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."
Programme: SynthSys
SEEK ID: https://fairdomhub.org/projects/92
Public web page: http://timing-metabolism.eu/
Organisms: Arabidopsis thaliana, Ostreococcus tauri
FAIRDOM PALs: No PALs for this Project
Project created: 16th Nov 2017
Related items
- People (5)
- Programmes (1)
- Institutions (3)
- Investigations (2)
- Studies (13)
- Assays (26+1)
- Strains (2)
- Data files (17)
- Models (2)
- Publications (4)
Projects: Millar group, TiMet
Institutions: University of Edinburgh
https://orcid.org/0000-0002-9258-583XProjects: 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 Edinburgh
https://orcid.org/0000-0003-1756-3654SynthSys is the University of Edinburgh's research organisation in interdisciplinary, Synthetic and Systems Biology, founded in 2012 as the successor to the Centre for Systems Biology at Edinburgh (CSBE).
Projects: Millar group, PHYTOCAL: Phytochrome Control of Resource Allocation and Growth in Arabidopsis and in Brassicaceae crops, TiMet, POP - the Parameter Optimisation Problem, Regulation of flowering time in natural conditions, PlaSMo model repository
Web page: http://www.synthsys.ed.ac.uk
Data, FMv2 model and simulations for the Chew et al. 2017 paper (bioRxiv https://doi.org/10.1101/105437 ), updated in 2022, mostly on the prr7 prr9 double mutant, with controls in lsf1 and prr7 single mutants. This is one of the outputs from the EU FP7 TiMet project, https://fairdomhub.org/projects/92.
This data archive was updated during submisson to the journal _in Silico _Plants in 2022, and a Snapshot was published. The updates are not changing the core data or the FMv2 model that has been ...
Submitter: Andrew Millar
Studies: Analysis of Framework Model version 2 (FMv2), Construction of Framework Model version 2 (FMv2), Test of FMv2, follow-on: mechanisms of malate/fumarate accumulation, Test of FMv2, photoperiodic flowering and hypocotyl elongation, Test of FMv2, study Gibberellins 1, Test of FMv2, study Laurel & Hardy 1, Test of FMv2, study Laurel & Hardy 2, Test of FMv2, study Laurel & Hardy 3, Tests of FMv2, compilations and figures
Assays: Assimilation and partitioning of 14CO2 at night, Biomass and metabolites, Biomass and metabolites, Biomass and metabolites, Biomass, leaf area and gas exchange data, Biomass, leaf number and metabolites, Circadian period analysis, Composition of FMv2, FMv2 simulation, FMv2 simulation, FMv2 simulation, Mizuno lab, Flowering time in clock mutants, Mizuno lab, Hypocotyl length in clock mutants, Relationship among FMv2 outputs, Sensitivity analysis of FMv2, Simulating clock gene expression with model P2011.1.2, Thiamine vitamers, TiMet WP1.1, Clock gene expression in clock mutants, TiMet WP1.1a Metabolite analysis of clock mutants
Snapshots: Snapshot 1
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.
Submitter: Andrew Millar
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
Snapshots: Snapshot 1, Snapshot 2
Modelling and experiments for FMv2 components.
Submitter: Andrew Millar
Investigation: Prediction and analysis of phenotypes in the Ar...
Assays: Composition of FMv2, Simulating clock gene expression with model P2011.1.2, TiMet WP1.1, Clock gene expression in clock mutants, TiMet WP1.1a Metabolite analysis of clock mutants
Snapshots: No snapshots
Simulations, parameter sensitivity analysis etc. for FMv2
Submitter: Andrew Millar
Investigation: Prediction and analysis of phenotypes in the Ar...
Assays: Relationship among FMv2 outputs, Sensitivity analysis of FMv2
Snapshots: No snapshots
Modelling and experiments for FMv2 as a whole; Testing Framework Model version 2 (FMv2)
Submitter: Andrew Millar
Investigation: Prediction and analysis of phenotypes in the Ar...
