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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Expression data from rho+ and rho0 budding yeast celles harvetsed from complete medium with 2% glucose before or after shifting to complete medium without glucose

ABSTRACT: This experiment compares mRNA expression in cells with and without mitochondrial DNA (M-OM-^A+ and M-OM-^A0 cells respectively). We used global RNA profiling to measure mRNA expression in M-OM-^A+ and M-OM-^A0 cells harvested at log phase from synthetic medium with glucose (CM + 2% glucose, "CMD"), and at 4 hours after transfer to the same medium without glucose (CM). This profiling provided new clues about the ways in which nutirent signaling is reprogrammed in cells lacking mitocondrial DNA. mRNA expression was assessed by analyzing the RNA from three biological replicates obtained under four conditions: M-OM-^A+ cells in glucose, M-OM-^A+ cells no glucose, M-OM-^A0 cells in glucose, M-OM-^A0 cells no glucose.

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Michael Schultz

PROVIDER: E-GEOD-49002 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Expression data from rho+ and rho0 budding yeast celles harvetsed from complete medium with 2% glucose before or after shifting to complete medium without glucose

Project description:This experiment compares mRNA expression in cells with and without mitochondrial DNA (ρ+ and ρ0 cells respectively). We used global RNA profiling to measure mRNA expression in ρ+ and ρ0 cells harvested at log phase from synthetic medium with glucose (CM + 2% glucose, "CMD"), and at 4 hours after transfer to the same medium without glucose (CM). This profiling provided new clues about the ways in which nutirent signaling is reprogrammed in cells lacking mitocondrial DNA.

2013-12-31 | GSE49002 | GEO

Transcription profiling of yeast grwon in high glucose medium and shifted to low glucose medium

Project description:Time series expression profile of yeast cells grown at high glucose and shifted to low glucose containing medium. Lowess normalized data in raw data files.

2008-09-01 | E-MTAB-22 | biostudies-arrayexpress

Transcription profiling timecourse of aging human myotubes cultured in low or high glucose medium

Project description:Aging of skeletal muscle tissue is characterized by loss of metabolic and contractile competence. It is thought that this phenomenon is driven via extrinsic and intrinsic factors. In order to identify age-dependent changes intrinsic to the muscle cell, microarray transcriptional profiles and measurements of glucose metabolism were performed in primary cultured human myotubes at different time points over seven weeks. Aging in culture tended to reduce myotube glucose metabolism, oxidative and storage capacities, despite elevation of glucose transport. The mitochondrial membrane potential slightly increased, whereas peroxidation of cell membrane lipids declined and membrane integrity was preserved. Transcriptional analysis revealed a fall in genes involved in glucose metabolism and oxidative phosphorylation, while stress defense genes were elevated. Expression of numerous genes coding for muscle contractile proteins and calcium-regulating proteins, was gradually decreased during aging of cultured myotubes. Transcripts of genes involved in cell growth, matrix and motility markedly rose while those involved in cell adhesion dropped. In conclusion, aging myotubes in culture exhibit a loss of glucose metabolic capacity. They are characterized by a shift from a contractile to a growth-survival, matrix-remodeling phenotype. This pattern of changes, linked to intrinsic factors, displays significant similarities with aging of muscle from primates and human subjects.

2007-07-19 | E-GEOD-1144 | biostudies-arrayexpress

Genome-wide analysis of FNR and M-OM-^C70 in E. coli under aerobic and anaerobic growth conditions.

Project description:We found many binding sites for FNR under glucose fermentative anaerobic growth conditions. Also, many binding sites were identified for M-OM-^C70 under both aerobic and anaerobic growthin conditions. Descirbed in the manuscript "Genome-scale Analysis of E. coli FNR Reveals the Complexity of Bacterial Regulon Structure" Examination of occupancy of FNR adn M-OM-^C70 under aerobic and anaerobic growth in conditions.

