Data files

1363 Data files visible to you, out of a total of 2258

Data file for PLaSMo accesssion ID PLM_23, version 1

Creators: BioData SynthSys, Robert Muetzelfeldt

Contributor: BioData SynthSys

No description specified

Creator: Alexey Kolodkin

Contributor: Alexey Kolodkin

WT (Cy5) vs. trxB (Cy3)_stationary growth phase_DyeFlip

Creator: Daniel Hönicke

Contributor: Daniel Hönicke

WT (Cy3) vs. trxB (Cy5)_stationary growth phase

Creator: Daniel Hönicke

Contributor: Daniel Hönicke

WT (Cy3) vs. trxB (Cy5)_exp. growth phase

Creator: Daniel Hönicke

Contributor: Daniel Hönicke

Experiment conducted in early April 2014
Intact rosette is pictured, with plant number and genotype in handwritten labels, and ruler for scale.
Then dissected leaves are organised in sequence of age,
if necessary with small cuts to let them lie flat.

Areas are then measured in image processing.

Intact rosette is pictured, with plant number and genotype in handwritten labels, and ruler for scale.
Then dissected leaves are organised in sequence of age, if necessary with small cuts to let them lie flat.
Areas are then measured in image processing.

E. faecalis was gucose-pulsed after resuspension in 100 mM MES buffer at pH 6.5
Intra- and extracellular metabolites concentrations were followed in time

Creator: Martijn Bekker

Contributor: Martijn Bekker

Growth curves of the PA1008 strain of Pseudomonas aeruginosa with multiple concentrations of meropenem. Data set 1 is used to parametrise the model in our project. This consists of three biological replicates, each with three technical repeats. The meropenem concentrations used for this data set were: 0, 2, 4, 10, 20, 40, 200 ug/ml.

Creators: Chloe Spalding, Sara Jabbari

Contributor: Chloe Spalding

Growth curves of the PA1008 strain of Pseudomonas aeruginosa with multiple concentrations of meropenem. Data set 1 is used to parametrise the model in our project. This consists of three biological replicates, each with three technical repeats. The meropenem concentrations used for this data set were: 0, 0.5, 1, 5, 10, 50, 100 ug/ml.

Creators: Chloe Spalding, Sara Jabbari

Contributor: Chloe Spalding

just cell counts, the area of the grains is separate.

NHA1 ENA1-5 TOK1 TRK1 TRK2

Creator: Silvia Petrezselyova

Contributor: The JERM Harvester

Data file for PLaSMo accesssion ID PLM_64, version 1

Data file for PLaSMo accesssion ID PLM_6, version 1

Creators: BioData SynthSys, Alexandra Pokhilko, Andrew Millar

Contributor: BioData SynthSys

Data file for PLaSMo accesssion ID PLM_24, version 1

Creators: BioData SynthSys, Jonathan Massheder

Contributor: BioData SynthSys

Data file for PLaSMo accesssion ID PLM_42, version 1

Creators: BioData SynthSys, Jonathan Massheder

Contributor: BioData SynthSys

This is a pdf showing a graph of the dissolved oxygen tension of the culture during an aerobic to anaerobic transition.

This is a pdf showing a graph of the dissolved oxygen tension of the culture during an anaerobic to aerobic transition.

The distribution of enzymes involved in oxidative Stickland reactions among archaea was estimated using BLAST searches (BLOSUM62) with the protein sequences of acetate-CoA ligase (EC 6.2.1.13, ACS), ketoisovalerate oxidoreductase (EC 1.2.7.7, BC-OR) and indolepyruvate oxdoreductase (EC 1.2.7.8, AR-OR) from Pyrococcus furiosus (Pfu) and Sulfolobus solfataricus (Sso) against all archaea. Positive results are indicated by a '+' (homologue found, e-value 1e-20).

Simulation of double mutants and perturbations and time series samples using for Sample 1 only OE mutants of which we update the enzyme concentrations. For each second mutant the enzyme concentrations in case of OE and KO mutants in updated and the metabolite concentrations of the second sample are loaded in the model.
Using this approach the model approximately predicts combinatorial effects of OE mutations with other mutations, perturbations and time series concentrations.

Creator: Niels Zondervan

Contributor: Niels Zondervan

Contains a Jupyter notebook file that uses libroadrunner and tellurium to run all simmulations and analysis based on the 40 independent samples. The Readme.txt file contains information on how to recreate the complete modelling environment used for all simmulations and analysis using Anaconda.

Creator: Niels Zondervan

Contributor: Niels Zondervan

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.

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,
...

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.

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