Assays: Biomass and metabolites, FMv2 simulation
Snapshots: No snapshots
Modelling and experiments for FMv2 as a whole; Testing Framework Model version 2 (FMv2)
Submitter: Andrew Millar
Investigation: Prediction and analysis of phenotypes in the Ar...
Assays: Biomass and metabolites, FMv2 simulation
Snapshots: No snapshots
Modelling and experiments for FMv2 as a whole; Testing Framework Model version 2 (FMv2)
Submitter: Andrew Millar
Investigation: Prediction and analysis of phenotypes in the Ar...
Snapshots: No snapshots
Model simulations compared to experimental data from the literature (publications from Mizuno lab are linked), testing the FMv2.
Submitter: Andrew Millar
Investigation: Prediction and analysis of phenotypes in the Ar...
Assays: Mizuno lab, Flowering time in clock mutants, Mizuno lab, Hypocotyl length in clock mutants
Snapshots: No snapshots
Modelling and experiments for FMv2 as a whole; Testing Framework Model version 2 (FMv2)
Submitter: Andrew Millar
Investigation: Prediction and analysis of phenotypes in the Ar...
Assays: Biomass, leaf number and metabolites, FMv2 simulation
Snapshots: No snapshots
Follow-up to the validation experiments on FMv2, testing candidate mechanisms for high malate and fumarate accumulation in the Arabidopsis double mutant prr7prr9 and its parent accession Col. New collaborations with the groups of Teresa Fitzpatrick and TiMet partner Samuel Zeeman.
Submitter: Andrew Millar
Investigation: Prediction and analysis of phenotypes in the Ar...
Assays: Assimilation and partitioning of 14CO2 at night, Thiamine vitamers
Snapshots: No snapshots
Assorted files prepared during the publication process of the FMv2, its validation and testing, mostly focussed on the Arabidopsis double mutant prr7prr9 and its parent accession Col. Data from other studies that are described separately, and linked by Atribution to the File records under this Study.
Submitter: Andrew Millar
Investigation: Prediction and analysis of phenotypes in the Ar...
Snapshots: No snapshots
Literature data used in the Seaton et al. 2017 study; data processing by Daniel Seaton.
Submitter: Andrew Millar
Investigation: Photoperiodic control of the Arabidopsis proteo...
Assays: Blasing et al, 2005, diurnal microarray in 12L:12D, Stitt lab, TiMet photoperiod microarrays
Snapshots: No snapshots
Experimental data reported in the Seaton et al. 2017 study; data processing by Alex Graf. Part of the EU FP7 TiMet project.
Submitter: Andrew Millar
Investigation: Photoperiodic control of the Arabidopsis proteo...
Assays: Photoperiod proteomics
Snapshots: No snapshots
Literature data and associated scripts analysed in the Seaton et al. 2017 study; data processing by Daniel Seaton.
Submitter: Andrew Millar
Investigation: Photoperiodic control of the Arabidopsis proteo...
Assays: Aryal et al, 2011, metabolic labelling of Cyanothece protein synthesis, Estimation of rates of translation and turnover from proteomics datasets, Martin et al, 2012, Ostreococcus N15 labelling proteomics data
Snapshots: No snapshots
Data analysis and modelling scripts and results for the Seaton et al. 2017 study, from Daniel Seaton.
Submitter: Andrew Millar
Investigation: Photoperiodic control of the Arabidopsis proteo...
Assays: Translational coincidence model
Snapshots: No snapshots
Metabolite analysis in clock mutants: Col-0 parent and mutants gi-201, toc1-101 and prr7prr9; WS parent and lhy/cca1 double mutant. Plants grown in Golm and harvested at End of Day and End of Night, , assays 22 major metabolites. More detail on TiMet wiki if required. Heteroscedastic t-tests to highlight most significant changes, without multiple-testing correction.
Submitter: Andrew Millar
Assay type: Metabolite Concentration
Technology type: Chromatography
Investigation: Prediction and analysis of phenotypes in the Ar...
