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General Information
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
Organism Escherichia coli
Strain WT K-12 BW25113 and mutants
Data type enzyme/protein concentrations
Data units (mg-protein/g-dry cell weight)
Execution date not specified


Experimental Details
Temperature (°C) 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 Measurement method: LC-MS/MS, 2D gel-MALDI-TOF

Methods description - Notes

Absolute protein quantification - to obtain absolute measurements of protein concentrations in complex samples we used a liquid chromatography / tandem mass spectrometry (LC-MS/MS) method that is a modification of previous work in absolute quantification making use of either ...

-----------------References--------------------
[1] S. A. Gerber, J. Rush, O. Stemman, M. W. Kirschner, S. P. Gygi, Proc. Natl. Acad. Sci. U. S. A. 100, 6940 (2003). http://doi.org/d2ztfh
[2] W. Wang et al., Anal. Chem. 75, 4818 (2003). http://doi.org/bmzr3v
[3] L. Anderson, C. L. Hunter, Mol. Cell Proteomics 5, 573 (2006). http://doi.org/c8f5g7
[4] K. Shinoda et al., J. Proteome Res. 5, 3312 (2006). http://doi.org/dqdj7x

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