DataEntryID 126
    General information
      Manuscript title: Pseudo-transition Analysis Identifies the Key Regulators of Dynamic Metabolic Adaptations from Steady-State Data.
      PubMed ID: http://www.ncbi.nlm.nih.gov/pubmed/27136056
      Journal: Cell Systems
      Year: 2015
      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: https://kimosys.org/rails/active_storage/blobs/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBdkVFIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--86727b525a3a35c44ada2a1e5893d6616038f44b/Gerosa_2015.pdf
      Project name: not specified

    Experiment description
      Organism: Escherichia coli
      Strain: BW25113
      Data type: metabolites at steady-state
      Data units: µmol * gCDW-1
      Execution date: not specified

    Experimental details
      Temperature (°C): 37
      pH: not specified
      Carbon source: acetate, fructose, galactose, glucose, glycerol, gluconate, pyruvate, succinate
      Culture mode: batch
      Process condition: aerobic
      Dilution rate (h⁻¹): —
      Working volume: 0.0035 L
      Biomass concentration (g/L): see worksheet
      Medium composition: LB cultures were used to inoculate M9 medium precultures with the indicated carbon sources for overnight cultivation.
      General protocol information: Sampling Method: 1 ml aliquots were taken in a 37°C room from exponential phase cultures.; Quenching: 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 list: boiling ethanol; Analysis list: LC-MS;
      Methods description: 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 [1] 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.
---------------------------------------------------References---------------------------------------------
[1] Buescher, J.M., Moco, S., Sauer, U., and Zamboni, N. (2010). Anal. Chem. 82, 4403–4412. http://doi.org/dsp5gb
      Data file: http://kimosys.org/repository/126/download?parameter=1264; 
      Alternative formats: no files uploaded

    Submission and curation
      Entered by: Administrator KiMoSys
      Created: 2018-10-01 08:52:44 UTC
      Updated: 2020-04-24 16:10:37 UTC
      Version: 0
      Status: (reviewed) 2018-10-01 08:56:07 UTC
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      Downloads: 51