Organisms: Arabidopsis thaliana : Col-0 wild type (wild-type / wild-type), Arabidopsis thaliana : prr7-3 prr9-1 (T-DNA insertion PRR9;T-DNA insertion PRR7 / 28h circadian rhythm), Arabidopsis thaliana
SOPs: No SOPs
Data files: TiMet WP1.1a metabolite data, ED-EN in clock mu...
Snapshots: No snapshots
Leaf number at flowering data from literature for prr7 prr9 and Col wild-type plants under long photoperiods and short photoperiods
Submitter: Andrew Millar
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Prediction and analysis of phenotypes in the Ar...
Organisms: Arabidopsis thaliana : Col-0 wild type (wild-type / wild-type), Arabidopsis thaliana : prr7-3 prr9-1 (T-DNA insertion PRR9;T-DNA insertion PRR7 / 28h circadian rhythm)
SOPs: No SOPs
Data files: Flowering time in WT vs prr7prr9 (Nakamichi et ...
Snapshots: No snapshots
Seedling hypocotyl data from literature for prr7 prr9 and Col wild-type plants under various photoperiods
Submitter: Andrew Millar
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Prediction and analysis of phenotypes in the Ar...
Organisms: Arabidopsis thaliana : Col-0 wild type (wild-type / wild-type), Arabidopsis thaliana : prr7-3 prr9-1 (T-DNA insertion PRR9;T-DNA insertion PRR7 / 28h circadian rhythm)
SOPs: No SOPs
Data files: Hypocotyl lengths in WT vs prr7prr9 across phot...
Snapshots: No snapshots
RNA timeseries data from TiMet for clock genes in prr7 prr9 and Col wild-type plants under 12L:12D cycle and LL
Submitter: Andrew Millar
Assay type: Gene Expression Profiling
Technology type: qRT-PCR
Investigation: Prediction and analysis of phenotypes in the Ar...
Organisms: Arabidopsis thaliana : Col-0 wild type (wild-type / wild-type), Arabidopsis thaliana : prr7-3 prr9-1 (T-DNA insertion PRR9;T-DNA insertion PRR7 / 28h circadian rhythm), Arabidopsis thaliana
SOPs: No SOPs
Data files: TiMet WP1.1 qRT-PCR LD to LL and DD
Snapshots: No snapshots
effects of 1% increase in each parameter, more detailed analysis of water content
Submitter: Andrew Millar
Biological problem addressed: Model Analysis Type
Investigation: Prediction and analysis of phenotypes in the Ar...
Organisms: Arabidopsis thaliana : Col-0 wild type (wild-type / wild-type)
Models: No Models
SOPs: No SOPs
Data files: Sensitivity analysis results (.mat file)
Snapshots: No snapshots
correlations of starch mobilisation and fresh weight under single parameter changes
Submitter: Andrew Millar
Biological problem addressed: Model Analysis Type
Investigation: Prediction and analysis of phenotypes in the Ar...
Organisms: Arabidopsis thaliana : Col-0 wild type (wild-type / wild-type)
Models: No Models
SOPs: No SOPs
Data files: Sensitivity analysis results (.mat file)
Snapshots: No snapshots
Combination of multiple sub-models to form Framework Model version 2
Submitter: Andrew Millar
Biological problem addressed: Model Analysis Type
Investigation: Prediction and analysis of phenotypes in the Ar...
Organisms: Arabidopsis thaliana : Col-0 wild type (wild-type / wild-type)
Models: Arabidopsis - starch and the circadian clock, M..., Chew_et_al_2014_Framework_Model version 1, Matl..., Framework Model v2, Modelling circadian regulation of flowering tim...
SOPs: No SOPs
Data files: No Data files
Snapshots: No snapshots
Comparison of simulated wild-type and prr7prr9 double mutant under 12L:12D cycles. Simulation with CVODE simulator via SBSI v1.5 framework.
Submitter: Andrew Millar
Biological problem addressed: Model Analysis Type
Investigation: Prediction and analysis of phenotypes in the Ar...
