Supplementary information to
Pathogen-specific isotope tracing approach reveals metabolic activities and fluxes of intracellular Salmonella
Karin Mitosch1, Martin Beyß2,3, Prasad Phapale4,5, Bernhard Drotleff4, Katharina Nöh2*, Theodore Alexandrov4,6,7,8*, Kiran R. Patil6,9*, Athanasios Typas1,6*
1 Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
2 Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
3 RWTH Aachen University, Computational Systems Biotechnology, Aachen, Germany
4 Metabolomics Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
5 Current address: Leibniz-Institut für Analytische Wissenschaften – ISAS – e.V., Dortmund, Germany
6 Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
7 Molecular Medicine Partnership Unit, European Molecular Biology Laboratory, Heidelberg, Germany
8 BioInnovation Institute, Copenhagen, Denmark
9 Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
* Corresponding authors:
- [email protected] (KN)
- [email protected] (TA)
- [email protected] (KRP)
- [email protected] (AT)
The raw data is available on zenodo doi:10.5281/zenodo.7896186 It contains the results of the MCMC sampling (i.e. fluxes) as well as the simulated MS measurements.
The jupyter notebook can be executed top down to reproduce all figures and tables. If the raw data is not present it will be fetched from zenodo
- The notebook generates the file
out/Fig_4_omix.csv. - Open Omix (the free Light version is sufficient) and open
ressources/STm_Omix.omx - In the Property Editor on the right hand side, find the entry Input File and set it to
Figure 4/omix.csv - Chose Start Visualization on the top
- By using the slider next to Select Row you can switch between the low (row 0) and high (row 1) glucose concentration
- Figure 4 is generated with the low glucose concentration