Assays
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McWatters A.t. Col-0 WT clock RNA timeseries
| Property | Value |
|---|---|
| BioDare ID | 3488 |
| Author | Harriet G. McWatters |
| Institution | University of Oxford |
| License | CC_BY |
Description
Literature data from: 'Defining the robust behaviour of the plant clock gene circuit with absolute RNA timeseries and open infrastructure.' by: Harriet G. McWatters.
data are col0 8 d seedlings grown on sucrose in either LD 12:12 at 20 oC or WC 27:12 in LL. Gene ...
Submitter: Daniel Thedie
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Flis Anna
Study: Flis et al. (2015)
Clock gene RNAs under RD-RR in clock mutants, expt 4
| Property | Value |
|---|---|
| BioDare ID | 13228357183121 |
| Author | Locke |
| Institution | |
| License |
Description
Literature data from: 'Extension of a genetic network model by iterative experimentation and mathematical analysis.' by: Locke.
First, heroic large-scale RNA profile screen by real-time qPCR in 96-well format, by Megan Southern in 2005. Experiment 4 of 4.
Purpose
Testing effects of clock ...
Submitter: Daniel Thedie
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Flis Anna
Study: Flis et al. (2015)
Clock gene RNAs under RD-RR in clock mutants, expt 3
| Property | Value |
|---|---|
| BioDare ID | 13228357055348 |
| Author | Locke |
| Institution | |
| License |
Description
Literature data from: 'Extension of a genetic network model by iterative experimentation and mathematical analysis.' by: Locke.
First, heroic large-scale RNA profile screen by real-time qPCR in 96-well format, by Megan Southern in 2005. Experiment 3 of 4.
Purpose
Testing effects of clock ...
Submitter: Daniel Thedie
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Flis Anna
Study: Flis et al. (2015)
Clock gene RNAs under RD-RR in clock mutants, expt 2
| Property | Value |
|---|---|
| BioDare ID | 13227619871305 |
| Author | Locke |
| Institution | |
| License |
Description
Literature data from: 'Extension of a genetic network model by iterative experimentation and mathematical analysis.' by: Locke.
First, heroic large-scale RNA profile screen by real-time qPCR in 96-well format, by Megan Southern in 2005. Experiment 2 of 4.
Purpose
Testing effects of clock ...
Submitter: Daniel Thedie
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Flis Anna
Study: Flis et al. (2015)
Clock gene RNAs under RD-RR in clock mutants, expt 1
| Property | Value |
|---|---|
| BioDare ID | 13228298288040 |
| Author | Locke |
| Institution | University of Warwick |
| License |
Description
Literature data from: 'Extension of a genetic network model by iterative experimentation and mathematical analysis.' by: Locke.
First, heroic large-scale RNA profile screen by real-time qPCR in 96-well format, by Megan Southern in 2005. Data are noisy (especially ...
Submitter: Daniel Thedie
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Flis Anna
Study: Flis et al. (2015)
Q-PCR LD (12:12) 17C ELF3
| Property | Value |
|---|---|
| BioDare ID | 12962294335805 |
| Author | Aurora Pinas-Fernandez |
| Institution | University of Edinburgh |
| License |
Description
Seedlings were entrained for 7 days at 22C in 12:12 white light. Then shifted to 17C 12:12 white light. Samples were collected on the 6th day at 17 degrees.
Purpose
Experiment carry out to reparameterize the clock off Succrose
Comments
Sample time 24h. 24h sample ...
Submitter: Daniel Thedie
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Flis Anna
Study: Flis et al. (2015)
Q-PCR LD (12:12) 17C ELF4
| Property | Value |
|---|---|
| BioDare ID | 12962296599986 |
| Author | Aurora Pinas-Fernandez |
| Institution | University of Edinburgh |
| License | CC_BY |
Description
Seedlings were entrained for 7 days at 22C in 12:12 white light. Then shifted to 17C 12:12 white light. Samples were collected on the 6th day at 17 degrees.
Purpose
Experiment carry out to reparameterize the clock off Succrose
Comments
Sample time 24h. 24h ...
Submitter: Daniel Thedie
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Flis Anna
Study: Flis et al. (2015)
Q-PCR LD (12:12) 17C CAB2
| Property | Value |
|---|---|
| BioDare ID | 13228354371807 |
| Author | Aurora Pinas-Fernandez |
| Institution | University of Edinburgh |
| License | CC_BY |
Description
Seedlings were entrained for 7 days at 22C in 12:12 white light. Then shifted to 17C 12:12 white light. Samples were collected on the 6th day at 17 degrees.
Purpose
Experiment carry out to reparameterize the clock off Succrose
Comments
Sample time 24h. 24h ...
