Research Software Engineer in the Biological Research Data Management team (BioRDM) at the University of Edinburgh.
SEEK ID: https://fairdomhub.org/people/2847
Location:
United Kingdom
ORCID:
https://orcid.org/0000-0002-1352-7245
Joined: 19th May 2026
Expertise: Data Management, Python, R, Programming, microscopy, fluorescence protein fusions, Software Engineering
Tools: Data Management, Python, R, Fluorescence and confocal microscopy, Time-lapse fluorescence microscopy Flow cytometry, Fluorecence based reporter gene analyses/single cell analyses
Related items
- Programmes (1)
- Projects (2)
- Institutions (2)
- Investigations (26)
- Studies (32)
- Assays (173)
- Data files (1320)
- Publications (6)
The Centre for Engineering Biology is the University of Edinburgh's research organisation in interdisciplinary, Synthetic and Systems Biology, founded in 2023 as the successor to SynthSys, itself founded in 2012 as the successor to the Centre for Systems Biology at Edinburgh (CSBE). CSBE was newly founded in 2007. The Centre for Engineering Biology is a hub organisation that links across multiple, major funding awards, including an Engineering Biology Mission Hub, and EPSRC C-loop.
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, BioDare1
Web page: https://biology.ed.ac.uk/centre-engineering-biology
Experiment data previously hosted on the original version of BioDare (biodare.ed.ac.uk).
Programme: Centre for Engineering Biology (prev. SynthSys)
Public web page: Not specified
Organisms: Not specified
Andrew Millar's research group, University of Edinburgh
Programme: Centre for Engineering Biology (prev. SynthSys)
Public web page: http://www.amillar.org
Organisms: Escherichia coli, Arabidopsis thaliana, Ostreococcus tauri
ROR ID: Not specified
Department: Not specified
Country:
United Kingdom
City: Edinburgh
Web page: http://www.ed.ac.uk/
ROR ID: https://ror.org/https://ror.org/01nrxwf90
Department: School of Biological Sciences
Country:
United Kingdom
City: Edinburgh
Web page: https://www.ed.ac.uk
Collection of experiments created by Hibberd Victoria on the original BioDare and automatically transferred to FAIRDOM Hub.
Submitter: Daniel Thedie
Studies: Unpublished
Assays: cca1 lhy Long #1 CAB2 marker, cca1 lhy Long #1 CCA1 marker, cca1 lhy Long #1 CCR2 marker
Snapshots: No snapshots
Collection of experiments created by Kim, W.Y. on the original BioDare and automatically transferred to FAIRDOM Hub.
Submitter: Daniel Thedie
Studies: Unpublished
Assays: Kim et al. (2005); CO, FT; 16L:8D; WT, elf3, Kim2007 ZTL in blue light
Snapshots: No snapshots
Collection of experiments created by Sawa, M. on the original BioDare and automatically transferred to FAIRDOM Hub.
Snapshots: No snapshots
Collection of experiments created by Ito, S. on the original BioDare and automatically transferred to FAIRDOM Hub.
Submitter: Daniel Thedie
Studies: Unpublished
Assays: Ito 2007 wt LD PRR9 protein, Ito et al. (2008); GI, FKF1, CDF1, CO, FT; 16L:8D, 10L:14D; WT, toc1, pr...
Snapshots: No snapshots
Collection of experiments created by Niwa Y. on the original BioDare and automatically transferred to FAIRDOM Hub.
Submitter: Daniel Thedie
Studies: Unpublished
Assays: Niwa et al. (2007); GI, FKF1, CDF1, CO, FT mRNA; 10L:14D; WT, cca1;lhy, ...
Snapshots: No snapshots
Collection of experiments created by Ven Tee Wei on the original BioDare and automatically transferred to FAIRDOM Hub.
Snapshots: No snapshots
Collection of experiments created by Carrington Jamie on the original BioDare and automatically transferred to FAIRDOM Hub.
Snapshots: No snapshots
Collection of experiments created by Hodge Sarah on the original BioDare and automatically transferred to FAIRDOM Hub.
Snapshots: No snapshots
Collection of experiments created by Nakamichi Norihito on the original BioDare and automatically transferred to FAIRDOM Hub.
Submitter: Daniel Thedie
Studies: Unpublished
Assays: Nakamichi et al. (2007); FKF1, CDF1, CO, FT; 16L:8D, 10L:14D; WT, prr7;5..., Nakamichi_2010_draft: PRR9,PRR7,PRR5
Snapshots: No snapshots
Collection of experiments created by Somers DE on the original BioDare and automatically transferred to FAIRDOM Hub.
