systems. Although widely appreciated that such experiments may result in indirect effects, these frequently remain uncharacterized. Here, genome-wide expression reanalysis of functionally unrelated Saccharyomyces cerevisiae deletion strains reveals a common expression signature. One property shared by these strains is slower growth, with increased presence of the signature in more slowly growing strains. The slow growth signature is highly similar to the environmental stress response, an expression response common to diverse environmental perturbations. Both environmental and genetic perturbations result in growth rate changes. These are accompanied by a change in the distribution of cells over different cell cycle phases. Rather than representing a direct expression response, the slow growth signature is a consequence of the redistribution of cells over different cell cycle phases, primarily characterized by an increase in the G1 population. The findings have implications for any study of perturbation that is accompanied by growth rate changes. Strategies to counter these effects are presented and discussed. This series shows the effect of phosphate limitation on gene expression
2014-05-14 | GSE54527 | GEO
Project description:Alteration of growth condition or disruption of gene function are commonly used strategies to study cellular systems. Although widely appreciated that such experiments may result in indirect effects, these frequently remain uncharacterized. Here, genome-wide expression reanalysis of functionally unrelated Saccharyomyces cerevisiae deletion strains reveals a common expression signature. One property shared by these strains is slower growth, with increased presence of the signature in more slowly growing strains. The slow growth signature is highly similar to the environmental stress response, an expression response common to diverse environmental perturbations. Both environmental and genetic perturbations result in growth rate changes. These are accompanied by a change in the distribution of cells over different cell cycle phases. Rather than representing a direct expression response, the slow growth signature is a consequence of the redistribution of cells over different cell cycle phases, primarily characterized by an increase in the G1 population. The findings have implications for any study of perturbation that is accompanied by growth rate changes. Strategies to counter these effects are presented and discussed. In this series, the effects, over time, of heatshock (shifting cells from 30 to 37 C) or the reverse (cold 'shock') are studied. Two channel microarrays were used. RNA isolated from a large amount of wt yeast from a single culture was used as a common reference. Two independent cultures were hybridized on two separate microarrays. For the first hybridization the Cy5 (red) labeled cRNA from the test sample is hybridized together with the Cy3 (green) labeled cRNA from the common reference. For the replicate hybridization, the labels are swapped. In the statistical analysis, factor levels are compared using the common reference as an intermediate.
2014-05-14 | E-GEOD-54528 | biostudies-arrayexpress
Project description:Alteration of growth condition or disruption of gene function are commonly used strategies to study cellular systems. Although widely appreciated that such experiments may result in indirect effects, these frequently remain uncharacterized. Here, genome-wide expression reanalysis of functionally unrelated Saccharyomyces cerevisiae deletion strains reveals a common expression signature. One property shared by these strains is slower growth, with increased presence of the signature in more slowly growing strains. The slow growth signature is highly similar to the environmental stress response, an expression response common to diverse environmental perturbations. Both environmental and genetic perturbations result in growth rate changes. These are accompanied by a change in the distribution of cells over different cell cycle phases. Rather than representing a direct expression response, the slow growth signature is a consequence of the redistribution of cells over different cell cycle phases, primarily characterized by an increase in the G1 population. The findings have implications for any study of perturbation that is accompanied by growth rate changes. Strategies to counter these effects are presented and discussed. This series shows the effect of phosphate limitation on gene expression Two channel microarrays were used. RNA isolated from a large amount of wt yeast from a single culture was used as a common reference. Two independent cultures were hybridized on two separate microarrays. For the first hybridization the Cy5 (red) labeled cRNA from the test sample is hybridized together with the Cy3 (green) labeled cRNA from the common reference. For the replicate hybridization, the labels are swapped. In the statistical analysis, factor levels are compared using the common reference as an intermediate.
