Data files

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Agenda for the satellite data management tutorial of Synthetic Biology 2017.

Creator: Natalie Stanford

Contributor: Natalie Stanford

No description specified

Creator: Ulrike Wittig

Contributor: Ulrike Wittig

No description specified

Creator: Ulrike Wittig

Contributor: Ulrike Wittig

No description specified

Creator: Ulrike Wittig

Contributor: Ulrike Wittig

Output of the 3D-structures modeled by comparative modeling tool for LDH enzymes from four LABs (in the PDB format, tarred). Four LABs include Enterococcus faecalis, Lactococcus lactis, Streptococcus pyogenes and Lactobacillus plantarum. Output of the SEEK Model https://seek.sysmo-db.org/models/118.

The modeling was performed against a x-ray structure of LDH from B. stearothermophilis (template, PDH ID: 1LDN).

The Table represents the simulation results of how the presence of phosphate ions (Pi) in the solution might affect the activity of four LDH enzymes. This includes the algorithmic analysis of the binding energies values computed by the GRID program (see Part 4, model) for each enzyme in presence and absence of FBP molecule at pH 6 and 7. The analysis was performed by using the algorithm proposed in Part 5, model.

Output files of phosphate probe binding on the surface of LDH from lactococcus lactis type 1. File with extension XPLOR can be visualized with a program VMD to identify the most favorable position for the phosphate binding. This relates to the Model "Part 4".

L. lactis cultures were grown at different dilution rates in glucose-limited chemostat conditions and were analyzed with respect to physiological parameters. Amino acid consumption, glucose consumption and production of fermentation products were measured in steady-state conditions,

Creator: Martijn Bekker

Contributor: Martijn Bekker

Simulation results of experimental data of the reconstituted gluconeogenic system

Simulation results of temperature degradation of gluconeogenic intermediates

Simulation results of TPI experimental data for GAP and DHAP saturation.

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

Simulation results of FBPAase of experimental data for DHAP and GAP saturation

Excel sheet contains:

- flux distribution solution from best iteration cluster
- quality of the fit (experimental MIDs vs. simulated MIDs)
- Sensitivity analysis for 95% flux parameter confidence interval using a Monte-Carlo approach

Excel sheet contains:

- flux distribution solution from best iteration cluster
- quality of the fit (experimental MIDs vs. simulated MIDs)
- Sensitivity analysis for 95% flux parameter confidence interval using a Monte-Carlo approach

Excel sheet contains:

- flux distribution solution from best iteration cluster
- quality of the fit (experimental MIDs vs. simulated MIDs)
- Sensitivity analysis for 95% flux parameter confidence interval using a Monte-Carlo approach

Simulation results of GAPDH experimental data for BPG, NADPH, NADP, GAP, and Pi

Simulation results of PGK experimental data for ADP, ATP, 3PG and BPG saturation.

No description specified

The file contains simulated data of the electron transport chain model (EcoliETC1) for varying parameter values, i.e. a local sensitivity analysis.

Filtering of data in Perseus and t-test between conditions
Perseus save file

Maxquant output.

Proteomics data comparing LXX cultures cultivated on mineral and in continuous culture:
mineral samples:
LNU-LXX9-Si00-14B-P-B-Pr
LNU-LXX9-Si00-14B-P-C-Pr
LNU-LXX9-Si00-14B-P-D-Pr
conitnuous culture samples:
LNU-LXX9-Si00-CnA-P-B2-Pr
LNU-LXX9-Si00-CnA-P-B3-Pr
LNU-LXX9-Si00-CnA-P-B4-Pr
LNU-LXX9-Si00-CnA-P-B5-Pr
LNU-LXX9-Si00-CnA-P-B6-Pr
LNU-LXX9-Si00-CnA-P-B7-Pr

Link to the repository for functional annotation

Comparison between axenic and planktonic readcounts with deseq2

Genbank file for the L.ferriphilum chromosome, annotated with prokka 1.12beta

Comparison for LFQs with t-test in Perseus

Table combining data for L.ferriphilum.
RNAseq data, Proteomics LFQs, Functional annotation

No description specified
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