Snapshots: No snapshots
Collection of experiments created by Matsushika A on the original BioDare and automatically transferred to FAIRDOM Hub.
Snapshots: No snapshots
Collection of experiments created by Kim JY on the original BioDare and automatically transferred to FAIRDOM Hub.
Snapshots: No snapshots
Collection of experiments created by Song, Y.H. on the original BioDare and automatically transferred to FAIRDOM Hub.
Submitter: Daniel Thedie
Studies: Unpublished
Assays: Song et al. (2012); WT, fkf1, COox, COox;fkf1 and COoxCDF1ox in SD and L..., Song et al. (2012); WT, fkf1, COox, COox;fkf1 and COoxCDF1ox in SD and L...
Snapshots: No snapshots
Collection of experiments created by Hall A on the original BioDare and automatically transferred to FAIRDOM Hub.
Submitter: Daniel Thedie
Studies: Unpublished
Assays: The TIME FOR COFFEE Gene Maintains the Amplitude and Timing of Arabidops...
Snapshots: No snapshots
Collection of experiments created by Tsuyoshi Mizoguchi on the original BioDare and automatically transferred to FAIRDOM Hub.
Submitter: Daniel Thedie
Studies: Unpublished
Assays: Mizoguchi2002 LHY CCA1 redundancy, Mizoguchi2002_wt_gi_LL_LHY_CCA1, Mizoguchi2002_wt_lhycca1_16L8D_TOC1_GI_LHYL1_COL1, Mizoguchi_wt_lhycca1_LD_TOC1
Snapshots: No snapshots
Collection of experiments created by Helfer A on the original BioDare and automatically transferred to FAIRDOM Hub.
Snapshots: No snapshots
Collection of experiments created by Gould Peter on the original BioDare and automatically transferred to FAIRDOM Hub.
Submitter: Daniel Thedie
Studies: Unpublished
Assays: 12C BL-cryptochrome paper-rep1, 12C BL-cryptochrome paper-rep2, 12C BL-cryptochrome paper-rep3, 12C RBL-cryptochrome paper-rep1, 12C RBL-cryptochrome paper-rep2, 12C RBL-cryptochrome paper-rep3, 12C RL-cryptochrome paper-rep1, 12C RL-cryptochrome paper-rep2, 12C RL-cryptochrome paper-rep3, 12C RL-cryptochrome paper-rep4, 17C BL-cryptochrome paper-rep1, 17C BL-cryptochrome paper-rep2, 17C BL-cryptochrome paper-rep3, 17C RBL-cryptochrome paper-rep1, 17C RBL-cryptochrome paper-rep2, 17C RBL-cryptochrome paper-rep3, 17C RL-cryptochrome paper-rep1, 17C RL-cryptochrome paper-rep2, 17C RL-cryptochrome paper-rep3, 17C RL-cryptochrome paper-rep4, 27C BL-cryptochrome paper-rep1, 27C BL-cryptochrome paper-rep2, 27C BL-cryptochrome paper-rep3, 27C RBL-cryptochrome paper-rep1, 27C RBL-cryptochrome paper-rep2, 27C RBL-cryptochrome paper-rep3, 27C RL-cryptochrome paper-rep1, 27C RL-cryptochrome paper-rep2, 27C RL-cryptochrome paper-rep3, 27C RL-cryptochrome paper-rep4, LUC CAB CCR2 MUT BL30 2LD to 5LL 17C 05/10/11
Snapshots: No snapshots
Collection of experiments created by Kozma-Bognar Laszlo on the original BioDare and automatically transferred to FAIRDOM Hub.
Snapshots: No snapshots
Collection of experiments created by Thomson Adrian on the original BioDare and automatically transferred to FAIRDOM Hub.
Submitter: Daniel Thedie
Studies: Unpublished
Assays: AT0005 4x SD-3xLL, AT0006 4x LD-3xLL, AT0007 4x 03:21-LL, AT0009 4x 9:15-LL, AT0010 4x 15:9-LL, AT0011 4x 12:12-LL, AT0028: 4x 3:21-LL, AT0030: 4x 9:15-LL, AT0032: 4x15:9-LL, AT0033: 4x18:6-LL, AT0039: 6:18 then DD, AT0040: 4x 9:15-DD, AT0045: 4x15:9-DD, AT0046: 4x18:6-DD, AT0053: 4x3:21-LL, AT0055: 4x9:15-LL, AT0057: 4x12:12-LL, AT0059: 4x15:09-LL, AT0061: 4x18:6-LL, AT0062: 4x6:18-LL, AT0064: 4x3:21-LL, AT0066: 4x6:18-LL, AT0068: 4x3:21-DD, AT0070: 4x6:18-DD, AT0072: 4x9:15-DD, AT0073: 4x12:12-DD, AT0074: 4x15:9-DD, AT0075: 4x18:6-DD, AT0077: 4x3:21-DD, AT0079: 4x12:12-DD, AT0091: 4x12:12-LL
Snapshots: No snapshots
Collection of experiments created by Munoz Felipe on the original BioDare and automatically transferred to FAIRDOM Hub.