Submitter: Daniel Thedie
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Flis Anna
Study: Flis et al. (2015)
Q-PCR LD (12:12) 17C LUX
| Property | Value |
|---|---|
| BioDare ID | 12820610913763 |
| Author | Aurora Pinas-Fernandez |
| Institution | University of Edinburgh |
| License | CC_BY |
Description
Seedlings were entrained for 7 days at 22C in 12:12 white light. Then shifted to 17C 12:12 white light. Samples were collected on the 6th day at 17 degrees.
Purpose
Experiment carry out to reparameterize the clock off Succrose
Comments
Sample time 24h. 24h ...
Submitter: Daniel Thedie
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Flis Anna
Study: Flis et al. (2015)
Q-PCR LD (12:12) 17C GI
| Property | Value |
|---|---|
| BioDare ID | 12820606741450 |
| Author | Aurora Pinas-Fernandez |
| Institution | University of Edinburgh |
| License | CC_BY |
Description
Seedlings were entrained for 7 days at 22C in 12:12 white light. Then shifted to 17C 12:12 white light. Samples were collected on the 6th day at 17 degrees.
Purpose
Experiment carry out to reparameterize the clock off Succrose
Comments
Sample time 24h. 24h ...
Submitter: Daniel Thedie
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Flis Anna
Study: Flis et al. (2015)
Q-PCR LD (12:12) 17C TOC1
| Property | Value |
|---|---|
| BioDare ID | 12820611587928 |
| Author | Aurora Pinas-Fernandez |
| Institution | University of Edinburgh |
| License | CC_BY |
Description
Seedlings were entrained for 7 days at 22C in 12:12 white light. Then shifted to 17C 12:12 white light. Samples were collected on the 6th day at 17 degrees.
Purpose
Experiment carry out to reparameterize the clock off Succrose
Comments
Sample time 24h. 24h ...
Submitter: Daniel Thedie
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Flis Anna
Study: Flis et al. (2015)
Q-PCR LD (12:12) 17C PRR5
| Property | Value |
|---|---|
| BioDare ID | 12820611188065 |
| Author | Aurora Pinas-Fernandez |
| Institution | University of Edinburgh |
| License | CC_BY |
Description
Seedlings were entrained for 7 days at 22C in 12:12 white light. Then shifted to 17C 12:12 white light. Samples were collected on the 6th day at 17 degrees.
Purpose
Experiment carry out to reparameterize the clock off Succrose
Comments
Sample time 24h. 24h ...
Submitter: Daniel Thedie
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Flis Anna
Study: Flis et al. (2015)
Q-PCR LD (12:12) 17C PRR7
| Property | Value |
|---|---|
| BioDare ID | 12820611319996 |
| Author | Aurora Pinas-Fernandez |
| Institution | University of Edinburgh |
| License | CC_BY |
Description
Seedlings were entrained for 7 days at 22C in 12:12 white light. Then shifted to 17C 12:12 white light. Samples were collected on the 6th day at 17 degrees.
Purpose
Experiment carry out to reparameterize the clock off Succrose
Comments
Sample time 24h. 24h ...
Submitter: Daniel Thedie
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Flis Anna
Study: Flis et al. (2015)
Q-PCR LD (12:12) 17C PRR9
| Property | Value |
|---|---|
| BioDare ID | 12820610743262 |
| Author | Aurora Pinas-Fernandez |
| Institution | University of Edinburgh |
| License | CC_BY |
Description
Seedlings were entrained for 7 days at 22C in 12:12 white light. Then shifted to 17C 12:12 white light. Samples were collected on the 6th day at 17 degrees.
Purpose
Experiment carry out to reparameterize the clock off Succrose
Comments
Sample time 24h. 24h ...
Submitter: Daniel Thedie
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Flis Anna
Study: Flis et al. (2015)
Q-PCR LD (12:12) 17C CCA1
| Property | Value |
|---|---|
| BioDare ID | 12820611467827 |
| Author | Aurora Pinas-Fernandez |
| Institution | University of Edinburgh |
| License | CC_BY |
Description
Seedlings were entrained for 7 days at 22C in 12:12 white light. Then shifted to 17C 12:12 white light. Samples were collected on the 6th day at 17 degrees.
Purpose
Experiment carry out to reparameterize the clock off Succrose
Comments
Sample time 24h. 24h ...
