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General Information info

Manuscript title Pseudo-transition Analysis Identifies the Key Regulators of Dynamic Metabolic Adaptations from Steady-State Data.
PubMed ID 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 Downloadarticle Gerosa_2015.pdf
Project name not specified

Experiment Description info

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

Experimental Details info

Temperature (0C) 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 (L) 0.0035
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 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 [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.
[1] Buescher, J.M., Moco, S., Sauer, U., and Zamboni, N. (2010). Anal. Chem. 82, 4403–4412.

Data file
Downloadmetabolites KIMODATAID126_v0.xlsx
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Submission and curation info

Entered by Administrator KiMoSysFirst name: Administrator
Affiliation: INESC-ID/IST
Interests: mathematical modeling, accessible data, use of data

Created 2018-10-01 08:52:44 UTC

Updated 2018-10-01 08:52:44 UTC

Version 0

Status (reviewed) 2018-10-01 08:56:07 UTC

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