Organisms: Arabidopsis thaliana : Col-0 wild type (wild-type / wild-type), Arabidopsis thaliana : prr7-3 prr9-1 (T-DNA insertion PRR9;T-DNA insertion PRR7 / 28h circadian rhythm)
Models: Arabidopsis clock model P2011.1.2, P2011.1.2_directupload
SOPs: No SOPs
Data files: P2011.1.2 simulations and data in prr7 prr9 mut..., P2011.1.2 simulations of clock genes under LD c..., P2011.1.2 simulations vs. data for WT, normalis..., TiMet WP1.1 qRT-PCR LD to LL and DD
Snapshots: No snapshots
Biomass, leaf number and metabolites in Col0 (WT), prr7, prr7prr9, and lsf1. Metabolite data from plants after 28 days of growth were analysed most (27 days 'end of night', 28 days 'end of day' and 'end of night'). The data file also includes data from 21 days of growth ('end of day' and 'end of night'), which is useful for comparison to early-flowering plants not tested here, such as the lhycca1 double mutant, that flower before 28 days, altering their physiology.
Submitter: Daniel Seaton
Assay type: Organism or Strain Characteristics
Technology type: Technology Type
Investigation: Prediction and analysis of phenotypes in the Ar...
Organisms: Arabidopsis thaliana : Col-0 wild type (wild-type / wild-type), Arabidopsis thaliana : prr7-3 prr9-1 (T-DNA insertion PRR9;T-DNA insertion PRR7 / 28h circadian rhythm), Arabidopsis thaliana : lsf1-1 (T-DNA insertion 104bp upstream of ATG codon LSF1 / wild-type), Arabidopsis thaliana : prr7-3 (T-DNA insertion PRR7 / slight effects on clock period in LL)
SOPs: No SOPs
Data files: Laurel and Hardy 1 - Experimental data (excel), Laurel and Hardy 1 - experimental data (.mat file)
Snapshots: No snapshots
Submitter: Daniel Seaton
Biological problem addressed: Model Analysis Type
Investigation: Prediction and analysis of phenotypes in the Ar...
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: Laurel and Hardy 1 - simulation data (.mat file), Laurel and Hardy 1 mean data and simulations
Snapshots: No snapshots
Biomass (fresh mass, dry mass), leaf numbers, leaf area, gas exchange and 12 metabolites in Col0 (WT), prr7prr9, and lsf1 (presented in the preprint/paper) and pgm (not analysed further).
Submitter: Daniel Seaton
Assay type: Organism or Strain Characteristics
Technology type: Technology Type
Investigation: Prediction and analysis of phenotypes in the Ar...
Organisms: Arabidopsis thaliana : prr7-3 prr9-1 (T-DNA insertion PRR9;T-DNA insertion PRR7 / 28h circadian rhythm), Arabidopsis thaliana : Col-0 wild type (wild-type / wild-type), Arabidopsis thaliana : lsf1-1 (T-DNA insertion 104bp upstream of ATG codon LSF1 / wild-type), Arabidopsis thaliana : pgm (EMS AT5G51820 / starch deficient)
SOPs: No SOPs
Data files: Laurel and Hardy 2 - Experimental data (excel), Laurel and Hardy 2 - complete data, Laurel and Hardy 2 - experimental data (.mat file)
Snapshots: No snapshots
Biomass (fresh mass, dry mass), leaf numbers, leaf area, gas exchange and 12 metabolites in Col0 (WT), prr7prr9, and pgm at days 29 and 35, presented in the preprint/publication, with most data also for Col and lhycca1 at days 21/22/23, not analysed further.
We suggest that the lower carbon assimilation rate measured in lhycca1 (see gas exchange data) might allow a calibirated simulation in the FMv2 model in future to incorporate the indirect effects of nightly carbon starvation in this genotype ...
Submitter: Daniel Seaton
Assay type: Organism or Strain Characteristics
Technology type: Technology Type
Investigation: Prediction and analysis of phenotypes in the Ar...
