Detail View - Data AccessID 38
General Information
Manuscript title | Modeling and simulation of the main metabolism in Escherichia coli and its several single-gene knockout mutants with experimental verification. |
PubMed ID | 21092096 |
Journal | Microbial Cell Factories |
Year | 2010 |
Authors | Tuty AA Kadir, Ahmad A Mannan, Andrzej M Kierzek, Johnjoe McFadden and Kazuyuki Shimizu |
Affiliations | Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Japan |
Keywords | Specific Growth Rate, Flux Balance Analysis, Oxidative Pentose Phosphate Pathway, Main Metabolic Pathway, Isotopomer Distribution |
Full text article | Kadir_2010.pdf |
Project name | not specified |
Experiment Description
Organism | Escherichia coli |
Strain | K-12 BW25113 and ppc, pyk mutants |
Data type | time-series data of metabolites |
Data units | g/L |
Execution date | not specified |
Experimental Details
Temperature (°C) | 37.0 |
pH | 7.0 |
Carbon source | glucose |
Culture mode | batch |
Process condition | aerobic |
Dilution rate (h⁻¹) | — |
Working volume (L) | 1.0 |
Biomass concentration (g/L) | not specified |
Medium composition | M9 sythetic medium: 48 mM Na2HPO4, 22 mM KH2PO4, 10 mM NaCl, 40 mM (NH4)zSO4 and 4 g/l of glucose. Components filter-sterilized separatory and then added (per liter of final volume): 1 ml 1 M MgSO4, 1 ml vitamin B1 (1 mgl stock), 1 ml 0.1 mM CaCl2, and 10 ml trace element solution containing (per liter): 0.55g CaCl2 1g FeCl3, 0.1 mg/l MnCl2.4H2O, 0.17 g ZnCl2, 0.043 g CuCl2.2H2O, 0.06 g CoCl2.2H2O, and 0.06 g Na2MoO4.2H2O). |
General protocol information |
Sampling method:
5ml from the culture broth Quenching procedure: 15ml of 60% (v/v) aqueous methanol containing 70mM HEPES at -80ºC Extraction technique: enzymatic, perchloric acid Sample analyzing method: enzymatic |
Methods description - Notes | Cells were separated from the culture by centrifugation at 10,000 ×g for 15 min at 0°C. To extract intracellular metabolites from the cell pellet, 500 ml of 50% methanol was added, and the cells were re-suspended by vortexing the mixture. Then 2 ml of 35% of perchloric acid ... Read more |
Data file |
KIMODATAID38_v1.xlsx
|
Alternative format(s) |
KIMODATAID38_wt_timeseries.csv
Preview
KIMODATAID38_pyk_timeseries.csv Preview KIMODATAID38_ppc_timseries.csv Preview |
Export metadata |
RDF:
metadataDataEntryID38.rdf
XML: metadataDataEntryID38.xml Plain text: metadataDataEntryID38.txt |
Related Data: AccessID 30 | AccessID 35 | AccessID 41 | AccessID 44 | AccessID 51 | AccessID 52 | AccessID 54 | AccessID 63 | AccessID 64 | AccessID 65 | AccessID 67 | AccessID 68 | AccessID 74 | AccessID 75 | AccessID 78 | AccessID 79 | AccessID 80 | AccessID 86 | AccessID 87 | AccessID 92 | AccessID 96 | AccessID 101 | AccessID 102 | AccessID 103 | AccessID 104 | AccessID 105 | AccessID 106 | AccessID 107 | AccessID 108 | AccessID 109 | AccessID 110 | AccessID 112 | AccessID 116 | AccessID 118 | AccessID 119 | AccessID 125 | AccessID 126
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: 2013-04-24 14:37:13 UTC
Updated: 2020-04-24 16:10:29 UTC
Version: 1
Status: (reviewed) 2013-12-06 17:17:38 UTC
Views: 595
Downloads: 105
Associated Models
Here we can find relevant models associated with Data EntryID 38:
Model EntryID |
Model name | Category | Model Type | Data used for | Access |
---|---|---|---|---|---|
16 | glycolysis Escherichia coli model | Metabolism | ordinary differential equations | Model validation | |
38 | E. coli Central Carbon Metabolism | Metabolism | ordinary differential equations | Model building and Model validation | |
45 | Batch kinetic model of Escherichia coli | Metabolism | ordinary differential equations | Model building |
Associate models to data
- Several models can be associated.