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General Information
Manuscript title Absolute Quantification of Protein and mRNA Abundances Demonstrate Variability in Gene-Specific Translation Efficiency in Yeast.
PubMed ID 28365149
Journal Cell Systems
Year 2017
Authors Petri-Jaan Lahtvee, Benjamín J. Sánchez, Agata Smialowska, Sergo Kasvandik, Ibrahim E. Elsemman, Francesco Gatto, Jens Nielsen
Affiliations Department of Biology and Biological Engineering, Systems and Synthetic Biology, Chalmers University of Technology, Kemivägen 10, 412 96 Gothenburg, Sweden.
Keywords integrative data analysis, absolute proteome, absolute transcriptome, protein turnover, protein degradation rates, translation efficiency, genome-scale metabolic modeling, translational control
Full text article Lahtvee_2017.pdf
Project name not specified

Experiment Description
Organism Saccharomyces cerevisiae
Strain CEN.PK113-7D ΔLYS1
Data type enzyme/protein concentrations
Data units pgDW
Execution date not specified

Experimental Details
Temperature (°C) 30
pH 5.5
Carbon source glucose
Culture mode chemostat
Process condition aerobic
Dilution rate (h⁻¹) 0.1
Working volume (L) 1
Biomass concentration (g/L) see original paper
Medium composition

Base medium used contained 10 g glucose, 5 g (NH4)2SO4, 3 g KH2PO4 and 0.5 g MgSO4 per litre, in addition to 1 mL of trace elements solution and 1 mL of vitamin solution. The trace element solution contained, per litre (pH=4): EDTA (sodium salt), 15.0 g; ZnSO4⋅7H2O, 4.5 g; MnCl2⋅2H2O, 0.84 g; CoCl2⋅6H2O, 0.3 g; CuSO4⋅5H2O, 0.3 g; Na2MoO4⋅2H2O, 0.4 g; CaCl2⋅2H2O, 4.5 g; FeSO4⋅7H2O, 3.0 g; H3BO3, 1.0 g; and KI, 0.10 g.). The vitamin solution contained, per liter (pH=6.5): biotin, 0.05 g; p-amino benzoic acid, 0.2 g; nicotinic acid, 1 g; Ca-pantothenate, 1 g; pyridoxine-HCl, 1 g; thiamine-HCl, 1 g and myo-inositol, 25 g.

General protocol information Measurement method: LC-MS/MS

Methods description - Notes

Quantitative Proteome Measurements: The peak intensity-based absolute quantification method iBAQ was chosen for protein quantification [1]. First, a lysine auxotrophic strain was created by deleting the LYS1 gene. Latter strain was cultivated with a labelled heavy 15N, 13C-l ...

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Data file
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