Submitter: Daniel Thedie
Studies: Unpublished
Assays: Analysis of Control Strains Neurospora crassa, Carbon Source, Controls, Entrainment Control Analysis
Snapshots: No snapshots
Unpublished
DOI: none
Submitter: Daniel Thedie
Investigation: Hibberd Victoria
Assays: cca1 lhy Long #1 CAB2 marker, cca1 lhy Long #1 CCA1 marker, cca1 lhy Long #1 CCR2 marker
Snapshots: No snapshots
Unpublished
DOI: none
Snapshots: No snapshots
Unpublished
DOI: none
Submitter: Daniel Thedie
Investigation: Kim, W.Y.
Assays: Kim et al. (2005); CO, FT; 16L:8D; WT, elf3, Kim2007 ZTL in blue light
Snapshots: No snapshots
Unpublished
DOI: none
Snapshots: No snapshots
Unpublished
DOI: none
Submitter: Daniel Thedie
Investigation: Ito, S.
Assays: Ito 2007 wt LD PRR9 protein, Ito et al. (2008); GI, FKF1, CDF1, CO, FT; 16L:8D, 10L:14D; WT, toc1, pr...
Snapshots: No snapshots
Unpublished
DOI: none
Submitter: Daniel Thedie
Investigation: Niwa Y.
Assays: Niwa et al. (2007); GI, FKF1, CDF1, CO, FT mRNA; 10L:14D; WT, cca1;lhy, ...
Snapshots: No snapshots
Unpublished
DOI: none
Snapshots: No snapshots
Unpublished
DOI: none
Snapshots: No snapshots
Unpublished
DOI: none
Snapshots: No snapshots
Unpublished
DOI: none
Submitter: Daniel Thedie
Investigation: Nakamichi Norihito
Assays: Nakamichi et al. (2007); FKF1, CDF1, CO, FT; 16L:8D, 10L:14D; WT, prr7;5..., Nakamichi_2010_draft: PRR9,PRR7,PRR5
Snapshots: No snapshots
Unpublished
DOI: none
Snapshots: No snapshots
Unpublished
DOI: none
Snapshots: No snapshots
Unpublished
DOI: none
Snapshots: No snapshots
Unpublished
DOI: none
Submitter: Daniel Thedie
Investigation: Song, Y.H.
Assays: Song et al. (2012); WT, fkf1, COox, COox;fkf1 and COoxCDF1ox in SD and L..., Song et al. (2012); WT, fkf1, COox, COox;fkf1 and COoxCDF1ox in SD and L...
Snapshots: No snapshots
Unpublished
DOI: none
Submitter: Daniel Thedie
Investigation: Hall A
Assays: The TIME FOR COFFEE Gene Maintains the Amplitude and Timing of Arabidops...
