DataEntryID 38
    General information
      Manuscript title: Modeling and simulation of the main metabolism in Escherichia coli and its several single-gene knockout mutants with experimental verification.
      PubMed ID: http://www.ncbi.nlm.nih.gov/pubmed/21092096
      Journal: Microbial Cell Factories
      Year: 2010
      Authors: Tuty AA Kadir, Ahmad A Mannan, Andrzej M Kierzek, Johnjoe McFadden and Kazuyuki Shimizu
      Affiliations: Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Japan 
      Keywords: Specific Growth Rate, Flux Balance Analysis, Oxidative Pentose Phosphate Pathway, Main Metabolic Pathway, Isotopomer Distribution
      Full text article: https://kimosys.org/rails/active_storage/blobs/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBbWtFIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--6eff591c69c77951c6332c9d72b2a8c03656e2a1/Kadir_2010.pdf
      Project name: not specified

    Experiment description
      Organism: Escherichia coli
      Strain: K-12 BW25113 and ppc, pyk mutants
      Data type: time-series data of metabolites
      Data units: g/L
      Execution date: not specified

    Experimental details
      Temperature (°C): 37.0
      pH: 7.0
      Carbon source: glucose
      Culture mode: batch
      Process condition: aerobic
      Dilution rate (h⁻¹): —
      Working volume: 1.0 L
      Biomass concentration (g/L): not specified
      Medium composition: M9 sythetic medium: 48 mM Na2HPO4, 22 mM KH2PO4, 10 mM NaCl, 40 mM (NH4)zSO4 and 4 g/l of glucose. Components filter-sterilized separatory and then added (per liter of final volume): 1 ml 1 M MgSO4, 1 ml vitamin B1 (1 mgl stock), 1 ml 0.1 mM CaCl2, and 10 ml trace element solution containing (per liter): 0.55g CaCl2 1g FeCl3, 0.1 mg/l MnCl2.4H2O, 0.17 g ZnCl2, 0.043 g CuCl2.2H2O, 0.06 g CoCl2.2H2O, and 0.06 g Na2MoO4.2H2O).
      General protocol information: Sampling Method: 5ml from the culture broth; Quenching: 15ml of 60% (v/v) aqueous methanol containing 70mM HEPES at -80ºC; Extraction list: enzymatic, perchloric acid; Analysis list: enzymatic;
      Methods description: Cells were separated from the culture by centrifugation at 10,000 ×g for 15 min at 0°C. To extract intracellular metabolites from the cell pellet, 500 ml of 50% methanol was added, and the cells were re-suspended by vortexing the mixture. Then 2 ml of 35% of perchloric acid was added, which was pre-cooled on ice, and vortexed again for 10 s. After one freeze-thaw cycle, proteins and cell fragments were removed by centrifugation at 12,000 ×g for 30 min at 0°C. Clear suparnatant was neutralized by adding collected supernatant, and then 895 μm of 5 M K2KO3 was added. Precipitated perchlorates were removed by another centrifugation step (12,000 ×g at 0°C for 10 min), the clear supernatant was collected, and they were stored as 200 μm aliquots at -20°C for  analysis.
      Data file: http://kimosys.org/repository/38/download?parameter=1128; 
      Alternative formats: http://kimosys.org/repository/38/attached_files/22/download; http://kimosys.org/repository/38/attached_files/21/download; http://kimosys.org/repository/38/attached_files/20/download; 

    Submission and curation
      Entered by: Administrator KiMoSys
      Created: 2013-04-24 14:37:13 UTC
      Updated: 2020-04-24 16:10:29 UTC
      Version: 1
      Status: (reviewed) 2013-12-06 17:17:38 UTC
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