In vivo bioluminescence of clock protein-NanoLUC fusions: example experiment
Seedlings of the transgenic lines complemented with CCA1-NL and TOC1-NL were tested under 12L:12D cycles followed by constant light, to test how well the reporter signal in living plants reflected the expected patterns of protein expression. One example is linked below, from the BioDare2 repository record, because FAIRDOMHub's Data File is not accepting these URLs.
BioDare2 ID 11391; Plate reader experiment CCA1 TOC1 NanoLUC; permalink: https://biodare2.ed.ac.uk/experiment/11391
SEEK ID: https://fairdomhub.org/assays/2491
Experimental assay
Projects: Millar group
Investigation: Absolute units for proteins in Arabidopsis clock models up to U2020.5
Study: Measuring absolute levels of clock proteins with calibrated NanoLUC assays
Assay position:
Assay type: Protein Quantification
Technology type: Imaging
Organisms: Arabidopsis thaliana : Col-0 wild type (wild-type / wild-type) (batch)
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Created: 28th Aug 2024 at 18:34
Last updated: 19th Dec 2024 at 11:28
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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
Andrew Millar's research group, University of Edinburgh
Programme: SynthSys
Public web page: http://www.amillar.org
The dataset presents mathematical models of the gene regulatory network of the circadian clock, in the plant Arabidopsis thaliana. The work will be published as Urquiza-Garcia, Molina, Halliday and Millar, title "Abundant clock proteins point to missing molecular regulation in the plant circadian clock", in Molecular Systems Biology, 2025.
Starting from the U2019.3 and U2020.3 models, this project rescales parameters to match protein levels that were predicted using a simple model from the TiMet ...
Submitter: Andrew Millar
Studies: Construction of NanoLUC-tagged plants, Estimating DNA-binding affinities for Arabidopsis proteins, Measuring absolute levels of clock proteins with calibrated NanoLUC assays, Predicting absolute levels of clock proteins with a simple model, Recalibrating the clock models for absolute protein levels, to create mo..., Reproducibility documentation
Assays: Clock protein number determination with NanoLUC calibration, Clock proteins NanoLUC fusion raw data, Gatway maps of genomic regions of clock genes, In vivo bioluminescence of clock protein-NanoLUC fusions: example experi..., Jupyter notebook Predicting Protein Numbers, Propagating scaling factors into model parameters for U2019.4->U2019.5 a..., Protein level time series, Python packages, Reproducibility tool set, Selection of complemented transgenic lines, TiMet RNA timeseries data, promoter binding affinity calculations on the genome based on PBMs and E...
