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- Daniel Seaton
SEEK ID: https://fairdomhub.org/people/851
Location:
United Kingdom
Expertise: Not specified
Tools: Not specified
Related items
- Projects (3)
- Institutions (1)
- Investigations (2)
- Studies (0+4)
- Assays (7+9)
- Data files (10+14)
- Models (3+2)
- Publications (14)
Research programme in the Takato Imaizumi lab, with multiple collaborators. Published in Song et al. Nature Plants 2018; Kinmonth-Schultz et al., in silico Plant 2019.
Programme: SynthSys
Public web page: https://faculty.washington.edu/takato/
Organisms: Arabidopsis thaliana
Andrew Millar's research group, University of Edinburgh
Programme: SynthSys
Public web page: http://www.amillar.org
Organisms: Escherichia coli, Arabidopsis thaliana, Ostreococcus tauri
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
Public web page: http://timing-metabolism.eu/
Organisms: Arabidopsis thaliana, Ostreococcus tauri
Project to test effects of temperature cycles on expression of Arabidopsis florigen gene FT, and whether these are mediated by temperature-dependent leaf development or temperature-specific FT expression, or both. Re-used and extended Arabidopsis Framework Model v1 to address this question. Led by Hannah Kinmonth-Schultz in Kim and Imaizumi labs, collaborating with Millar lab.
Snapshots: No snapshots
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.
Snapshots: Snapshot 1, Snapshot 2
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
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
Snapshots: No snapshots
Investigation: Photoperiodic control of the Arabidopsis proteo...
Study: Photoperiod-specific proteome data for Arabidopsis
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...
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.
Investigation: Photoperiodic control of the Arabidopsis proteo...
Study: Modelling and analysis of translational coincid...
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
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
Snapshots: No snapshots
Investigation: Photoperiodic control of the Arabidopsis proteo...
Study: Rhythmic and photoperiod-specific transcriptome...
Organisms: Arabidopsis thaliana : Col-0 wild type (wild-type / wild-type)
SOPs: No SOPs
Data files: Flis et al, 2016, Supplemental Table S4, Global...
Submitter: Daniel Seaton
Assay type: Gene Expression Profiling
Technology type: Microarray
Snapshots: No snapshots
Investigation: Photoperiodic control of the Arabidopsis proteo...
Study: Rhythmic and photoperiod-specific transcriptome...
Organisms: Arabidopsis thaliana : Col-0 wild type (wild-type / wild-type)
SOPs: No SOPs
Data files: Blasing et al, 2005, diurnal microarray dataset...
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
Snapshots: No snapshots
Investigation: Photoperiodic control of the Arabidopsis proteo...
Study: Proteome and translation rate data for the Ostr...
Organisms: No organisms
SOPs: No SOPs
Data files: Martin et al, 2012, Ostreococcus N15 labelling ...
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
Snapshots: No snapshots
Investigation: Photoperiodic control of the Arabidopsis proteo...
Study: Proteome and translation rate data for the Ostr...
Organisms: No organisms
SOPs: No SOPs
Data files: Aryal et al, 2011, metabolic labelling of Cyano...
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.
Investigation: Photoperiodic control of the Arabidopsis proteo...
Study: Proteome and translation rate data for the Ostr...
Organisms: Ostreococcus tauri
Models: Estimation of translation and turnover - python...
SOPs: No SOPs
Data files: Aryal et al, 2011, metabolic labelling of Cyano..., Calculated rates of protein degradation in Cyan..., Calculated rates of protein degradation in Ostr..., Calculated rates of protein synthesis in the li..., Calculated rates of protein synthesis in the li..., Martin et al, 2012, Ostreococcus N15 labelling ...
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
Proteomics data for N15 incorporation into protein in Ostreococcus grown in 12L:12D light:dark cycles.
Creators: Daniel Seaton, Andrew Millar
Submitter: Daniel Seaton
Quantitative proteomic analysis of Cyanothece ATCC51142 grown in 12L:12D light:dark cycles, using partial metabolic labeling and LC-MS analysis.
Creators: Daniel Seaton, Andrew Millar
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 Arabid...
Studies: 1 hidden item
Modelling analyses: 1 hidden item
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.
Creators: Daniel Seaton, Andrew Millar
Submitter: Daniel Seaton
Model type: Not specified
Model format: Not specified
Environment: Not specified
Organism: Not specified
Investigations: Photoperiodic control of the Arabidopsis proteo...
Studies: Proteome and translation rate data for the Ostr...
Modelling analyses: Estimation of rates of translation and turnover...
Creator: Daniel Seaton
Submitter: Daniel Seaton
Model type: Algebraic equations
Model format: Not specified
Environment: Not specified
Organism: Arabidopsis thaliana
Investigations: Photoperiodic control of the Arabidopsis proteo...
Studies: Modelling and analysis of translational coincid...
