Sample description table for Proteomics data file submission to PRIDE, PXD006848 Version 1
ExploreThis 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 replicates on each of the two large gels used to process all samples). These 4 gold standard samples in 7 fractions explain 28 extra samples. Third, we did not have 168 but 166 samples in the photoperiod set. Fractions 1 and 2 of sample 43 (Photoperiod 2, bio replicate 1, tech. replicate 2) were lost during sample preparation. While the remaining fractions were measured and are included in the PRIDE upload and the table, this sample was not used in the data analysis. Photoperiod 2 bio rep. 1 was only used with one technical replicate in the calculations.
SEEK ID: https://fairdomhub.org/data_files/3704?version=1
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TiMet PhotoPeriod Samples_Seaton_2018.xlsx
Format: Spreadsheet
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Created: 26th Mar 2020 at 22:01
Last updated: 26th Mar 2020 at 22:02
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Version 1 (earliest) Created 26th Mar 2020 at 22:01 by Andrew Millar
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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 Edinburgh
https://orcid.org/0000-0003-1756-3654
SynthSys 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
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/
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
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
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...
