Assays

This script take the scaling paramters using synthetic protein data updates model paramaters

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

Jupyter lab notebook that contains the models and data that for predicting protein levels based on mRNA data from TiMet projecto

RNA timeseries data for Arabidopsis Col wild-type plants and clock mutants, as separate mean and SD files. The raw data is available on BioDare.ed.ac.uk, and is linked as 'Attribution' from elsewhere on FAIRDOMHub.

Protein time series for clock proteins colected from the literature. Protein expression profiles were derived from images of western blot or or from plots that the orignal authors derived from quantitative western blots

Insertion of events that rescued mutant phenotypes were selected for performing absolute quantification using calibration curves of recombinant purified MBP-NanoLUC-3Flag-10his. Seeds were sterilised with 5% houshold bleach for 10 min and washed three time with deionised water. The seeds were then put for stratifyication at 4ºC in darkenss for 48 hours in 1.5 ml polyproplyen tubes in dionised water. After 48 hours seeds wered plated on ROBUST agar (1/2 MS salts, 1.2% Agar pH 5.8 ajudsted with ...

Information about the BioProject submission of all whole-genome-sequenced samples used in this study

Sequencing of 150 bp paired-end reads on an Illumina NextSeq 500 or 2000

Files connected to study: _S_P5_SxF_lavandulol

Short Name: LA_myc-GC-MS Assay Class: WET Assay Type: GC-MS Title: Detection of lavandulyl acetate in SxF mycelium extracts Description: Detection of lavandulyl acetate in solvent extracts of SxF mycelia by GC-MS-MS pISA Assay creation date: 2021-12-23 pISA Assay creator: Sandra Vacas Phenodata: None Featuredata: Data: https://doi.org/10.5281/zenodo.6559159

Short Name: L_liq-GC-MS Assay Class: WET Assay Type: GC-MS Title: Detection of lavandulol in extracts of SxF liquid cultures Description: Detection of lavandulol in solvent extracts of SxF liquid cultures by GC-MS-MS pISA Assay creation date: 2021-12-23 pISA Assay creator: Sandra Vacas Phenodata: None Featuredata: Data: https://doi.org/10.5281/zenodo.6559450

Short Name: L_myc-GC-MS Assay Class: WET Assay Type: GC-MS Title: Dectection of lavandulol in SxF mycelium extracts Description: Detection of lavandulol in solvent extracts of SxF mycelia by GC-MS-MS pISA Assay creation date: 2021-12-23 pISA Assay creator: Sandra Vacas Phenodata: None Featuredata: Data: https://doi.org/10.5281/zenodo.6559481

Files connected to investigation: _I_T33_MonoterpenoidsFungi

Files connected to study: _S_P5_SxF_lav_ac

Short Name: LA_liq-GC-MS Assay Class: WET Assay Type: GC-MS Title: Detection of lavandulyl acetate in extracts of SxF liquid cultures Description: Detection of lavandulyl acetate in solvent extracts of SxF liquid cultures by GC-MS-MS pISA Assay creation date: 2021-12-23 pISA Assay creator: Sandra Vacas Phenodata: None Featuredata: Data: https://doi.org/10.5281/zenodo.6559101

Files connected to investigation: _I_T32_CandidateGeneExpressionTesting

Files connected to study: _S_TransientLPPSCPPS

Short Name: TransientCompLPPSCPPS-GCMS Assay Class: WET Assay Type: GCMS Title: Transient expression of LPPS and CPPS genes in Nicotiana benthamiana plants Description: The purpose of this assay is to check the transient expression of the LPPS and CPPS genes in Nicotiana benthamiana plants. Two different Agrobacterium strains were assayed and compared the levels of production between them. Volatile monoterpenoid levels were measured by GCMS of samples. pISA Assay creation date: 2021-12-03 pISA ...