Assays
What is an Assay?Filters
Biosense Vtg assay measuring concentrations of vitellogenin in cod blood plasma
Submitter: Karina Dale
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: 1 hidden item
Study: Caging study - Kollevåg
Submitter: Jacqueline Wolf
Assay type: RNA-seq Profiling
Technology type: Rna-seq
Investigation: Amino acid degradation in Sulfolobus solfataric...
Submitter: Jacqueline Wolf
Assay type: Proteomics
Technology type: Tandem Mass Spectrometry
Investigation: Amino acid degradation in Sulfolobus solfataric...
Intracellular and extracellular metabolome analysis
Submitter: Jacqueline Wolf
Assay type: Metabolite Profiling
Technology type: Gas Chromatography Mass Spectrometry
Investigation: Amino acid degradation in Sulfolobus solfataric...
Growth on D-glucose served as reference scenario
Submitter: Jacqueline Wolf
Biological problem addressed: Genome Scale
Investigation: Amino acid degradation in Sulfolobus solfataric...
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
Submitter: Andrew Millar
Assay type: Cultivation Experiment
Technology type: Cultivation experiment
Investigation: Arabidopsis Framework Model v1, predicting rose...
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 ...
Submitter: Andrew Millar
Assay type: Cultivation Experiment
Technology type: Cultivation experiment
Investigation: Arabidopsis Framework Model v1, predicting rose...
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 ...
Submitter: Andrew Millar
Assay type: Cultivation Experiment
Technology type: Cultivation experiment
Investigation: Arabidopsis Framework Model v1, predicting rose...
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; ...
Submitter: Andrew Millar
Assay type: Cultivation Experiment
Technology type: Cultivation experiment
Investigation: Arabidopsis Framework Model v1, predicting rose...
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)
Submitter: Andrew Millar
Biological problem addressed: Model Analysis Type
Investigation: Arabidopsis Framework Model v1, predicting rose...
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.
Submitter: Andrew Millar
Assay type: Cultivation Experiment
Technology type: Cultivation experiment
Investigation: Arabidopsis Framework Model v1, predicting rose...
Submitter: Jacky Snoep
Biological problem addressed: Model Analysis Type
Investigation: Karin et al (2017) Molecular Systems Biology
Submitter: Jacky Snoep
Biological problem addressed: Model Analysis Type
Investigation: Karin et al (2017) Molecular Systems Biology
Submitter: Jacky Snoep
Biological problem addressed: Model Analysis Type
Investigation: Karin et al (2017) Molecular Systems Biology
Submitter: Jacky Snoep
Biological problem addressed: Model Analysis Type
Investigation: Karin et al (2017) Molecular Systems Biology
Submitter: Jacky Snoep
Biological problem addressed: Model Analysis Type
Investigation: Karin et al (2017) Molecular Systems Biology
Submitter: Jacky Snoep
Biological problem addressed: Model Analysis Type
Investigation: Karin et al (2017) Molecular Systems Biology
Submitter: Jacky Snoep
Biological problem addressed: Model Analysis Type
Investigation: Karin et al (2017) Molecular Systems Biology
Submitter: Jacky Snoep
Biological problem addressed: Model Analysis Type
Investigation: Martins et al (2016) Molecular Systems Biology
Submitter: Jacky Snoep
Biological problem addressed: Model Analysis Type
Investigation: Martins et al (2016) Molecular Systems Biology
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Investigation: Glycolytic oscillations in individual isolated ...
Model of glycolytic oscillations in individual yeast cells in microfluidic flow chamber
Submitter: Dawie van Niekerk
Biological problem addressed: Model Analysis Type
Investigation: Glycolytic oscillations in individual isolated ...
This Excel template is the general (master) template for any type of metabolomics data. It can be used as it is, or extended and modified to create a more specific templates for particular technologies and assay types.
Submitter: Katy Wolstencroft
Assay type: Metabolomics
Technology type: Technology Type
Investigation: Creating data sheet template for 'omics data
These Python scripts define and simulate the translational coincidence model. This model takes measured transcript dynamics (Blasing et al, 2005) in 12L:12D, measured synthesis rates of protein in light compared to dark (Pal et al, 2013), and outputs predicted changes in protein abundance between short (6h) and long (18h) photoperiods. These are compared to the photoperiod proteomics dataset we generated.
Submitter: Daniel Seaton
Biological problem addressed: Model Analysis Type
Investigation: Photoperiodic control of the Arabidopsis proteo...
Transcript profiling by microarray in 4, 6, 8, 12 and 18 h photoperiods, originally published in Flis et al, 2016, Photoperiod-dependent changes in the phase of core clock transcripts and global transcriptional outputs at dawn and dusk in Arabidopsis. doi: 10.1111/pce.12754.
Submitter: Daniel Seaton
Assay type: Gene Expression Profiling
Technology type: Microarray
Investigation: Photoperiodic control of the Arabidopsis proteo...
Submitter: Daniel Seaton
Assay type: Gene Expression Profiling
Technology type: Microarray
Investigation: Photoperiodic control of the Arabidopsis proteo...
Proteomics data for N15 incorporation into protein in Ostreococcus grown in 12L:12D light:dark cycles.
Submitter: Daniel Seaton
Assay type: Proteomics
Technology type: Mass Spectrometry
Investigation: Photoperiodic control of the Arabidopsis proteo...
Quantitative proteomic analysis of Cyanothece ATCC51142 grown in 12L:12D light:dark cycles, using partial metabolic labeling and LC-MS analysis.
Submitter: Daniel Seaton
Assay type: Proteomics
Technology type: Mass Spectrometry
Investigation: Photoperiodic control of the Arabidopsis proteo...
Data and Python scripts to run the analysis of literature data that estimates rates of protein synthesis in the light and dark, and overall rates of protein turnover, in Cyanothece and Ostrecoccus tauri.
Submitter: Daniel Seaton
Biological problem addressed: Model Analysis Type
Investigation: Photoperiodic control of the Arabidopsis proteo...
RNAseq data for L.ferriphilum samples
Submitter: Malte Herold
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Multi -omics reveal lifestyle of acidophile, mi...
Study: Omics_data_analysis