Millar group

Data, model 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.

Data, models and simulations for the Chew et al. 2017 paper (bioRxiv https://doi.org/10.1101/105437 ), mostly on the prr7 prr9 double mutant, with controls in lsf1 and prr7 single mutants.

Literature data used in the Seaton et al. 2017 study; data processing by Daniel Seaton.

Experimental data reported in the Seaton et al. 2017 study; data processing by Alex Graf. Part of the EU FP7 TiMet project.

Literature data and associated scripts analysed in the Seaton et al. 2017 study; data processing by Daniel Seaton.

Data analysis and modelling scripts and results for the Seaton et al. 2017 study, from Daniel Seaton.

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.

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.

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
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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.

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.

Microarray data at end of day (ED) and end of night (EN) in 4, 6, 8, 12, and 18h photoperiods.

Mean and standard deviation of protein abundances in 6h, 8h, 12h, and 18h photoperiods.

Results of the statistical analysis, identifying proteins that change in abundance significantly across photoperiods.

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.

Exactly the same as model 243, but uploaded as a file rather than copied from PlaSMo.

This version is P2011.1.2, model ID PLM_71 version 1. Dynamics identical to P2011.1.1 of the Pokhilko et al. 2012 publication.

http://www.plasmo.ed.ac.uk/plasmo/models/download.shtml?accession=PLM_71&version=1

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.

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Outline report of joint research conducted during MSBnet-funded visit of Sanu Shameer to Millar lab