Assays

Test Assay description

Assay for transcriptional profiling time course in yeast

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Assay to measure gene expression of Saccharomyces cerevisiae (yeast) under different nutrient limitations

Limiting Nutrients: ethanol, nitrogen, glucose, phosphorus, carbon, sulfur, sulphur

This data is public data taken from the BioInvestigation Index.

(http://www.ebi.ac.uk/bioinvindex/study.seam?studyId=BII-S-1)

Assay to measure metabolites of yeast saccharomyces cerevisiae under different nutrient limitations

Limiting Nutrients: ethanol, nitrogen, glucose, phosphorus, carbon, sulfur, sulphur

This data is public data taken from the BioInvestigation Index. (http://www.ebi.ac.uk/bioinvindex/study.seam?studyId=BII-S-1)

Assay to measure protein expression in yeast saccharomyces cerevisiae under different nutrient limitations

Limiting Nutrients: ethanol, nitrogen, glucose, phosphorus, carbon, sulfur, sulphur

This data is public data taken from the BioInvestigation Index. (http://www.ebi.ac.uk/bioinvindex/study.seam?studyId=BII-S-1)

Assay for transcriptional profiling time course in yeast treated with rapamycin

This is public data from the BioInvestigation Index (http://www.ebi.ac.uk/bioinvindex/study.seam?studyId=BII-S-2)

Glycolysis in Saccharomyces cerevisiae

Detailed glycolytic model in Lactococcus lactis

A kinetic model of the glycerol synthesis pathway has been constructed. Kinetic parameters were collected from published values. Maximal enzyme activities and intracellular effector concentrations were determined experimentally.

An assay to measure exttracellular glycerol using HPLC

Intracellular metabolite concentrations were determined enzymatically by measuring the oxidation or reduction of NADH or NAD+, respectively, at 340 nm in a Beckman Coulter DU640 spectrophotometer

Kinetic characterisation of Phosphoglycerokinase

Kinetic characterization of the FBPA/ase with respect to GAP en DHAP saturation.

GAP and DHAP concentrations were measured over time at 70C.

The temperature dependent degradation of DHAP and GAP is modelled as an exponential decay process using experimental data for the disintegration at 70C.

Mathematical model for FBPAase kinetics, saturation of GAP and DHAP

Mathematical model for PGK kinetics, saturation with ADP, ATP, 3PG and BPG.

Mathematical model for GAPDH kinetics, saturation of GAP, BPG, NADP, NADPH and Pi.

Mathematical model for TPI kinetics, saturation of GAP and DHAP.

Mathematical model for the analysis of carbon loss of BPG, GAP and DHAP in reconstituted system of S. solfataricus at 70C.

The four purified enzymes were incubated in assay buffer and consumption of 3PG and production of F6P were measured in time, together with GAP and DHAP concentrations.

Mathematical model for the reconstituted system with PGK, GAPDH, TPI and FBPAase.

Varying the relative amounts of PGK and FBPAase and analyse the 3PG uptake and F6P production rates.

Experimental analysis of pathway fluxes with varying PGK and FBPAase concentrations in the incubation assay.

Sharing well-annotated research data helps the systems biology process.

This practical is about how to easily structure your experimental data such that it becomes well annotated, standard compliant, reproducible, and re-usable (also for others). While much big data travels from machine to machine without human intervention, we will focus on exchange of small data describing experiments which is (to our experience) mostly handled via MS Excel and similar tools. First we give an outline talk about ...

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