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General Information info

Manuscript title Linking high-resolution metabolic flux phenotypes and transcriptional regulation in yeast modulated by the global regulator Gcn4p.
PubMed ID 19346491
Journal Proc Natl Acad Sci USA
Year 2009
Authors Joel F. Moxley, Michael C. Jewett, Maciek R. Antoniewicz, Silas G. Villas-Boas, Hal Alper, Robert T. Wheeler, Lily Tong, Alan G. Hinnebusch, Trey Ideker, Jens Nielsen, and Gregory Stephanopoulos
Affiliations Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
Keywords amino acid stress response, fluxomics, gcn4, systems biology
Full text article Downloadarticle Moxley_2009.pdf
Project name not specified

Experiment Description info

Organism Saccharomyces cerevisiae
Strain WT S288C and gcn4-knockout
Data type flux measurements
Data units not specified
Execution date not specified

Experimental Details info

Temperature (0C) 30
pH 5.0
Carbon source glucose,
Culture mode chemostat
Process condition aerobic
Dilution rate (h-1) 0.1
Working volume (L) 1.0
Biomass concentration (g/L) not specified
Medium composition

unsupplemented YNB minimal media.

General protocol information Flux analysis method: 13C constrained MFA

Platform: GC-MS

Methods description - Notes

Metabolic fluxes were determined using the Metran software, using the elementary metabolite units (EMU) algorithm [1, 2]. Metran accepts as input a user-defined metabolic network model consisting of biochemical reactions and atom transitions, and a set of 13C-measurements and external fluxes; it produces as output metabolic fluxes for the entire network, confidence intervals for all fluxes, and statistical analysis of the goodness-of-fit [3].
--------------------------------------------References---------------------------------------
[1] Yoo H, Antoniewicz MR, Stephanopoulos G, Kelleher JK(2008). J Biol Chem 283:20621–20627. http://doi.org/fsrtj5
[2] Antoniewicz MR, Kelleher JK, Stephanopoulos G (2007). Metab Eng 9:68–86. http://doi.org/b97p7s
[3] Antoniewicz MR, Kelleher JK, Stephanopoulos G (2006). Metab Eng, 324–337. http://doi.org/fbgz85

Data file
Downloadfluxes KIMODATAID122_v1.xlsx
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Submission and curation info

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 2018-09-12 09:46:26 UTC

Updated 2018-09-12 10:07:01 UTC

Version 1

Status (reviewed) 2018-09-12 09:47:23 UTC




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