Transcription profiling of wild type, gis1 knockout, rph1 knockout and gis1/rph1 double knockout yeast at different growth phases
Ontology highlight
ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
SUBMITTER: Jakub Orzechowski Westholm
PROVIDER: E-TABM-496 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Gene regulatory significance of the JmjC domain H235A point mutation in the yeast transcription factor Rph1, in log and post-diauxic shift (pds) phase
2014-08-27 | E-MTAB-2147 | biostudies-arrayexpress
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, AgmR. Like TrmB, its thermophilic archaeal homolog, AgmR regulates glycolytic and gluconeogenic pathways in response to sugar availability. However, using high throughput genome-scale experiments, we find that AgmR directly governs the transcription of nearly 100 additional genes encoding enzymes in diverse metabolic pathways. Genome-scale in vivo binding site location data reveals that >60% of these are direct targets. Integration of these systems-scale datasets with metabolic reconstruction models suggests that AgmR, a sequence-specific bacterial-like regulator, interacts with the general transcription factor machinery to coordinate nitrogen and carbon metabolism with the de novo synthesis of cognate cofactors and reducing equivalents, achieving system-wide redox and energy balance. Halobacterium salinarum NRC-1 (ATCC700922) ura3 parent and VNG1451C strains were grown in rich medium (CM, 250 NaCl, 20 g/L MgSO4?7H2O, 3 g/L sodium citrate, 2 g/L KCl, 10 g/L peptone) with or without varying concentrations of glucose or glycerol at 37ºC under full-spectrum white light. The cells were cross-linked with 1.2% formaldehyde, then lysed and DNA sheared via sonication. Next cleared cell lysate was subject to immunoprecipitation against an anti-myc antibody. Protein-DNA complexes were purified and DNA was isolated after protease and RNAase treatment. DNA was amplified using universal linkers, labeled directly using Kreatech 547 and 647 dyes. Samples were grown in biological duplicate. Each DNA sample was hybridized against 2 microarrays as dyefilps. At least two experiments (including biological duplicates) were carried out.
2010-05-06 | E-GEOD-13498 | biostudies-arrayexpress
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 rich medium during growth to show that the expression of many metabolic genes is perturbed in the VNG1451C deletion mutant. Halobacterium salinarum NRC-1 (ATCC700922) ura3 parent and VNG1451C strains were grown in complex medium (CM; 250g/L NaCl, 20g/L MgSO4.7H2O, 3g/L sodium citrate, 2g/L KCl, 10g/L peptone) at 37ºC under full-spectrum white light. Biological replicate samples were removed throughout the growth curve at early log, mid log, late log, and stationary phase to measure genome-wide transcription.
2010-05-06 | E-GEOD-13531 | biostudies-arrayexpress
Project description:We have used three complementary deep sequencing approaches to characterise the temporal order of genome replication in S. cerevisiae. Each approach measures the increase in DNA copy number as a genomic region is replicated (in a large population of cells). We find that the use of deep sequencing provided high spatial resolution. For maximum temporal resolution we have measured replication dynamics at multiple time points during a synchronous S phase. To pinpoint replication origins we have synchronously released a checkpoint mutant (rad53-delta) into S phase under conditions of depleted dNTPs (200 mM hydroxyurea; HU) and measured the increase in DNA copy number after 60 minutes. Finally for rapid characterisation of replication dynamics in wild-type cells from an unperturbed cell cycle we have obtained replicating (S phase) and non-replicating (G2 phase) cells by fluorescence activated cell sorting (FACS) and subjected the DNA to copy number analysis. We have compared and contrasted these approaches and developed the tools required for interpreting the deep sequencing data. Measurement of genome replication time for various S. cerevisiae strains. For each strain two samples were analysed: a replicating sample (from S phase) and a non-replicating sample (from G2 phase).