2014-05-14 | E-GEOD-54527 | biostudies-arrayexpress
Project description:Bacteria regulate their cellular resource allocation to enable their fast growth-adaptation to a variety of environmental niches. We studied the ribosomal allocation, growth and expression profile of two sets of fast-growing mutants of Escherichia coli K-12 MG1655. Mutants with 3 copies of the stronger ribosomal RNA operons grew faster than the wild-type strain in minimal media and show similar phenotype to previously studied rpoB mutants. All of them displayed increased ribosomal content, a longer diauxic shift and a reduced activity of the aceBAK operon, indicative of repressed gluconeogenic pathways. Transcriptomic profiles of fast-growing mutants showed common downregulation of hedging functions and upregulated growth functions. Proteome allocation estimations showed an increase in the growth-related proteome for fast-growing strains, but not an increased cellular budget for recombinant protein production. These results show that two different regulatory perturbations (rRNA promoters or rpoB mutations) increasing ribosomal allocation optimize the proteome for growth with a concomitant fitness cost.
2022-02-21 | GSE180830 | GEO
Project description:Colorectal cancer (CRC) is characterized by extensive intra-tumor heterogeneity. The cancer stem cell (CSC) theory may explain the mechanisms underlying the non-genetic heterogeneity and their characteristics of prominent plasticity are emerging to be elucidated. By tracking the spheroid formation and growth capacity of CRC CSCs with a single-cell resolution using an organoid culture, we revealed CSCs consisted of subpopulations with a dual (fast and slow)-growing pattern. When isolated, the slow-growing CSCs remained slow-growing and converted into dual-growing CSCs under certain conditions. The slow-growing cells showed low levels of MAP kinase activity and were resistant to a MEK1/2 inhibitor as well as chemo-drugs. The MSI1 gene was down-regulated in the slow-growing CSCs and played a key role in the transition between slow- and dual-growing CSCs. Isolation of slow-growing CSCs will provide a platform to elucidate the role of the plasticity of CSCs in drug resistance and tumor recurrence. To disclose the molecular characteristics of the CSC subclones with the distinct growth features, we analyzed the differentially expressed genes between the subgroups.
2021-10-01 | GSE185012 | GEO
Project description:We analysed the transcriptomic signature associated to fast and slow growing microcolonies generated after the encapsulation of single cells belonging to a clonal wild-type population, in alginate microspheres. This allowed us to identify particular gene expression signatures associated to each subpopulation. In particular, we found that slow growing cells display an increased expression of respiratory genes even when growing in glucose rich media.
2017-02-10 | GSE72092 | GEO
Project description:Background: Food supply is a major factor influencing growth rates in animals. This has important implications for both natural and farmed fish populations, since food restriction may difficult reproduction. However, a study on the effects of food supply on the development of juvenile gonads has never been transcriptionally described in fish. Methods and Findings: This study investigated the consequences of growth on gonadal transcriptome of European sea bass in: 1) 4-month-old sexually undifferentiated fish, comparing the gonads of fish with the highest vs. the lowest growth, to explore a possible link between transcriptome and future sex, and 2) testis from 11-month-old juveniles where growth had been manipulated through changes in food supply. The four groups used were: i) sustained fast growth, ii) sustained slow growth, iii) accelerated growth, iv) decelerated growth. The transcriptome of undifferentiated gonads was not drastically affected by initial natural differences in growth. Further, changes in the expression of genes associated with protein turnover were seen, favoring catabolism in slow-growing fish and anabolism in fast-growing fish. Moreover, while fast-growing fish took energy from glucose, as deduced from the pathways affected and the analysis of protein-protein interactions examined, in slow-growing fish lipid metabolism and gluconeogenesis was favored. Interestingly, the highest transcriptomic differences were found when forcing initially fast-growing fish to decelerate their growth, while accelerating growth of initially slow-growing fish resulted in full transcriptomic convergence with sustained fast-growing fish. Conclusions: Food availability during sex differentiation shapes the juvenile testis transcriptome, as evidenced by adaptations to different energy balances. Remarkably, this occurs in absence of major histological changes in the testis. Thus, fish are able to recover transcriptionally their testes if they are provided with enough food supply during sex differentiation; however, an initial fast growth does not represent any advantage in terms of transcriptional fitness if later food becomes scarce.
2014-12-25 | GSE54362 | GEO