Assays
What is an Assay?Filters
Global sensitivity analysis of a kinetic model to determine the sensitivities for each parameter, over a wide parameter range. We used the elementary effects method.
Submitter: Mark Musters
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Investigation of glycolysis and pyruvate branch...
Lumped kinetic model of L. lactis glycolysis, formulated with ordinary differential equations. Simulations are in line with experimental data
Submitter: Mark Musters
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Investigation of glycolysis and pyruvate branch...
This experiment uses a low-copy plasmid based system (MG1655 Δlac FF(-41.5)/RW50) for measuring FNR activity. Initial acetate calibration of the chemostat with the MG1655 Δlac strain was carried out, with β-galactosidase activity from the FF(-41.5)/RW50 reporter plasmid measured at 100%, 80%, 50%, 20% and 0% aerobiosis levels. Finally, the aerobiosis levels were re-determined by calculating the actual acetate flux in the sampled chemostat runs.
Note: the strain used (MG1655 Δlac) is not the same ...
Submitter: Michael Ederer
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Steady state studies for different oxygen avail...
The task of this assay is to determine the impact of oxygen availability on the concentrations of metabolites from different central metabolic pathways. The focus lies on metabolites connected to glycolysis, tri-carbon-acid-cycle and energy metabolism. All strains have been cultured and analysed according to the SOPs listed below
Submitter: Stefan Stagge
Assay type: Metabolomics
Technology type: Liquid Chromatography Mass Spectrometry
Investigation: Steady state studies for different oxygen avail...
Theoretical analysis of hypothetical sigma factor competition. Based on the model 'transcription factor competition' possible dynamics of sigma factor competition are simulated and analysed using Lineweaver-Burk representations.
Submitter: Ulf Liebal
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: The transition from growing to non-growing Baci...
experimentally measured extracellular fluxes in yeast Saccharomyces cerevisiae in anaerobic glucose limited chemostat (D=0.1 h-1) on minimal medium
Submitter: Maksim Zakhartsev
Assay type: Metabolite Profiling
Technology type: HPLC
Investigation: Steady state metabolic fluxes and metabolite co...
Steady state concentrations of extracellular metabolites in yeast Saccharomyces cerevisiae in anaerobic chemostat at D = 0.1 h-1 on minimal medium
Submitter: Maksim Zakhartsev
Assay type: Metabolite Profiling
Technology type: HPLC
Investigation: Steady state metabolic fluxes and metabolite co...
Submitter: Maksim Zakhartsev
Assay type: Metabolite Profiling
Technology type: Gas Chromatography Mass Spectrometry
Investigation: Steady state metabolic fluxes and metabolite co...
Biomass weight during glucose pulse. Glucose pulse was performed in anaerobically growing yeast Saccharomyces cerevisiae in steady state chemostat (D = 0.1 h-1) and transent concentrations of the extra- and intracellular metabolites from central carbon metabolism (e.g. glycolysis, PPP, glycerol, purines, etc) were measured.
Submitter: Maksim Zakhartsev
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Kinetic analysis of metabolic system using tran...
Dynamics of extracellular metabolites (glc, pyr, suc, lac, gly, ac, etoh, fum, mal, cit, including loss of akg, g3p, 2pg, 3pg, r5p, f6p, g6p, 6pg) during glucose pulse. Glucose pulse was performed in anaerobically growing yeast Saccharomyces cerevisiae in steady state chemostat (D = 0.1 h-1) and transent concentrations of the extra- and intracellular metabolites from central carbon metabolism (e.g. glycolysis, PPP, glycerol, purines, etc) were measured.
Submitter: Maksim Zakhartsev
Assay type: Metabolite Profiling
Technology type: HPLC
Investigation: Kinetic analysis of metabolic system using tran...
Dynamics of intracellular metabolites (pyr, suc, fum, mal, akg, pep, g3p, 2pg, 3pg, cit, r5p, f6p, g6p, 6pg, ATP, ADP, AMP, UTP, GTP, inosine, NAD+, IMP, UDP, NADP+, CTP, AdenyloSuccinate, NADPH, trehalose) during glucose pulse. Glucose pulse was performed in anaerobically growing yeast Saccharomyces cerevisiae in steady state chemostat (D = 0.1 h-1) and transent concentrations of the extra- and intracellular metabolites from central carbon metabolism (e.g. glycolysis, PPP, glycerol, purines, ...
Submitter: Maksim Zakhartsev
Assay type: Metabolite Profiling
Technology type: Gas Chromatography Mass Spectrometry
Investigation: Kinetic analysis of metabolic system using tran...
Dynamics of macromolecules (total RNA) during glucose pulse. Glucose pulse was performed in anaerobically growing yeast Saccharomyces cerevisiae in steady state chemostat (D = 0.1 h-1) and transent concentrations of the extra- and intracellular metabolites from central carbon metabolism (e.g. glycolysis, PPP, glycerol, purines, etc) were measured.
Submitter: Maksim Zakhartsev
Assay type: Metabolomics
Technology type: Technology Type
Investigation: Kinetic analysis of metabolic system using tran...
These files show physiological measurements from the Sheffield Infors chemostat which were made during acetate calibration and also when sampling for the steady-state transcriptional profiles.
Submitter: Matthew Rolfe
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Steady state studies for different oxygen avail...