Organisms: Arabidopsis thaliana : prr7-3 prr9-1 (T-DNA insertion PRR9;T-DNA insertion PRR7 / 28h circadian rhythm), Arabidopsis thaliana : Col-0 wild type (wild-type / wild-type), Arabidopsis thaliana, Arabidopsis thaliana : pgm (EMS AT5G51820 / starch deficient)
SOPs: No SOPs
Data files: Laurel and Hardy 3 - Experimental data (excel), Laurel and Hardy 3 - complete data, Laurel and Hardy 3 - experimental data (.mat file)
Snapshots: No snapshots
Simulation data from FMv2 calibrated for experiment L&H2, an experiment run at 18.5C instead of the 20.5C of the replicate and related studies. The Excel file includes the mean and SD of the relevant experimental data, and the figure panels.
Submitter: Daniel Seaton
Biological problem addressed: Model Analysis Type
Investigation: Prediction and analysis of phenotypes in the Ar...
Organisms: Arabidopsis thaliana : prr7-3 prr9-1 (T-DNA insertion PRR9;T-DNA insertion PRR7 / 28h circadian rhythm), Arabidopsis thaliana : Col-0 wild type (wild-type / wild-type), Arabidopsis thaliana : lsf1-1 (T-DNA insertion 104bp upstream of ATG codon LSF1 / wild-type)
Models: No Models
SOPs: No SOPs
Data files: Laurel and Hardy 2 - simulation data (.mat file), Laurel and Hardy 2 mean data and simulations
Snapshots: No snapshots
Submitter: Daniel Seaton
Biological problem addressed: Model Analysis Type
Investigation: Prediction and analysis of phenotypes in the Ar...
Organisms: No organisms
Models: No Models
SOPs: No SOPs
Data files: Laurel and Hardy 3 - simulation data (.mat file), Laurel and Hardy 3 mean data and simulations
Snapshots: No snapshots
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...
Organisms: Arabidopsis thaliana : Col-0 wild type (wild-type / wild-type)
SOPs: No SOPs
Data files: Flis et al, 2016, Supplemental Table S4, Global...
Snapshots: No snapshots
Plant material The same plant material used for transcriptome analysis in (Flis et al., 2016) was the basis of our proteome study. Briefly, Arabidopsis thaliana Col-0 plants were grown on GS 90 soil mixed in a ratio 2:1 (v/v) with vermiculite. Plants were grown for 1 week in a 16 h light (250 μmol m−2 s−1, 20 °C)/8 h dark (6 °C) regime followed by an 8 h light (160 μmol m−2 s−1, 20 °C)/16 h dark (16 °C) regime for one week. Plants were then replanted with five seedlings per pot, transferred for ...
Submitter: Daniel Seaton
Assay type: Protein Quantification
Technology type: Mass Spectrometry
Investigation: Photoperiodic control of the Arabidopsis proteo...
Organisms: Arabidopsis thaliana : Col-0 wild type (wild-type / wild-type)
SOPs: No SOPs
Data files: Proteomics data file submission to PRIDE, PXD00..., Sample description table for Proteomics data fi..., Table EV1 - Quantitative proteomics dataset, Table EV3, Statistical analysis of protein chan...
Snapshots: No snapshots
Submitter: Daniel Seaton
Assay type: Gene Expression Profiling
Technology type: Microarray
Investigation: Photoperiodic control of the Arabidopsis proteo...
Organisms: Arabidopsis thaliana : Col-0 wild type (wild-type / wild-type)
SOPs: No SOPs
Data files: Blasing et al, 2005, diurnal microarray dataset...
Snapshots: No snapshots
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...
Organisms: Arabidopsis thaliana : Col-0 wild type (wild-type / wild-type)
Models: Translational coincidence modelling - python sc...
SOPs: No SOPs
Data files: Blasing et al, 2005, diurnal microarray dataset..., Table EV1 - Quantitative proteomics dataset
Snapshots: No snapshots
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...
Organisms: No organisms
SOPs: No SOPs
Data files: Martin et al, 2012, Ostreococcus N15 labelling ...
Snapshots: No snapshots
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...
Organisms: No organisms
SOPs: No SOPs
Data files: Aryal et al, 2011, metabolic labelling of Cyano...
