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General Information info

Manuscript title Multiple High-Throughput Analyses Monitor the Response of E. coli to Perturbations.
PubMed ID 17379776
Journal Science
Year 2007
Authors Nobuyoshi Ishii, Kenji Nakahigashi, Tomoya Baba, Martin Robert, Tomoyoshi Soga, Akio Kanai, Takashi Hirasawa, Miki Naba, Kenta Hirai, Aminul Hoque, Pei Yee Ho, Yuji Kakazu, Kaori Sugawara, Saori Igarashi, Satoshi Harada, Takeshi Masuda, Naoyuki Sugiyama, Takashi Togashi, Miki Hasegawa, Yuki Takai, Katsuyuki Yugi, Kazuharu Arakawa, Nayuta Iwata, Yoshihiro Toya, Yoichi Nakayama, Takaaki Nishioka, Kazuyuki Shimizu, Hirotada Mori, Masaru Tomita
Affiliations Institute for Advanced Biosciences, Keio University
Keywords Escheirchia coli, perturbations response, chemostat, single knockouts
Full text article no file uploaded
Project name not specified

Experiment Description info

Organism Escherichia coli
Strain WT K-12 BW25113 and mutants
Data type metabolites at steady-state
Data units mM
Execution date not specified

Experimental Details info

Temperature (0C) 37.0
pH 7.0
Carbon source glucose,
Culture mode chemostat
Process condition aerobic
Dilution rate (h-1) 0.1, 0.2, 0.4, 0.5 and 0.7
Working volume (L) 1.0
Biomass concentration (g/L) See Supplementary files of the original article (Tabel S3).
Medium composition

Synthetic medium: 48mM Na2HPO4, 22mM KH2PO4, 10mM NaCl, 45mM (NH4)2SO4, 4g/L glucose, 1mM MgSO4, 1mg/L thiamin.HCL, 5.6 mg/L CaCl2, 8 mg/L FeCl3, 1 mg/L MnCl2.4H2O, 1.7 mg/L ZnCl2, 0.43 mg/L CuCl2.2H2O, 0.6 mg/L CoCl2.2H2O and 0.6 mg/L Na2MoO4.2H2O

General protocol information Sampling method: Aliquots of 10 mL were withdrawn at OD600 0.85

Quenching procedure: Cells were filter (0.45-µm), washed with 10 mL of Milli-Q water and plunged into 1 mL of methanol containing 10µL of 0.56 mM PIPES

Extraction technique: chloroform

Sample analyzing method: CE-MS

Methods description - Notes

Metabolites were quantified using peak areas obtained from measurements of chemical standards mixtures that were analyzed in parallel with experimental samples. See more details in the original article.

Data file
Downloadmetabolites KIMODATAID41_v1.xlsx
Alternative format(s)
no file uploaded


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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 2013-05-02 17:35:25 UTC

Updated 2014-05-19 15:22:32 UTC

Version 1

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

Associated Models

Here we can find relevant models associated with Data EntryID 41:

Model name Category Model Type Data used for Access Json
Authors: Ahmad A. Mannan, Yoshihiro Toya, Kazuyuki Shimizu, Johnjoe McFadden, Andrzej M. Kierzek , Andrea Rocco

Original paper: Integrating Kinetic Model of E. coli with Genome Scale Metabolic Fluxes Overcomes Its Open System Problem and Reveals Bistability in Central Metabolism.

kinetic model of the central carbon metabolism of E. coli Metabolism ordinary differential equations Model building Visto4 {"affiliation":"Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, GU2 7XH, United Kingdom ","article_file_name":null,"authors":"Ahmad A. Mannan, Yoshihiro Toya, Kazuyuki Shimizu, Johnjoe McFadden, Andrzej M. Kierzek , Andrea Rocco","biomodels_id":"","category":"Metabolism","combine_archive_content_type":null,"combine_archive_file_name":null,"combine_archive_file_size":null,"combine_archive_updated_at":null,"comments":"For the analysis and evaluation of the kinetic model, the solver ode15s was used.","control":null,"dilution_rate":"0.2","id":42,"journal":"Plos One","keywords":"E. coli, Bistability, Central Metabolism","main_organism":"Escherichia coli","manuscript_title":"Integrating Kinetic Model of E. coli with Genome Scale Metabolic Fluxes Overcomes Its Open System Problem and Reveals Bistability in Central Metabolism.","model_name":"kinetic model of the central carbon metabolism of E. coli ","model_type":"ordinary differential equations","organism_id":null,"project_name":"","pubmed_id":"26469081","review_journal_id":null,"sbml_file_name":"Mannan_2015.PDF","software":"MATLAB\u00ae R2007b (version 7.5.0)","used_for":"---\n- Model building\n","year":2015} Administrator KiMoSys

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