General Information info
|Manuscript title||Pseudo-transition Analysis Identifies the Key Regulators of Dynamic Metabolic Adaptations from Steady-State Data.|
|Authors||Luca Gerosa, Bart R.B., Haverkorn van Rijsewijk, Dimitris Christodoulou, Karl Kochanowski, Thomas S.B. Schmidt, Elad Noor, Uwe Sauer|
|Affiliations||Institute of Molecular Systems Biology, ETH Zurich, Zurich 8093, Switzerland; Systems Biology Graduate School, Zurich 8057, Switzerland.|
|Keywords||computational biology; metabolism; metabolomics; regulation network; transcription factor|
|Full text article||Gerosa_2015.pdf|
|Project name||not specified|
Experiment Description info
|Data type||metabolites at steady-state|
|Data units||µmol * gCDW-1|
|Execution date||not specified|
Experimental Details info
|Carbon source||acetate, fructose, galactose, glucose, glycerol, gluconate, pyruvate, succinate|
|Dilution rate (h-1)||—|
|Working volume (L)||0.0035|
|Biomass concentration (g/L)||see worksheet|
LB cultures were used to inoculate M9 medium precultures with the indicated carbon sources for overnight cultivation.
|General protocol information||
1 ml aliquots were taken in a 37°C room from exponential phase cultures.
Quenching procedure: Filters were directly subjected to cold extraction (-20°C) with 40:40:20 acetonitrile/methanol/water containing 200 μl of internal standard (fully 13C-labelled S. cerevisiae extract).
Extraction technique: boiling ethanol
Sample analyzing method: LC-MS
|Methods description - Notes||
Cell extracts were thawed, dried at 120 μbar, and resuspended in 100 μl deionized H2O of which 15 μl were transferred into rubber-sealed HPLC tubes. Metabolite abundances were determined by ion-pairing ultra-high performance liquid chromatography (UPLC)-tandem MS  and quantified through a dilution series of a mix containing all metabolites and internal standard. Intracellular metabolite concentrations in μmol/mL were calculated from metabolite abundances in μmol/gCDW using a previously determined conversion factor to intracellular cytosolic volume.
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