Snapshots: No snapshots
Submitter: Andrew Millar
Provider Name: Andrew Millar
Provider's strain ID: Not specified
Organism: Arabidopsis thaliana
Genotypes: T-DNA LHY;T-DNA CCA1
Phenotypes: short circadian period, early flowering
Comment: Probably contains a chromosomal rearrangement, as the T-DNA's can segregate as if they are genetically linked in the Millar lab's experience, whereas the target genes are on different chromosomes
Submitter: Andrew Millar
Provider Name: Mark Stitt
Provider's strain ID: Not specified
Organism: Arabidopsis thaliana
Genotypes: EMS AT5G51820
Phenotypes: starch deficient
Comment: I assume pgm-1
Analysis of carbon metabolites in clock mutants by Anna Flis and Ronan Sulpice, Mark Stitt lab
Creators: Andrew Millar, Anna Flis, Ronan Sulpice, Mark Stitt
Submitter: Andrew Millar
Investigations: Prediction and analysis of phenotypes in the Ar... and 1 hidden item
Studies: Construction of Framework Model version 2 (FMv2) and 1 hidden item
Assays: TiMet WP1.1a Metabolite analysis of clock mutants and 1 hidden item
Excel spreadsheet with data and simulations used to prepare figures for publication, see Metadata sheet for conditions. Data Fresh (not dry) rosette leaf biomass, measured in samples of 5 plants each on multiple days, as mean and SD; Simulation outputs from FMv2 for Col Wild Type plants, and two simulations for prr7prr9 where the mutation affects only starch degradation or both starch degradation and malate/fumarate store mobilisation.
Starch levels in carbon units (not C6) measured on on days ...
Creators: Daniel Seaton, Yin Hoon Chew, Virginie Mengin
Submitter: Andrew Millar
Investigations: Prediction and analysis of phenotypes in the Ar...
Studies: Test of FMv2, study Laurel & Hardy 3
Assays: FMv2 simulation
Excel workbook with included Read.Me sheet, including FW and DW biomass data derived from files linked elsewhere; a compilation of the rosette area and gas exchange data for every plant measured of the Col, lsf1 and prr7prr9 genotypes; statistical analysis across the experiments; and charts of the compiled data, some of which are presented as figure panels in the 2022 versions.
Creators: Yin Hoon Chew, Andrew Millar
Submitter: Andrew Millar
Investigations: Prediction and analysis of phenotypes in the Ar...
Biomass data for individual plants at day 35, fresh and dry weights, as well as mean and SD, from study Gibberellins 1
Creators: Yin Hoon Chew, Andrew Millar
Submitter: Andrew Millar
Investigations: Prediction and analysis of phenotypes in the Ar...
Studies: Test of FMv2, study Gibberellins 1
Assays: Biomass and metabolites
Excel sheet with mean and SD biomass data and charts, individual metabolite replicates, mean, SD and charts Details on Read.ME worksheet
Creators: Virginie Mengin, Yin Hoon Chew, Andrew Millar
Submitter: Andrew Millar
Investigations: Prediction and analysis of phenotypes in the Ar...
Studies: Test of FMv2, study Gibberellins 1
Assays: Biomass and metabolites
14CO2 assimilation in the night-time, in plants of Col, prr7prr9; Ws, lhycca1 genotypes at 18 and 28 days, and partitioning among cellular fractions.
Creator: Gavin George, Samuel Zeeman
Submitter: Andrew Millar
Excel file with data on levels of thiamine and its metabolites TMP and active cofactor TDP, tested in Col and prr7prr9 samples from study Laurel and Hardy 3. Altered levels of TDP could potentially affect enzymes with TDP cofactors that metabolise malate and fumarate levels, altering their levels in prr7prr9.
Creators: Yin Hoon Chew, Michael Moulin, Teresa Fitzpatrick
Submitter: Andrew Millar
Investigations: Prediction and analysis of phenotypes in the Ar...
Studies: Test of FMv2, follow-on: mechanisms of malate/f...
