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General Information
Manuscript title Temporal system-level organization of the switch from glycolytic to gluconeogenic operation in yeast.
PubMed ID 23549479
Journal Molecular Systems Biology
Year 2013
Authors Guillermo G Zampar, Anne Kümmel, Jennifer Ewald, Stefan Jol, Bastian Niebel, Paola Picotti, Ruedi Aebersold, Uwe Sauer, Nicola Zamboni and Matthias Heinemann
Affiliations ETH Zurich, Institute of Molecular Systems Biology, Zurich, Switzerland
Keywords diauxic shift, metabolome, S. cerevisiae, intracellular
Full text article Zampar_2013.pdf
Project name not specified


Experiment Description
Organism Saccharomyces cerevisiae
Strain FY4
Data type time-series data of metabolites
Data units (mmol/L) of total cell volume
Execution date not specified


Experimental Details
Temperature (°C) 30.0
pH 5.0
Carbon source glucose,
Culture mode batch
Process condition aerobic
Dilution rate (h⁻¹)
Working volume (L) 2.0
Biomass concentration (g/L) correlation of OD with biomass: 0.486 gDW/L OD
Medium composition

Minimal defined medium with 5 g/L glucose

General protocol information Sampling method: withdrawn from the culture at specific time points.

Quenching procedure: four samples of 1-4ml at each sampling time point were quenched in 4 volumes of 60% methanol in 10mM ammonium acetate pH 7.5 at -40ºC. After centrifuging for 3min at 14000 rpm and -9ºC, frozen in liquid nitrogen and stored at -80ºC.

Extraction technique: hot ethanol

Sample analyzing method: LC-MS, GC-TOF

Methods description - Notes

Intracellular metabolites were extracted by incubation in 75% ethanol 10mM ammonium acetate pH 7.5 for 3 min at 95ºC. The supernatant was retained by centrifuging at −9 °C, samples were dried in a vacuum centrifuge and two samples each were prepared for either LC-MS/MS of GC ...

--------------References------------------
[1] Ewald JC, Heux S, Zamboni N (2009). High-throughput quantitative metabolomics: workflow for cultivation, quenching, and analysis of yeast in a multiwell format. Anal Chem 81: 3623–3629. http://doi.org/chgtcq
[2] Buscher JM, Czernik D, Ewald JC, Sauer U, Zamboni N (2009). Cross-platform comparison of methods for quantitative metabolomics of primary metabolism. Anal Chem 81: 2135–2143. http://doi.org/cjqg95
[3] Luo B, Groenke K, Takors R, Wandrey C, Oldiges M (2007). Simultaneous determination of multiple intracellular metabolites in glycolysis, pentose phosphate pathway and tricarboxylic acid cycle by liquid chromatography-mass spectrometry. J Chromatogr A 1147: 153–164. http://doi.org/cxdj7w

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Submission and curation

Entered by: Administrator KiMoSysFirst name: Administrator
Affiliation: INESC-ID/IST
Homepage: http://kdbio.inesc-id.pt/kimosys
Interests: mathematical modeling, accessible data, use of data

Created: 2013-06-12 00:04:24 UTC

Updated: 2020-04-24 16:10:32 UTC

Version: 0

Status: (reviewed) 2013-12-06 17:17:38 UTC

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