Submitter: Daniel Thedie
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Flis Anna
Study: Flis et al. (2015)
TiMet WP1.1 WS seedling vs rosette
| Property | Value |
|---|---|
| BioDare ID | 2843 |
| Author | Anna Flis |
| Institution | MPI of Molecular Plant Physiology |
| License | CC_BY |
Description
Ws in biological duplicates, from diurnal cycle (12L/12D) with different plants age: 9 and 20 days. Numbers are in transcript copy per cell, obtained assuming 1 g FW contains 25000000 cells.
Purpose
Compare clock important genes transcript levels in seedlings ...
Submitter: Daniel Thedie
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Flis Anna
Study: Flis et al. (2015)
TiMet WP1.1 qRT-PCR elf3 LD
| Property | Value |
|---|---|
| BioDare ID | 2842 |
| Author | Anna Flis |
| Institution | MPI of Molecular Plant Physiology |
| License | CC_BY |
Description
WT and elf3-4 mutants, in biological duplicates, diurnal light, harvest every 2 hours Numbers are in transcript copy per cell, obtained assuming 1 g FW contains 25000000 cells.
Purpose
TiMet focuses on an important and general biological problem – how are plant ...
Submitter: Daniel Thedie
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Flis Anna
Study: Flis et al. (2015)
TiMet WP1.1 qRT-PCR LD to LL and LD
| Property | Value |
|---|---|
| BioDare ID | 2841 |
| Author | Anna Flis |
| Institution | MPI of Molecular Plant Physiology, Golm, Germany |
| License | CC_BY |
Description
2 WT (Col, Ws) and 5 clock mutants, in biological duplicates, from three conditions: Diurnal cycle (12L/12D), Extended night (DD), Extended light (LL), harvest every 2 hours. Numbers are in transcript copy per cell, obtained ...
Submitter: Daniel Thedie
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Flis Anna
Study: Flis et al. (2015)
Maps of cloned genes for rescuing selected clock mutants
Submitter: Uriel Urquiza-Garcia
Assay type: Transformation
Technology type: Technology Type
Investigation: Absolute units for proteins in Arabidopsis cloc...
The reporter fusion constructs expressing clock proteins fused to NanoLUC or firefly FLUC were transformed into the cognate, clock-mutant host plants. Each host also contained a transcriptional FLUC fusion that was used to score the circadian period of each transgenic line in constant light. Transformants that expressed a functionally normal level of clock protein were selected by choosing lines that complemented the mutant's period defect back close to the wild type period. Note that the reporters ...
Submitter: Andrew Millar
Assay type: Transcriptional reporter gene
Technology type: Imaging
Investigation: Absolute units for proteins in Arabidopsis cloc...
The reporter fusion constructs expressing clock proteins fused to NanoLUC or firefly FLUC were transformed into the cognate, clock-mutant host plants. Each host also contained a transcriptional FLUC fusion that was used to score the circadian period of each transgenic line in constant light. Transformants that expressed a functionally normal level of clock protein were selected by choosing lines that complemented the mutant's period defect back close to the wild type period. Note that the reporters ...
Submitter: Andrew Millar
Assay type: Transcriptional reporter gene
Technology type: Imaging
Investigation: Absolute units for proteins in Arabidopsis cloc...
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
Submitter: Andrew Millar
Assay type: Protein Quantification
Technology type: Imaging
Investigation: Absolute units for proteins in Arabidopsis cloc...
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.
Submitter: Andrew Millar
Assay type: Q_PCR
Technology type: qRT-PCR
Investigation: Absolute units for proteins in Arabidopsis cloc...
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.
Submitter: Andrew Millar
Assay type: Q_PCR
Technology type: qRT-PCR
Investigation: Absolute units for proteins in Arabidopsis cloc...
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.
Submitter: Andrew Millar
Assay type: Q_PCR
Technology type: qRT-PCR
Investigation: Absolute units for proteins in Arabidopsis cloc...
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.
Submitter: Andrew Millar
Assay type: Q_PCR
Technology type: qRT-PCR
Investigation: Absolute units for proteins in Arabidopsis cloc...
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 ...
Submitter: Uriel Urquiza-Garcia
Assay type: Protein Quantification
Technology type: Enzymatic Activity Measurements
Investigation: Absolute units for proteins in Arabidopsis cloc...
Leaf number at flowering data from literature for prr7 prr9 and Col wild-type plants under long photoperiods and short photoperiods
Submitter: Andrew Millar
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Prediction and analysis of phenotypes in the Ar...
Leaf number at flowering data from literature for prr7 prr9 and Col wild-type plants under long photoperiods and short photoperiods
Submitter: Andrew Millar
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Prediction and analysis of phenotypes in the Ar...
Seedling hypocotyl data from literature for prr7 prr9 and Col wild-type plants under various photoperiods
Submitter: Andrew Millar
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Prediction and analysis of phenotypes in the Ar...