Assays: Thiamine vitamers
Excel spreadsheet with data and simulations used to prepare figures for publication, see Metadata sheet for conditions. Data Fresh (not dry) rosette leaf biomass, measured in samples of 5 plants each on multiple days, as mean and SD; Simulation outputs from FMv2 for Col Wild Type plants, lsf1, and two simulations for prr7prr9 where the mutation affects only starch degradation or both starch degradation and malate/fumarate store mobilisation.
Starch levels in carbon units (not C6) measured on on ...
Creators: Daniel Seaton, Yin Hoon Chew, Virginie Mengin
Submitter: Andrew Millar
Investigations: Prediction and analysis of phenotypes in the Ar...
Studies: Test of FMv2, study Laurel & Hardy 1
Assays: FMv2 simulation
SD values of clock gene RNA data in absolute units of RNA copies per cell (calculated from copies per gFW, / 25 million cells/gFW) from TiMet WP1.1, RNA dataset ros (from rosettes). Note the Col data are from WP1.1, not substituted with Col from the LD12:12 of the WP1.2 photoperiod data set, as they were in Flis et al. 2015. Note also that cL_m in these data is taken from CCA1 only, not the average of CCA1 and LHY as in the data sets used for optimisation of P2011.2.1 in Flis et al. 2015.
The ...
Creators: Andrew Millar, Uriel Urquiza Garcia
Submitter: Andrew Millar
Investigations: Absolute units for proteins in Arabidopsis cloc..., Absolute units in Arabidopsis clock models up t...
Studies: Predicting absolute levels of clock proteins wi..., Rescaling the P2011 model to match RNA data
Assays: TiMet RNA timeseries data, TiMet RNA timeseries data and starting models
Mean values of clock gene RNA data in absolute units of RNA copies per cell (calculated from copies per gFW, / 25 million cells/gFW) from TiMet WP1.1, RNA dataset ros (from rosettes). Note the Col data are from WP1.1, not substituted with Col from the LD12:12 of the WP1.2 photoperiod data set, as they were in Flis et al. 2015. Note also that cL_m in these data is taken from CCA1 only, not the average of CCA1 and LHY as in the data sets used for optimisation of P2011.2.1 in Flis et al. 2015.
The ...
Creators: Andrew Millar, Uriel Urquiza Garcia
Submitter: Andrew Millar
Investigations: Absolute units for proteins in Arabidopsis cloc..., Absolute units in Arabidopsis clock models up t...
Studies: Predicting absolute levels of clock proteins wi..., Rescaling the P2011 model to match RNA data
Assays: TiMet RNA timeseries data, TiMet RNA timeseries data and starting models
Data curation notes provided by Alex Graf via Willi Gruissem, in addition to the PRIDE deposition.
The Excel file gives the list of samples uploaded into PRIDE. here - https://fairdomhub.org/data_files/3704
The published experimental design might lead one to expect 4x3x2x7 = 168 samples. There are more than 168 samples in the PRIDE upload for the following reasons:
First, all of the measurements from the experiment had been uploaded, including files for measurements that were repeated because of ...
Creators: Andrew Millar, Alexander Graf, Katja Baerenfaller, Willi Gruissem
Submitter: Andrew Millar
Investigations: Photoperiodic control of the Arabidopsis proteo...
Studies: Photoperiod-specific proteome data for Arabidopsis
Assays: Photoperiod proteomics
This Excel file lists the samples uploaded in PRIDE. The table “Table Sorted PP and Replicates” in the Excel file has all the relevant annotation.
There are more than the expected 168 samples in the PRIDE upload for the following reasons:
First, all of the measurements from the experiment had been uploaded, including files for measurements that were repeated because of problems during the MS run. These samples are not annotated in the table. Second, we had included 4 Gold Standard samples (2 ...
Creators: Alexander Graf, Katja Baerenfaller, Willi Gruissem
Submitter: Andrew Millar
Investigations: Photoperiodic control of the Arabidopsis proteo...
Studies: Photoperiod-specific proteome data for Arabidopsis
Assays: Photoperiod proteomics
Supplementary information file from Chew et al. PNAS 2014, including full model description for Arabidopsis Framework Model v1, model simulations and experimental validations.