2013-10-02 | E-GEOD-48212 | biostudies-arrayexpress
Project description:Staphylococcus aureus is a Gram-positive human pathogen causing a variety of human diseases in both hospital and community settings. This bacterium is so closely associated with prophages that it is rare to find S. aureus isolates without prophages. Two phages are known to be important for staphylococcal virulence: the beta-hemolysin (hlb) converting phage and the Panton-Valentine Leukocidin (PVL) converting phage. The hlb-converting phage is found in more than 90% of clinical isolates of S. aureus. This phage produces exotoxins and immune modulatory molecules, which inhibit human innate immune responses. The PVL-converting phage produces the two-component exotoxin PVL, which can kill human leucocytes. This phage is wide-spread among community-associated methicillin resistant S. aureus (CA-MRSA). It also shows strong association with soft tissue infections and necrotizing pneumonia. Several lines of evidence suggest that staphylococcal prophages increase bacterial virulence not only by providing virulence factors but also by altering bacterial gene expression: 1) Transposon insertion into prophage regulatory genes, but not into the genes of virulence factors, reduced S. aureus killing of Caenorhabditis elegans.; 2) Although the toxins and immune modulatory molecules encoded by the hlb- converting phages do not function in the murine system, deletion of NM3, the hlb-converting phage in S. aureus Newman, reduced staphylococcal virulence in the murine abscess formation model. 3) In a preliminary microarray experiment, prophages in S. aureus Newman altered the expression of more than 300 genes. In this research proposal, using microarray and high-throughput quantitative RT-PCR (qRT-PCR) technologies, we will identify the effects of the two important staphylococcal phages on the gene expression of S. aureus in both in vitro and in vivo conditions. This project is intended to be completed within one year. All the data – microarray, qRT-PCR and all the primer sequences- will be made available to public 6 month after completion. Data from this project will help us to understand the role of prophages in the S. aureus pathogenesis and can lead to development of a strategy to interfere with the pathogenesis process. Staphylococcus aureus subsp.aureus strain Newman (reference) and Staphylococcus aureus subsp.aureus strain Newman yhcR knockout(query) were grown in TSA broth.Samples were grown under aerobic and anaerobic conditions and RNA samples harvested at mid log, stationary, and log phases.Samples were hybridized on aminosilane coated slides with 70-mer oligos.
2011-12-31 | E-GEOD-26585 | biostudies-arrayexpress
Project description:Transcriptional profiling of E. faecalis E99 WT and an isogenic ΔperA strain grown in THB + 1% glucose. Pathogenic E. faecalis are enriched for a pathogenicity island (PAI). This 150-kb island harbors a number of well characterized virulence genes plus a number of determinants of unknown function including one encoding a transcriptional regulator, designated PerA. In this work, we show that PerA coordinately regulates both metabolic and virulence genes, and influences the platelet binding ability of E. faecalis. Finally, we show that PerA responds to bicarbonate, an intestinal ion frequently used by pathogens to determine the site of infection. Together, these results indicate that PerA is a global transcriptional regulator that coordinately regulates genes responsible for enterococcal pathogenicity. These findings highlight a novel feature of PAI-mediated virulence regulation, namely the coordinate regulation of metabolic and virulence factors in the core genome by a horizontally acquired PAI-encoded transcriptional regulator. RNA was obtained from E. faecalis E99 ΔperA from mid-log (OD600 0.05), late log (OD600 0.5) and stationary phase (OD600 1.0) and compared to E. faecalis E99 WT RNA extracted from the same growth phases. Cultures were grown in THB + 1% glucose.
2012-08-16 | E-GEOD-31538 | biostudies-arrayexpress
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 37ºC 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
Project description:Assays 1-4: Effects of DnaA activity on S. meliloti chromosome, pSymA and pSymB replicon bias. Sheared DNA extracts of IPTG-induced vs uninduced cultures of DnaA (Assays 1,2) or Hda (Assays 3,4) overexpressors were labeled with Cy3 or Cy5 and hybridized applying dye-swap replicate design. Assay 5: Hybridization of sheared DNA of logarithmic (Cy3-labeled) vs stationary phase (Cy5-labeled) culture.
2015-10-04 | E-MTAB-3924 | biostudies-arrayexpress
Project description:JLP515, JLP1285, and JLP1288 were grown in EMM+LAUH supplemented with thiamine (B1) to repress nmt1 promoter driving cdc18* expression. Cells were grown at 32°C to late log phase, OD600 = ~0.500. Then cells were washed with water and used to inoculate a culture of EMM+LAUH lacking B1 and a culture of EMM+LAUH+ B1 to an OD600 = ~0.0125. Cells were put back at 32°C to grow. At 17, 21, and 25 hours post removal of B1, cells in EMM+LAUH-B1 were harvested for experimental samples. Cells in EMM+LAUH+B1 were harvested after 25 hours for control samples. Cultures were diluted periodically to ensure that cells remained in early log phase throughout time course.
2007-11-16 | E-MEXP-1128 | biostudies-arrayexpress
Project description:Candida glabrata were kept within human moncoyte-derived macrophages (MDM) for up to seven days to investigate the transcriptome of long-term residence within phagosomes. Samples were taken after 6h and 1, 2, 4, and 7 days. To control for general starvation, long-term exposure data for the growth media YPD, SD, and RPMI (with serum) were included. Experiments were performed as a common reference design, with log-phase YPD growth as Cy3-labeled reference for all arrays.
2023-05-31 | E-MTAB-11801 | biostudies-arrayexpress