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.
SEEK ID: https://fairdomhub.org/assays/633
Biological problem addressed: Model Analysis Type
Organisms: Ostreococcus tauri
- Aryal et al, 2011, metabolic labelling of Cyanothece protein synthesis
- Martin et al, 2012, Ostreococcus N15 labelling proteomics
- Calculated rates of protein degradation in Ostreococcus tauri
- Calculated rates of protein degradation in Cyanothece ATCC51142
- Calculated rates of protein synthesis in the light and dark in Ostreococcus tauri
- Calculated rates of protein synthesis in the light and dark in Cyanothece ATCC51142
Created: 15th Jan 2018 at 08:24
Last updated: 20th Feb 2018 at 23:03
Projects: Millar group, TiMet, PHYTOCAL: Phytochrome Control of Resource Allocation and Growth in Arabidopsis and in Brassicaceae crops, POP - the Parameter Optimisation Problem, Regulation of flowering time in natural conditions, PlaSMo model repository
Institutions: University of Edinburghhttps://orcid.org/0000-0003-1756-3654
EU FP7 collaborative project TiMet, award number 245143. Funded 2010-2015.
"TiMet assembles world leaders in experimental and theoretical plant systems biology to advance understanding of the regulatory interactions between the circadian clock and plant metabolism, and their emergent effects on whole-plant growth and productivity."
Click on Snapshot 2 to download data, models and analysis for Daniel Seaton et al.
biorXiv 2017 https://doi.org/10.1101/182071 and
Molecular Systems Biology, accepted Jan 2018, https://doi.org/10.15252/msb.20177962.
Note that the published paper cannot be fully linked into this record as the DOI above was not live when we made the Research Object from this Investigation on FAIRDOMHub.
Studies: Modelling and analysis of translational coincidence, Photoperiod-specific proteome data for Arabidopsis, Proteome and translation rate data for the Ostreococcus alga and for cya..., Rhythmic and photoperiod-specific transcriptome datasets for Arabidopsis
Assays: Aryal et al, 2011, metabolic labelling of Cyanothece protein synthesis, Blasing et al, 2005, diurnal microarray in 12L:12D, Estimation of rates of translation and turnover from proteomics datasets, Martin et al, 2012, Ostreococcus N15 labelling proteomics data, Photoperiod proteomics, Stitt lab, TiMet photoperiod microarrays, Translational coincidence model
Literature data and associated scripts analysed in the Seaton et al. 2017 study; data processing by Daniel Seaton.
Person responsible: Andrew Millar
Snapshots: No snapshots
Proteomics data for N15 incorporation into protein in Ostreococcus grown in 12L:12D light:dark cycles.
Quantitative proteomic analysis of Cyanothece ATCC51142 grown in 12L:12D light:dark cycles, using partial metabolic labeling and LC-MS analysis.
Python scripts to run the analysis estimating rates of protein synthesis in the light and dark, and overall rates of protein turnover, in Cyanothece and Ostrecoccus tauri.
Contributor: Daniel Seaton
Model type: Not specified
Model format: Not specified
Environment: Not specified
Organism: Not specified
Investigations: Photoperiodic control of the Arabidopsis proteo...
Modelling analyses: Estimation of rates of translation and turnover...