Data files

An example of a blank data sheet for Mass spectrometry data. This is not SysMO specific, but it is an example of MIAPE compliant data.

The shreadsheet contains macros to help you annotate your data with terms from controlled vocabularies and ontologies

Concentrations of vitellogenin in blood plasma in cod caged in Kollevåg and at reference location.

Measurement of oxidative stress (TBARS) assay in liver of cod caged in Kollevåg and at reference location.

Gene expression data of various genes from cod liver.

Gene expression data of genes involved in steroidogenic pathways, measured in cod ovaries.

Relative protein expression of the proteins Cyp3a and Mt in cod from the Kollevåg study

Concentrations of various contaminants in liver from cod caged in Kollevåg and at reference location.

Measurements of PAH metabolites in bile in fish caged in Kollevåg.

Concentrations of metals, PAHs and PCBs in sediment samples from Kollevåg and reference site.

Concentrations of E2 and T in cod plasma of female cod caged in Kollevåg measured by enzyme immunoassay.

Measurement of Gst and Cat enzyme activity in liver of fish caged in Kollevåg.

Biometry data of fish from Kollevåg caging study

RNA-Seq mapping results (part1): Sulfolobus solfataricus P2 grown on casaminoacids and d-glucose, mapped using bowtie2 against reference sequence of Sulfolobus solfataricus P2 (NBCI, see other data files of experiment).

RNA-Seq mapping results (part2): Sulfolobus solfataricus P2 grown on casaminoacids and d-glucose, mapped using bowtie2 against reference sequence of Sulfolobus solfataricus P2 (NBCI, see other data files of experiment).

RNA-Seq raw data: Sulfolobus solfataricus P2 grown on casaminoacids and d-glucose.

Reference genome of Sulfolobus solfataricus P2 used for mapping of RNA-seq results. Based on NCBI genome of Sulfolobus solfataricus.

Data for Figs. 2I, 2J, 2K in Chew et al. PNAS 2014
Fresh biomass, dry biomass (i.e. after baking out all water),
SLA - specific leaf area (area per g)

The same data are available on the BioDare resource, with additional experimental meta data on growth conditions.
BioDare ID 13790828881028, title "Physiology experiment using Col", the direct link is:
https://www.biodare.ed.ac.uk/robust/ShowExperiment.action?experimentId=13790828881028

Data for Figs. 3D, 3E in Chew et al. PNAS 2014
Fresh biomass, dry biomass (i.e. after baking out all water),
SLA - specific leaf area (area per g)
Also FMv1 model simulation results.

The same data are available on the BioDare resource, with additional experimental meta data on growth conditions.
BioDare ID 13790837647786, title "Physiology experiment using Fei", the direct link is:
https://www.biodare.ed.ac.uk/robust/ShowExperiment.action?experimentId=13790837647786

Data for Figs. 3A, 3B in Chew et al. PNAS 2014
Fresh biomass, dry biomass (i.e. after baking out all water),
SLA - specific leaf area (area per g)

Also contains model simulation data from the FMv1
The same data are available, with additional experimental meta data on growth conditions, from the BioDare resource:
BioDare experiment 13790834110003; title "Physiology experiment using Ler", the direct link is:
https://www.biodare.ed.ac.uk/robust/ShowExperiment.action?experimentId=13790834110003

Intact rosette is pictured, with plant number and genotype in handwritten labels, and ruler for scale.
Then dissected leaves are organised in sequence of age, if necessary with small cuts to let them lie flat.
Areas are then measured in image processing.

Data for Figs 3C, 3F and Supp 2 in Chew et al. PNAS 2014
Leaf number of the growing rosettes, from 4 to 37 days after sowing (DAS).
Data and also results of FMv1 model simulations.
Note that Fei-0 was previously tested by Mendez-Vigo et al, suggesting this line had a higher leaf appearance rate. We suggested that its larger final leaf number was more likely due to faster germination.

binary data file from "Hobo" environment multi-sensor + data logger, located next to the plants used in the experiment. Usually read in HOBOware software, free from Onsetcomp.com. Useful temperature record. Though light levels can usefully show changes they are not well calibrated.

Fig 5D

Figure 5D

Data for Fig. Supp 7B in Chew et al. PNAS 2014
Leaf number of the growing rosettes, from 5 to 37 days after sowing.
Data and also results of three FMv1 model simulations, with default, fitted and linear (i.e. no juvenile-adult transition in phyllochron)

Data for Figs. 5D, 5E and Supp 7C in Chew et al. PNAS 2014
FW - fresh weight
DW - dry weight (i.e. after baking out all water)
SLA - specific leaf area (area per g mass), indicates leaf thickness
Indiv, data for individual leaves rather than rosette

Experiment conducted in early April 2014
Intact rosette is pictured, with plant number and genotype in handwritten labels, and ruler for scale.
Then dissected leaves are organised in sequence of age,
if necessary with small cuts to let them lie flat.

Areas are then measured in image processing.

Supplementary information file from Chew et al. PNAS 2014, including full model description for Arabidopsis Framework Model v1, model simulations and experimental validations.

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