Data files

This template is for recording gene expression data from the NimbleGen platform. This template was taken from the GEO website (http://www.ncbi.nlm.nih.gov/geo/info/spreadsheet.html) and modified to conform to the SysMO-JERM (Just enough Results Model) for transcriptomics. Using these templates will mean easier submission to GEO/ArrayExpress and greater consistency of data in SEEK.

This template is for recording genome data from the NimbleGen platform. This template was taken from the GEO website (http://www.ncbi.nlm.nih.gov/geo/info/spreadsheet.html) and modified to conform to the SysMO-JERM (Just enough Results Model) for transcriptomics. Using these templates will mean easier submission to GEO/ArrayExpress and greater consistency of data in SEEK.

The file contains complete agenda of the SEEK users meeting , 26-27 March 2012 in Berlin

intracellular metabolites measured by LC/MS

extracellular metabolites concentrations [mM] measured by 1H-NMR i

intracellular metabolite measured by GC/MS

Cellular size and granularity (measured by FACS) during glucose pulse. Glucose pulse was performed in anaerobically growing yeast Saccharomyces cerevisiae in steady state chemostat (D = 0.1 h-1) and transent concentrations of the extra- and intracellular metabolites from central carbon metabolism (e.g. glycolysis, PPP, glycerol, purines, etc) were measured.

Dynamics of macromolecules (total RNA) during glucose pulse. Glucose pulse was performed in anaerobically growing yeast Saccharomyces cerevisiae in steady state chemostat (D = 0.1 h-1) and transent concentrations of the extra- and intracellular metabolites from central carbon metabolism (e.g. glycolysis, PPP, glycerol, purines, etc) were measured.

Biomass weight during glucose pulse. Glucose pulse was performed in anaerobically growing yeast Saccharomyces cerevisiae in steady state chemostat (D = 0.1 h-1) and transent concentrations of the extra- and intracellular metabolites from central carbon metabolism (e.g. glycolysis, PPP, glycerol, purines, etc) were measured.

Steady state concentrations of intracellular metabolites in yeast Saccharomyces cerevisiae anaerobic chemostat at D = 0.1 h-1 on minimal medium. All metabolite concentrations are in mmol/L(CV).

Steady state concentrations of extracellular metabolites in yeast Saccharomyces cerevisiae anaerobic chemostat at D = 0.1 h-1 on minimal medium. All metabolite concentrations are in mmol/L(R) except CO2, which is in parts of the partial pressure.

Steady state metabolic fluxes measured in glucose-limited chemostat of Saccharomyces cerevisiae at D = 0.1 h-1 growing on minimal medium. Fluxes are: glucose, ethanol, glycerol, acetate, succinate, pyruvate, lactate, citrate, malate, a-ketoglutarate, fumarate

Some home work for PALs to prepare Lightning Talks and ISBE/ESFRI Sessions

Monitoring of end products ethanol, acetone, butanol, acetate and butyrate during master fermentation of Clostridium acetobutylicum at the steady state pH values 5.5, 5.3, 5.1, 4.9 and 4.7.

This document outlines our plans for making it easier to publish assets from SEEK to enable people from outside the consortium to see them.

Confocal microscopy of CIN5-GFP from the collection of GFP strains at standard growth conditions (50 mM KCl)

Confocal microscopy of HOG1-GFP from GFP-strain collection under standard growth cionditions (50 mM KCl).

Confocal microscopy of Pma1-GFP cells after 60 min at 0 or 50 mM KCl .

Confocal microscopy of Nha1-GFP cells after 60 min at 0 or 50 mM KCl or at 1 M NaCl.

Confocal microscopy of Arl1-GFP cells after 60 min at 0 or 50 mM KCl or at 1 M NaCl.

Confocal microscopy of Ena1-GFP cells after 60 min at 0 or 50 mM KCl or at 1 M NaCl.

Micro array analysis of steady-state growing cells of Clostridium acetobutylicum at pH 5.7 (acidogenesis) in comparison to pH 4.5 (solventogenesis).

Monitoring of end products in mM of ethanol, acetone, butanol, acetate and butyrate during master fermentation of Clostridium acetobutylicum at the steady state pH values 5.7 (acidogenesis) and 4.5 (solventogenesis).

TRK1, TRK2

Micro array analyses of all mRNA levels of cells growing at steady state pH values 5.7, 5.5, 5.3, 5.1, 4.9, 4.7 compared to the same reference steady-state pH 4.5.

All spots and identified proteins of Clostridium acetobutylicum growing at steady-state pH 5.7 (acidogenesis) and pH 4.5 (solventogenesis), respectively, using 2D PAGE and Maldi-TOF analysis. The focus were cytosolic proteins with an isoelectric point bewteen 4 and 7 as well as a molecular weight of 180-10 kDa.