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 Views: 251 Downloads: 57