Assays
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SDtoLD 260410
| Property | Value |
|---|---|
| BioDare ID | 13982031569136 |
| Author | Laura Dixon |
| Institution | University of Edinburgh |
| License | CC_BY |
Description
pTOC plate 0683 pCAB plate0684 LHY plate 0685 control plate 0686 TOC plate0687 pLHY plate 0688
Purpose
Re-entrainment dynamics during the transition between light:dark cycles with different photoperiods, comparing Arabidopsis thaliana and Ostreococcus tauri. This expt in O. tauri ...
Submitter: Daniel Thedie
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Dixon Laura
Study: Dixon et al. (2014)
Edwards et al. (2010); WT in different light conditions.
| Property | Value |
|---|---|
| BioDare ID | 13227622661196 |
| Author | Edwards, K.D. |
| Institution | University of Edinburgh |
| License | CC_BY |
Description
Literature data from: 'Quantitative analysis of regulatory flexibility under changing environmental conditions.' by: Edwards, K.D..
Theory suggested that multiple loops contribute the flexibility for molecular rhythms to track multiple phases ...
Submitter: Daniel Thedie
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Kieron D Edwards
Study: Edwards et al. (2010)
Effects of GA on clock in WT and prr9prr7
| Property | Value |
|---|---|
| BioDare ID | 3838 |
| Author | Daniel Seaton |
| Institution | University of Edinburgh |
| License | CC_BY |
Description
Purpose
To test whether GA has any effect on circadian clock period in the WT, and whether this effect is altered in the prr9prr7 mutant.
Comments
Submitter: Daniel Thedie
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Chew Yin Hoon
Study: Chew et al. (2022)
Flis et al. TiMet clock gene comparison across photoperiods
| Property | Value |
|---|---|
| BioDare ID | 3967 |
| Author | Anna Flis |
| Institution | Max Planck Inst. Golm |
| License | CC_BY |
Description
Literature data from: 'Photoperiod-dependent changes in the phase of core clock transcripts and global transcriptional outputs at dawn and dusk in Arabidopsis' by: Anna Flis.
Col plants were grown in soil under 6, 8, 12 and 18h photoperiod for 21 days, and ...
Submitter: Daniel Thedie
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Flis Anna
Study: Flis et al. (2016)
Q-PCR LD (12:12) 17C LHY
| Property | Value |
|---|---|
| BioDare ID | 3492 |
| Author | Aurora Pinas-Fernandez |
| Institution | University of Edinburgh |
| License | CC_BY |
Description
Literature data from: 'Temp' by: Aurora Pinas-Fernandez.
Wild-type and clock-mutant 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, every 2h, for 24h.
Purpose
...
Submitter: Daniel Thedie
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Flis Anna
Study: Flis et al. (2015)
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)
The list of python packages used was obtained by typing inside the Docker image
pip list -- format==columns > python_packages_pip_installed.txt
This list the version of packages installed as we have observed issues related to the use of the most current version of some python packaged for example scipy
Submitter: Uriel Urquiza-Garcia
Biological problem addressed: Gene Expression
Investigation: Absolute units for proteins in Arabidopsis cloc...
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 promoter regions for clock genes that present a ChIP-seq signal were extracted from TAIR10 using costume python scripts using the gene list for Kamioka et al CCA1 or Daphne Ezer et al for LUX. The promoter was considered from the TSS of the gene until the annotated end of the upstream gene. Then, this region was scanned using the Energy Matrix derived using EMA working as a classifier for bound or unbound. After classification the calibrated PBM data calibrated using in vitro data was used ...
Submitter: Uriel Urquiza-Garcia
Biological problem addressed: Model Analysis 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...
This section contains the links to the tools used for reproducing the computational results presented in Urquiza-Garcia et al. 2022. This is required in particular because the SloppyCell model optimisation software is at some risk. Using Docker we can assure persistence for the computational environment that allows you to run SloppyCell.
The associated git repository can be found in https://hub.docker.com/r/uurquiza/urquiza2019a_tellurium_sloppycell/tags which can be cloned.
The docker image can ...
Submitter: Andrew Millar
Biological problem addressed: Model Analysis Type
Investigation: Absolute units for proteins in Arabidopsis cloc...
Analysis for inferring the number of molecules of clock proteins using recombinant NanoLUC
Submitter: Uriel Urquiza-Garcia
Biological problem addressed: Model Analysis Type
Investigation: Absolute units for proteins in Arabidopsis cloc...
This script take the scaling paramters using synthetic protein data updates model paramaters
Submitter: Uriel Urquiza-Garcia
Biological problem addressed: Model Analysis Type
Investigation: Absolute units for proteins in Arabidopsis cloc...