Modelling analyses: Translational coincidence model
Abstract (Expand)
Authors: Hannah A Kinmonth-Schultz, Melissa J S MacEwen, Daniel D Seaton, Andrew J Millar, Takato Imaizumi, Soo-Hyung Kim
Date Published: 2019
Publication Type: Journal
DOI: 10.1093/insilicoplants/diz006
Citation: in silico Plants 1(1),diz006
Abstract (Expand)
Authors: D. D. Seaton, R. W. Smith, Y. H. Song, D. R. MacGregor, K. Stewart, G. Steel, J. Foreman, S. Penfield, T. Imaizumi, A. J. Millar, K. J. Halliday
Date Published: 21st Jan 2015
Publication Type: Not specified
PubMed ID: 25600997
Citation: Mol Syst Biol. 2015 Jan 19;11(1):776. doi: 10.15252/msb.20145766.
Abstract (Expand)
Authors: D. D. Seaton, O. Ebenhoh, A. J. Millar, A. Pokhilko
Date Published: 18th Dec 2013
Publication Type: Not specified
PubMed ID: 24335560
Citation: J R Soc Interface. 2013 Dec 11;11(91):20130979. doi: 10.1098/rsif.2013.0979. Print 2014 Feb 6.
Abstract (Expand)
Authors: Y. Niwa, T. Yamashino, T. Mizuno
Date Published: 24th Feb 2009
Publication Type: Not specified
PubMed ID: 19233867
Citation: Plant Cell Physiol. 2009 Apr;50(4):838-54. doi: 10.1093/pcp/pcp028. Epub 2009 Feb 20.
Abstract (Expand)
Authors: N. Nakamichi, M. Kita, K. Niinuma, S. Ito, T. Yamashino, T. Mizoguchi, T. Mizuno
Date Published: 17th May 2007
Publication Type: Not specified
PubMed ID: 17504813
Citation: Plant Cell Physiol. 2007 Jun;48(6):822-32. Epub 2007 May 15.
Abstract (Expand)
Authors: Yin Hoon Chew, Daniel D. Seaton, Virginie Mengin, Anna Flis, Sam T. Mugford, Alison M. Smith, Mark Stitt, Andrew J Millar
Date Published: No date defined
Publication Type: Not specified
DOI: 10.1101/105437
Citation: Linking circadian time to growth rate quantitatively via carbon metabolism
Abstract (Expand)
Authors: Daniel Seaton, Alexander Graf, Katja Baerenfaller, Mark Stitt, Andrew Millar, Wilhelm Gruissem
Date Published: No date defined
Publication Type: Not specified
DOI: 10.1101/182071
Citation: Photoperiodic control of the Arabidopsis proteome reveals a translational coincidence mechanism
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.
Abstract (Expand)
Authors: B. Usadel, O. E. Blasing, Y. Gibon, K. Retzlaff, M. Hohne, M. Gunther, M. Stitt
Date Published: No date defined
Publication Type: Not specified
PubMed ID: 18305208
Citation: Plant Physiol. 2008 Apr;146(4):1834-61. doi: 10.1104/pp.107.115592. Epub 2008 Feb 27.
Abstract (Expand)
Authors: O. E. Blasing, Y. Gibon, M. Gunther, M. Hohne, R. Morcuende, D. Osuna, O. Thimm, B. Usadel, W. R. Scheible, M. Stitt
Date Published: No date defined
Publication Type: Not specified
PubMed ID: 16299223
Citation: Plant Cell. 2005 Dec;17(12):3257-81. doi: 10.1105/tpc.105.035261. Epub 2005 Nov 18.
Abstract (Expand)
Authors: U. K. Aryal, J. Stockel, R. K. Krovvidi, M. A. Gritsenko, M. E. Monroe, R. J. Moore, D. W. Koppenaal, R. D. Smith, H. B. Pakrasi, J. M. Jacobs
Date Published: No date defined
Publication Type: Not specified
PubMed ID: 22133144
Citation: BMC Syst Biol. 2011 Dec 1;5:194. doi: 10.1186/1752-0509-5-194.
Abstract (Expand)
Authors: S. F. Martin, V. S. Munagapati, E. Salvo-Chirnside, L. E. Kerr, T. Le Bihan
Date Published: No date defined
Publication Type: Not specified
PubMed ID: 22077659
Citation: J Proteome Res. 2012 Jan 1;11(1):476-86. doi: 10.1021/pr2009302. Epub 2011 Dec 1.
Abstract
Authors: Hannah A Kinmonth-Schultz, Melissa J MacEwen, Daniel D Seaton, Andrew J Millar, Takato Imaizumi, Soo-Hyung Kim
Date Published: No date defined
Publication Type: Not specified
DOI: 10.1101/267104
Citation: Mechanistic model of temperature influence on flowering through whole-plant accumulation of FT
Abstract (Expand)
Authors: Zeenat B. Noordally, Matthew M. Hindle, Sarah F. Martin, Daniel D. Seaton, Ian Simpson, Thierry Le Bihan, Andrew J. Millar
Date Published: No date defined
Publication Type: Not specified
DOI: 10.1101/287862
Citation: Circadian protein regulation in the green lineage I. A phospho-dawn anticipates light onset before proteins peak in daytime.