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General Information
Manuscript title Metabolic regulation analysis of wild-type and arcA mutant Escherichia coli under nitrate conditions using different levels of omics data.
PubMed ID 22790675
Journal Molecular BioSystems
Year 2012
Authors Yoshihiro Toya, Kenji Nakahigashi, Masaru Tomita and Kazuyuki Shimizu
Affiliations Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0017, Japan
Keywords Escherichia coli, intracelullar metabolites
Full text article no file uploaded
Project name not specified


Experiment Description
Organism Escherichia coli
Strain BW25113 and arcA mutant
Data type metabolites at steady-state
Data units (µM)
Execution date not specified


Experimental Details
Temperature (°C) 37.0
pH 7.0
Carbon source glucose
Culture mode chemostat
Process condition aerobic and anaerobic
Dilution rate (h⁻¹) 0.2
Working volume (L) 1.0
Biomass concentration (g/L) not specified
Medium composition

Synthetic medium for batch and continuous: 48 mM Na2HPO4, 22 mM KH2PO4, 10 mM NaCl, 45 mM (NH4)2SO4, 4 g/L glucose was supplemented with 1 mM MgSO4, 1 mg mL 1 thiamine, 0.056 mg/L CaCl2, 0.08 mg/L FeCl3, 0.01 mg/L MnCl2.4H2O, 0.017 mg/L ZnCl2, 0.0043 mg/L CuCl2.2H2O, 0.006 mg/L CoCl2.2H2O, and 0.06 mg/L Na2MoO4.2H2O. In addition, 40 mM of potassium nitrate was added to the medium for the cultures under nitrate conditions.
General protocol information Sampling method: 5 mg of cells were passed through a 0.45 mm pore filter (Millipore) filled with saline.

Quenching procedure: filter washed twice with 10 mL of Milli-Q water and quickly plunged into 5 mL of methanol containing 2 mM CSA and methionine sulfone as internal standards within 1 min.

Extraction technique: chloroform, sonication

Sample analyzing method: CE-TOF-MS
Methods description - Notes

Capillary electrophoresis time-of-flight mass spectrometry (CE-TOFMS) measurements were performed on an Agilent CE capillary electrophoresis system (Agilent Technologies) and an Agilent G3250AA LC/MSD TOF system (Agilent Technologies). The raw CE-TOFMS data were analyzed usi ...

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Data file
KIMODATAID79_v0.xlsx Preview file
Alternative format(s)
 KIMODATAID79_wt_nitrate.txt
KIMODATAID79_wt_anaerobic.txt
KIMODATAID79_wt_aerobic.txt
KIMODATAID79_arcA_nitrate.txt
KIMODATAID79_wt_nitrate_compound_SBtab.csv Preview
KIMODATAID79_wt_anaerobic_compound_SBtab.csv Preview
KIMODATAID79_wt_aerobic_compound_SBtab.csv Preview
KIMODATAID79_arcA_nitrate_compound_SBtab.csv Preview
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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: 2013-07-08 15:05:36 UTC

Updated: 2020-04-24 16:10:34 UTC

Version: 0

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

Views: 215

Downloads: 50



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