Creators: Andrew Millar, Yin Hoon Chew
Submitter: Andrew Millar
Investigations: Arabidopsis Framework Model v1, predicting rose...
Studies: Construction of Framework Model v1
Microarray data at end of day (ED) and end of night (EN) in 4, 6, 8, 12, and 18h photoperiods.
Creator: Daniel Seaton
Submitter: Daniel Seaton
Investigations: Photoperiodic control of the Arabidopsis proteo...
Mean and standard deviation of protein abundances in 6h, 8h, 12h, and 18h photoperiods.
Creators: Daniel Seaton, Andrew Millar
Submitter: Daniel Seaton
Results of the statistical analysis, identifying proteins that change in abundance significantly across photoperiods.
Creators: Daniel Seaton, Andrew Millar
Submitter: Daniel Seaton
Investigations: Photoperiodic control of the Arabidopsis proteo...
Studies: Photoperiod-specific proteome data for Arabidopsis
Assays: Photoperiod proteomics
Creator: Daniel Seaton
Submitter: Daniel Seaton
Framework Model for Arabidopsis vegetative growth, version 2 (FMv2), as described in Chew et al. bioRxiv 2017 (https://doi.org/10.1101/105437; please see linked Article file).
The FMv2 model record on FAIRDOMHub has the following versions, which represent the same FMv2 model: Version 1 is an archive of the github repository of MATLAB code for the Framework Model v2, downloaded from https://github.com/danielseaton/frameworkmodel on 06/02/17. This version was not licensed for further use and was ...
Creators: Daniel Seaton, Yin Hoon Chew, Andrew Millar
Submitter: Daniel Seaton
Model type: Not specified
Model format: Matlab package
Environment: Matlab
Organism: Arabidopsis thaliana
Investigations: Prediction and analysis of phenotypes in the Ar...
Studies: Construction of Framework Model version 2 (FMv2)
Assays: Composition of FMv2
Originally submitted model file for PLaSMo accession ID PLM_71, version 2
Creators: BioData SynthSys, Andrew Millar, Andrew Millar
Submitter: BioData SynthSys
Model type: Ordinary differential equations (ODE)
Model format: SBML
Environment: Copasi
Organism: Arabidopsis thaliana
Investigations: Millar, Andrew (ex-PlaSMo models)
Abstract (Expand)
Authors: Yin Hoon Chew, Daniel D Seaton, Virginie Mengin, Anna Flis, Sam T Mugford, Gavin M George, Michael Moulin, Alastair Hume, Samuel C Zeeman, Teresa B Fitzpatrick, Alison M Smith, Mark Stitt, Andrew J Millar
Date Published: 1st Jul 2022
Publication Type: Journal
DOI: 10.1093/insilicoplants/diac010
Citation: in silico Plants 4(2),diac010
Abstract (Expand)
Authors: Yin Hoon Chew, Daniel D. Seaton, Virginie Mengin, Anna Flis, Sam T. Mugford, Gavin M. George, Michael Moulin, Alastair Hume, Samuel C. Zeeman, Teresa B. Fitzpatrick, Alison M. Smith, Mark Stitt, Andrew J. Millar
Date Published: 6th Feb 2017
Publication Type: Tech report
DOI: 10.1101/105437
Citation: biorxiv;105437v2,[Preprint]
Abstract (Expand)
Authors: A. Pokhilko, A. P. Fernandez, K. D. Edwards, M. M. Southern, K. J. Halliday, A. J. Millar
Date Published: 6th Mar 2012
Publication Type: Not specified
PubMed ID: 22395476
Citation: Mol Syst Biol. 2012 Mar 6;8:574. doi: 10.1038/msb.2012.6.
Abstract (Expand)
Authors: A. Flis, R. Sulpice, D. D. Seaton, A. A. Ivakov, M. Liput, C. Abel, A. J. Millar, M. Stitt
Date Published: No date defined
Publication Type: Not specified
PubMed ID: 27075884
Citation: Plant Cell Environ. 2016 Sep;39(9):1955-81. doi: 10.1111/pce.12754. Epub 2016 Jul 15.