Assays

Chemical analyses in Kollevåg includes sediment contaminant concentrations, concentrations of various contaminants in cod liver and concentrations of PAH metabolites in cod bile.

Enzyme activity of glutathione-s-transferase (Gst) and catalase (Cat) in Kollevåg samples

Concentrations of steroid hormones E2 and T in female cod plasma from Kollevåg fish

Information about the fish from the Kollevåg study

Analyses of gene expression: qPCR analyses in liver (relative expression) and ovaries (absolute expression).

TBARS assay measured oxidative stress as levels of malondialdehyde in samples.
Performed in cod liver samples.

Biosense Vtg assay measuring concentrations of vitellogenin in cod blood plasma

Western blot results for Kollevåg samples.

Growth on D-glucose served as reference scenario

Intracellular and extracellular metabolome analysis

Data for Figure 2I-2K in Chew et al. PNAS 2014.
Experimental conditions: ∼21.3 °C; 12:12-h light/dark cycle; light intensity, 110 μmol·m−2·s−1;mean daytime CO2 level, 375 ppm. The error bars show the SEs of five plants
Further detail on the experimental conditions is contained in the public record on the BioDare resource, link to follow

Data for Figure 3G and Supplementary Figure 4, including gas exchange measurements and photo of the experimental setup. The 'Summary' sheets in the XLSX files often include published graphs. Simulation data are included from FMv1.

These data were acquired in a separate experiment from the biomass, in March 2013. Replication of the earlier biomass study was imperfect, as some plants became a little dry when watering was controlled to reduce moss growth. Sufficient plants grew strongly to measure
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Data for Figure 3A-3F and Supplementary Figures 2, 3, and 6, including leaf number, biomass and leaf areas. Image data for leaf areas are included in a .ZIP archive. The 'Summary' sheets in the XLSX files often include published graphs. Simulation data are included from FMv1.
These data were acquired in June 2012.
Experimental conditions: ~22C constant temperature; 12:12-h light/dark cycle; light intensity = 130 μmol·m−2·s−1; average daytime CO2 concentration = 375 ppm. 10 plants per genotype per
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Data for Figures 5D-5F and Supplementary Figure 7B, 7C, including biomass and leaf areas. Image data for leaf areas are included in a .ZIP archive, with two samples as published in 5D. The 'Summary' sheets in the XLSX files include published graphs. Simulation data are included from FMv1.
These data were acquired in April 2014, in a separate experiment from the La(er) and Fei-0.
Experimental conditions: ∼20.7 °C constant temperature; 12h:12h light/dark cycle; light intensity = 100μmol·m−2·s−1;
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In future we should split these versions into separate Assays, and link to the four, original component models, when they are imported with the PlaSMo resource into FairdomHub (expected late 2018)

Data for Figure 4, from the prior publication of Sulpice et al. Mol. Plant 2014: Biomass, net growth and starch levels at end of day and end of night, under light:dark cycles of 4:20, 6:18, 8:16, 12:12 and 18:6 hours.

Model of glycolytic oscillations in individual yeast cells in microfluidic flow chamber

General sandbox