Data files

All datapoints that were measured are displayed together with the accompanying simulations by the computational model

This files contains the parameter values, life-times, half-lives and errors associated with modeling the decay of the transcriptome, based on 3 models described in Deneke et al. "Complex degradation processes lead to non-exponential decay patters and age-dependent decay rates of messenger RNA". PLoS One. 2013;8(2):e55442

The file contains the normalized relative read counts (RPM) of 2 mRNA decay experiments. Columns in blue correspond to experiment 1, columns in violet correspond to experiment 2. The time points are in column headers. The last 3 columns contain parameters and half lives calculated from an exponantial fit of all data points. Normalization was done in 2 steps :first by calculating RPM i.e. reads per million of aligned reads to unique ORFs, second by normalizing this to the total amount of mRNA ...

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 GSH, and Spd.

An extended model description of the TryS model

The file contains the initial rate measurements of TbTryS obtained under different substrate and product initial concentrations.

Untargeted and targeted metabolic analysis on T. b. brucei 427 grown under oxidative stress with methylene blue has been carried out. This work has been completed with 11 bio-reps and found significant metabolic changes as you can see in the IDEOM file attached. 'Comparison' tab in the data spread sheet shows heat maps and fold change analysis regarding different metabolite levels (T: T brucei, TMB: T. brucei exposed to methylene blue, numbers: time points, 0, 5, 60 & 120min). If you double ...

Metabolic changes of 26 intracellular metabolites extracted from T. b. brucei 427 wild type and arginine kinase knockout cells under high pH stress (pH8.7)

Intracellular concentrations of 50 metabolites measured by LC-MS using isotope ratio based mass spectrometry technique

Concentrations of 22 extracellular metabolites (major medium components) from T. b. brucei 427

Metabolic changes of 26 intracellular metabolites extracted from T. b. brucei 427 wild type and arginine kinase knockout cells exposed to methylene blue

Describes the assumptions made, how to integrate the new reactions to the rest of the glycolysis model, the parameters needed and the preliminary parameter values collected from the litterature.

Arginine kinase has been thought of as a potential stress marker (see 'Metabolic changes by oxidative stress in T. b. brucei 427'), the gene knockout cells have been constructed.