2013-06-20 | E-GEOD-41187 | biostudies-arrayexpress

Expression analysis of the glucose deprivation-induced human tumor cell responses

Project description:The tumor microenvironment is characterized by low glucose and hypoxia. It is well known that changes in the tumor microenvironment, such as hypoxia and low glucose, can increase the production of VEGF. Although the role of hypoxia in the regulation of VEGF production is well understood, the mechanism linking glucose deprivation (GD) to tumor growth and angiogenesis is unclear. Here, GD (a physiological stimulus) was used to treat human tumor cells. The transcriptional reprogramming of tumor cells by GD was measured with microarray technology to provide a comprehensive analysis of the gene expression profile underlying the GD treatment. Our study suggested that GD initiates an angiogenic switch by increasing the expression of proangiogenic mediators (VEGF, FGF2, IL6, etc.) and decreasing the expression of angiogenesis inhibitors (THBS1, CXCL14 and CXCL10). The markers of Unfolded Protein Response (UPR) (Grp78/Bip, CHOP, ATF4, etc.) were significantly increased. The above results suggest GD may regulate angiogenesis through activation of the UPR. UM-SCC-81B cells (human oral squamous cell carcinoma cell line) were treated with glucose deprivation (GD) for 4 hours (UM-SCC-81B-GD-4) and 24 hours (UM-SCC-81B-GD24). Cells without treatment were used as a non-treatment control (UM-SCC-81B-NT). Each sample was analyzed once, i.e., without biological replicates. The expression of the genes of interest was confirmed with real-time PCR, ELISA and Western blot.

2012-10-25 | E-GEOD-38583 | biostudies-arrayexpress

Genome sequecing of yeast strain evolved under high glucose

Project description:A population of Saccharomyces cerevisiae was cultured for approximately 450 generations in the presence of high glucose to select for genetic variants. This experiment allows for a controlled model of adaptive evolution under natural selection. Using the parental strain BY4741 as the starting population, an evolved culture was obtained after continuous aerobic growth in a glucose-high medium for approximately 450 generations. After the evolution period three single colony isolates were selected for analysis. Next-generation Ion Torrent sequencing was used to evaluate genetic changes. Greater than 100 deletion/insertion changes were found with approximately half of these effecting genes. Additionally, over 180 single-nucleotide polymorphisms (SNPs) were identified with more than one quarter of these resulting in a non-synonymous mutation. Affymetrix DNA microarrays and RNseq analysis were used to determine differences in gene expression in the evolved strains compared to the parental strain. It was established that approximately 900 genes demonstrated significantly altered expression in the evolved strains relative to the parental strain. Many of these genes showed similar alterations in their expression in all three evolved strains. Interestingly, genes with altered expression in the three evolved strains included genes with a role in the TCA cycle. Overall these results are consistent with the physiological observations of decreased ethanol production and suggest that the underlying metabolism switched from fermentation to respiration during aerobic growth. Yeast strains were grown in the presence of high glucose for approximately 450 generations. Individual isolates were then grown and total RNA was collected to compare difference between the evolved strains and the parental strain.

2012-07-10 | E-GEOD-36518 | biostudies-arrayexpress

Expression data from human embryonic kidney cells (HEK293) cultivated in high and low glucose

Project description:Gene expression profiling of human embryonic kidney (HEK293) cells was performed to determine the effect of high and low glucose on gene expression. Microarrays were used to identify distinct classes of genes up-regulated in HEK293 cells during cultivation for 7 days in medium with physiological (low) glucose compared to high glucose. Human embryonic kidney cells (HEK293) were cultivated for 7 days in commercially available DMEM (supplemented with 10 % FCS) containing high glucose (450 mg/dl) or low glucose (100 mg/dl). Cells were harvested, total RNA was extracted and microarray gene expression profiling was performed to compare differential gene expression between low and high glucose conditions. Two biological replicates for each condition were made (high glucose: HEK-high-gluc-1 and HEK-high-gluc-2; and low glucose: HEK-low-gluc-1 and HEK-low-gluc-2).

