Assays
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Temperature degradation of BPG, GAP and DHAP
Submitter: Jacky Snoep
Assay type: Metabolite Concentration
Technology type: Technology Type
Investigation: Central Carbon Metabolism of Sulfolobus solfata...
Study: Model Gluconeogenesis
test
Submitter: Holger Janssen
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Systems Biology of Clostridium acetobutylicum -...
Submitter: John Raedts
Assay type: Metabolomics
Technology type: Technology Type
Investigation: Identification of regulatory metabolites in the...
We developed a new metabolomics protocol, which involved a comparison of different harvesting techniques, quenching solutions and extraction methods. Cell leakage and metabolite recovery was determined by ATP measurements
Submitter: John Raedts
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Identification of regulatory metabolites in the...
Using TFinfer2 to analyse data from "Characterization of MG1655 and mutant strains under conditions of glucose excess and limitation"
Submitter: Botond Cseke
Biological problem addressed: Model Analysis Type
Investigation: Analysis of the glucose transport in Escherichi...
Submitter: Sebastian Curth
Biological problem addressed: Model Analysis Type
Investigation: General Method Development
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...
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: Praveen kumar Sappa
Assay type: Transcriptomics
Technology type: Technology Type
Investigation: Redefining the Complete Transcriptome of Bacill...
Submitter: Falko Krause
Assay type: Transcriptomics
Technology type: Microarray
Investigation: K+ Starvation in Saccharomyces cerevisiae
Study: Transcriptional Profile
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
Time-dependent simulations of the dynamic switch between acidogenesis and solventogenesis based on the metabolic network and pH-dependent regulation of the enzymes.
Submitter: Sara Jabbari
Biological problem addressed: Metabolic Network
Investigation: The effect of pH upon the metabolic shift in Cl...
Kinetic characterisation of triose phosphate isomerase
Submitter: Jacky Snoep
Assay type: Enzymatic Assay
Technology type: Initial Rate Experiment
Investigation: Central Carbon Metabolism of Sulfolobus solfata...
Study: Model Gluconeogenesis
Mathematical model for TPI kinetics, saturation with GAP and DHAP, and inhibition by 3PG and PEP
Submitter: Jacky Snoep
Biological problem addressed: Enzymology
Investigation: Central Carbon Metabolism of Sulfolobus solfata...
Study: Model Gluconeogenesis
Submitter: Daniel Hönicke
Assay type: Transcriptomics
Technology type: Microarray
Investigation: Altering the expression pattern in Clostridium ...
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...
Transcriptome analysis for the samples harvested from Chemostat cultivated samples.
Submitter: Praveen kumar Sappa
Assay type: Transcriptomics
Technology type: Microarray
Investigation: Multiomics study of Bacillus subtilis under osm...
Submitter: Sebastian Curth
Assay type: Transcriptional Profiling
Technology type: Microarray
Investigation: Investigation on the effect of pulsed metabolit...
Submitter: Jay Moore
Assay type: Transcriptomics
Technology type: Custom Array
Investigation: Metabolism of Streptomyces coelicolor (SysMO ST...
Study: Timeseries 1
Submitter: Praveen kumar Sappa
Assay type: Transcriptomics
Technology type: Custom Array
Investigation: Identification of targets of the essential RNas...
This assay is designed to obtain the in vitro kinetic data of T. brucei recombinant trypanothione synthetase. The enzyme catalyzes the ATP-dependent ligation of spermidine (Spd) and GSH to generate glutathionylspermidine (Gsp) and also of Gsp and GSH to finally produce trypanothione (T(SH)2). The data was obtained in an spectrophotometric assay that links ADP production with NADH consumption through the piruvte kinase and lactate dehydrogenase.
Submitter: Alejandro Leroux
Assay type: Experimental Assay Type
Technology type: Enzymatic Activity Measurements
Investigation: Kinetic understanding of the T. brucei trypanot...
TbTryS activity was measured at 37°C in the in vivo-like buffer. All substrate stock solutions were prepared in the in vivo-like buffer and the pH was adjusted to 7.0. The assays were performed in a final volume of 2 ml and contained 0.2 mM NADH, 1 mM phosphoenolpyruvate, 4 units pyruvate kinase, 4 units L-lactate dehydrogenase, 0.17 µM TbTryS, 2.1 mM ATP and varying amounts of glutathione, and spermidine.
Submitter: Alejandro Leroux
Assay type: Discontinuous Enzymatic
Technology type: HPLC
Investigation: Kinetic understanding of the T. brucei trypanot...