This assay involved the determination of transcriptional profiles at 0, 2, 5, 10, 15 and 20 minutes through aerobic to anaerobic gas transitions and anaerobic to aerobic gas transitions. In each case an aerobic or anaerobic steady state was created, RNA sampled (0 min) and then the gas supply changed. RNA samples were then taken from the time at which the gas supply was changed.
For anaerobic conditions 5% CO2, 95% N2 was used.
The full transcriptional dataset is available from ArrayExpress ...
Submitter: Matthew Rolfe
Assay type: Transcriptional Profiling
Technology type: Microarray
Investigation: Dynamical studies for different oxygen availabi...
The transcriptional profiles of steady state E. coli cultures at a range of aerobiosis levels were determined. Two biological replicates and two technical replicates were carried out. Microarrays were carried out in a reference style (i.e. RNA vs a gDNA reference).
Submitter: Matthew Rolfe
Assay type: Transcriptomics
Technology type: Microarray
Investigation: Steady state studies for different oxygen avail...
This assay describes the determination of concentrations and ratio of metabolites of adenine nucleotides (NAD and NADH). These metabolites have been extracted from Escherichia coli MG1655 and isgenic mutant strains.
Submitter: Stefan Stagge
Assay type: Metabolomics
Technology type: Initial Rate Experiment
Investigation: Steady state studies for different oxygen avail...
This assay describes the determination of concentrations and ratio of metabolites of ubiquinones (oxidised and reduced form). These metabolites have been extracted from Escherichia coli MG1655 and isgenic mutant strains.
Submitter: Stefan Stagge
Assay type: Metabolomics
Technology type: HPLC
Investigation: Steady state studies for different oxygen avail...
This .csv file shows the numbers of different cytochrome molecules per cell from steady-state continuously-grown cultures at various aerobiosis levels (0%, 31%, 56%, 85% and 115% AAU).
Submitter: Alison Graham
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Steady state studies for different oxygen avail...
Submitter: Praveen kumar Sappa
Assay type: Glucose Pulse
Technology type: Technology Type
Investigation: The transition from growing to non-growing Baci...
B. subtilis was grown in SMM media with glucose as carbon source and the samples for RNA were harvested OD578nm- 1.0). The stress conditions that were applied over here are growthat 57°C, 16°C, 1.2M Nacl and 37°C(control). All the samples were analysed for transcriptome as biological triplicates.
Submitter: Praveen kumar Sappa
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Redefining the Complete Transcriptome of Bacill...
Submitter: Praveen kumar Sappa
Assay type: Transcriptomics
Technology type: Technology Type
Investigation: Redefining the Complete Transcriptome of Bacill...
B. subtilis was grown in M9 media with glucose as carbon source and the samples were harvested during exponential phase (OD600nm- 0.4), early stationary phase(OD600nm- 1.3), late stationary phase(OD600nm- 1.0). All the samples were analysed for transcriptome as biological triplicates.
Submitter: Praveen kumar Sappa
Assay type: Transcriptomics
Technology type: Microarray
Investigation: Redefining the Complete Transcriptome of Bacill...
Submitter: Jay Moore
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Metabolism of Streptomyces coelicolor (SysMO ST...
Study: Timeseries 1
Submitter: Jay Moore
Assay type: Transcriptomics
Technology type: Custom Array
Investigation: Metabolism of Streptomyces coelicolor (SysMO ST...
Study: Timeseries 1
Submitter: Falko Krause
Assay type: Transcriptomics
Technology type: Microarray
Investigation: K+ Starvation in Saccharomyces cerevisiae
Study: Transcriptional Profile
Submitter: Falko Krause
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: K+ Starvation in Saccharomyces cerevisiae
Study: Transcriptional Profile
Submitter: Falko Krause
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: K+ Starvation in Saccharomyces cerevisiae
Study: Transcriptional Profile
Is cell volume affected by potassium starvation?
The volume reduction as a response to the shift of cells from a medium of high potassium to potassium free medium will be studied in mutants lacking certain membrane transporters like Trk1,2 Nha1, etc. The conditions for the experiments follow Navarrete et al. (2010). Additionally knockouts of related regulation proteins (SAP155, SAP185) will be tested. For each mutant several time points will be measured to generate time courses.
Submitter: Falko Krause
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: K+ Starvation in Saccharomyces cerevisiae
Time courses of the internal pH changes under the conditions of Navarrete et al. (2010) will be obtained. The usage of different mutants (transport systems and regulation factors) will reveal the influence and key systems of pH regulation.
To estimate the changes of internal pH, the pH-dependent variant of GFP pHluorin is expressed in cells from a multicopy plasmid, and the changes in cell fluorescence are monitored during 5 hours of incubation in YNB-F growth media without added potassium.
Submitter: Falko Krause
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: K+ Starvation in Saccharomyces cerevisiae
How does internal potassium changes (decreases) during several hours of potassium starvation. Is there a limit for internal potassium decrease? Sampling potassium content in cells during starvation The relative membrane potential will be measured according to the conditions of Navarrete et al. (2010). Various mutants will be tested for their effect. To estimate the relative changes of plasma-membrane potential, the diSC3(3) fluorescent probe was used and the changes in cell fluorescence monitored ...
Submitter: Falko Krause
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: K+ Starvation in Saccharomyces cerevisiae