2009-04-08 | E-GEOD-15575 | biostudies-arrayexpress

Transcriptional profiling of glucose deprivation resistant and glucose deprivation sensitive clones derived from IGROV-1 and SKOV3 ovarian cancer models and cultivated under either normal-glucose or low-glucose condition

Project description:This microarray experiment was designed to identify genes and pathways modulated in glucose deprivation resistant (GDR) and glucose deprivation sensitive (GDS) clones of ovarian cancer xenografts. Tumors were established in NOD/SCID mice by s.c. injection of human ovarian cancer cells (IGROV-1 and SKOV3). After sacrifice GDR and GDS clones were obtained from ex vivo cultures of tumors. Once isolated, GDR and GDS clones were cultivated in normal-glucose (0h) or low-glucose condition (6 h and 24 h). Two different time points were selected to investigate both early (6 h) and late (24 h) transcriptional effects of glucose deprivation in IGROV-1 and SKOV3-derived clones. Total RNA was extracted from samples and hybridized on Affymetrix GeneChip™ PrimeView™ Human Gene Expression Arrays. Based on assessment of RNA quality and on quality control analyses (including MAplots and boxplots), only one sample, corresponding to GDR condition at 6 h of glucose deprivation in SKOV3 model, was excluded because it was deemed not suitable for data analysis. In order to evaluate the effects of glucose deprivation in the two models, expression data of IGROV-1 and SKOV3-derived GDR and GDS clones were normalized and analyzed separately. Raw microarray data and pre-processed data matrices are available together with the applied protocols. Results of differential expression analysis are provided as supplementary tables of the associated publication.

2023-05-31 | E-MTAB-12150 | biostudies-arrayexpress

Halobacterium NRC-1 VNG1451C deletion mutant growth in defined medium with and without glucose

Project description:Gene regulatory networks play an important role in coordinating biochemical fluxes through diverse metabolic pathways. The modulation of enzyme levels enables efficient utilization of limited resources as organisms dynamically acclimate to nutritional fluctuations in their environment. Here we have identified and characterized a novel nutrient-responsive transcription factor from the halophilic archaea, VNG1451C. In this experiment we used whole-genome microarray analysis in the VNG1451C deletion mutant vs. H. salinarum NRC-1 ura3 parent strain in defined medium during growth with and without glucose to show that the expression of many metabolic genes is perturbed in the VNG1451C deletion mutant in response to this sugar. Halobacterium salinarum NRC-1 (ATCC700922) ura3 parent and VNG1451C strains were grown in complete defined medium (CDM; 20 amino acids at concentrations defined by Shand and Perez, 1999. NaCl 250g/L, MgSO4 20 g/L, KCl 1 g/L, NaH2PO4 0.167mM, Biotin 0.02mM, Thiamin 0.015mM, Folic acid 0.0113 mM, MnSO4 0.01mM, FeSO4, 0.01mM, glucose added at 10% w/v where indicated in sample files) at 37ÂºC under full-spectrum white light. Biological replicate samples were removed throughout the growth curve at early log, mid log, and stationary phase to measure genome-wide transcription.

2010-05-06 | E-GEOD-13529 | biostudies-arrayexpress

Expression data for haploid Saccharomyces cerevisiae strains growing in a defined low glucose medium.

Project description:We used microarrays to assess differences in gene expression associated with single nucleotide polymorphisms occurred in three genes, PMA1, MDS3 and MKT1, as compared to a reference strain devoid of any mutations (Progenitor strain). Haploid yeast strains carrying no evolved alleles (progenitor - reference strain) or different combinations of the studied evolved alleles (PMA1e, MDS3e and MKT1e) and devoid of all other evolved alleles were used. The following genotypes were studied: ancestral, MDS3e, MKT1e, MDS3e_MKT1e and PMA1e_MKT1e (2 replicates each). Cells of the studied strains were grown overnight on liquid yeast peptone dextrose (YPD) medium and used to inoculate defined low glucose medium.

2011-05-20 | E-GEOD-29353 | biostudies-arrayexpress

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