Snapshots: No snapshots
Unpublished
DOI: none
Submitter: Daniel Thedie
Investigation: Kieron D Edwards
Assays: FLOWERING LOCUS C Controls Temperature Response of the Arabidopsis Clock
Snapshots: No snapshots
Unpublished
DOI: none
Submitter: Daniel Thedie
Investigation: Tsuyoshi Mizoguchi
Assays: Mizoguchi2002 LHY CCA1 redundancy, Mizoguchi2002_wt_gi_LL_LHY_CCA1, Mizoguchi2002_wt_lhycca1_16L8D_TOC1_GI_LHYL1_COL1, Mizoguchi_wt_lhycca1_LD_TOC1
Snapshots: No snapshots
Unpublished
DOI: none
Snapshots: No snapshots
Unpublished
DOI: none
Submitter: Daniel Thedie
Investigation: Gould Peter
Assays: 12C BL-cryptochrome paper-rep1, 12C BL-cryptochrome paper-rep2, 12C BL-cryptochrome paper-rep3, 12C RBL-cryptochrome paper-rep1, 12C RBL-cryptochrome paper-rep2, 12C RBL-cryptochrome paper-rep3, 12C RL-cryptochrome paper-rep1, 12C RL-cryptochrome paper-rep2, 12C RL-cryptochrome paper-rep3, 12C RL-cryptochrome paper-rep4, 17C BL-cryptochrome paper-rep1, 17C BL-cryptochrome paper-rep2, 17C BL-cryptochrome paper-rep3, 17C RBL-cryptochrome paper-rep1, 17C RBL-cryptochrome paper-rep2, 17C RBL-cryptochrome paper-rep3, 17C RL-cryptochrome paper-rep1, 17C RL-cryptochrome paper-rep2, 17C RL-cryptochrome paper-rep3, 17C RL-cryptochrome paper-rep4, 27C BL-cryptochrome paper-rep1, 27C BL-cryptochrome paper-rep2, 27C BL-cryptochrome paper-rep3, 27C RBL-cryptochrome paper-rep1, 27C RBL-cryptochrome paper-rep2, 27C RBL-cryptochrome paper-rep3, 27C RL-cryptochrome paper-rep1, 27C RL-cryptochrome paper-rep2, 27C RL-cryptochrome paper-rep3, 27C RL-cryptochrome paper-rep4, LUC CAB CCR2 MUT BL30 2LD to 5LL 17C 05/10/11
Snapshots: No snapshots
Unpublished
DOI: none
Snapshots: No snapshots
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)
Organisms: Arabidopsis thaliana
SOPs: No SOPs
Data files: BioDare_metadata, Primers_TiMet_AnnaFlis2013, RNA LD to Both LL and DD, Readme, Sample_list
Snapshots: No snapshots
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)
Organisms: Arabidopsis thaliana
SOPs: No SOPs
Data files: BioDare_metadata, Primers_TiMet_AnnaFlis2013, RNA ELF3 LD, Readme, Sample_list
Snapshots: No snapshots
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)
Organisms: Arabidopsis thaliana
SOPs: No SOPs
Data files: BioDare_metadata, Primers_TiMet_AnnaFlis2013, RNA LD seedling vs rosette, Readme, Sample_list
Snapshots: No snapshots
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)
Organisms: Arabidopsis thaliana
SOPs: No SOPs
Data files: 17C-LD-OS-wt-cca1, 17C-LD-OS-wt-lhy21, 17C-LD-OS-wt-prr-gi-lc-toc.1, 2011-12 CCA1 LD, BioDare_metadata, Plt15&16-CCA1-190710-Prog, Plt18-CCA1-270710-Prog, Plt19&20-CCA1-020810-Prog, Plt21-CCA1-180810-Prog, Readme, STANDARD_DATAFILE, STANDARD_RAWDATAFILE, Sample_list
Snapshots: No snapshots
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)
Organisms: Arabidopsis thaliana
SOPs: No SOPs
Data files: 17C-LD-OS-lhyccagi, 17C-LD-OS-wt-cca1, 17C-LD-OS-wt-lhy21, 17C-LD-OS-wt-prr-gi-lc-toc.1, 2011-12 PRR9 LD.2, BioDare_metadata, Plt15&16-PRR9-190710-Prog, Plt17-PRR9-260710-Prog, Plt18-PRR9-270710-Prog, Plt19&20-PRR9-020810-Prog, Readme, STANDARD_DATAFILE.2, STANDARD_RAWDATAFILE.2, Sample_list
Snapshots: No snapshots
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)
Organisms: Arabidopsis thaliana
SOPs: No SOPs
Data files: 17C-LD-OS-lhyccagi, 17C-LD-OS-wt-cca1, 17C-LD-OS-wt-lhy21, 17C-LD-OS-wt-prr-gi-lc-toc.1, 2011-12 PRR7 LD, BioDare_metadata, Plt15&16-PRR7-190710-Prog1, Plt17-PRR7-260710-Prog, Plt18-PRR7-080810-Prog, Plt19&20-PRR7-050810-Prog, Plt21-PRR7-190810-Prog, Readme, STANDARD_DATAFILE, STANDARD_RAWDATAFILE, Sample_list
Snapshots: No snapshots
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)
Organisms: Arabidopsis thaliana
SOPs: No SOPs
Data files: 17C-LD-OS-lhyccagi, 17C-LD-OS-prr7-3, 17C-LD-OS-wt-cca1, 17C-LD-OS-wt-lhy21, 17C-LD-OS-wt-prr-gi-lc-toc.1, 2011-12 PRR5 LD, BioDare_metadata, Plt15&16-PRR5-200710-Prog, Plt17-PRR5-260710-Prog, Plt18-PRR5-270710-Prog, Plt19&20-PRR5-020810-Prog, Plt21-PRR5-180810-Prog, Readme, STANDARD_DATAFILE, STANDARD_RAWDATAFILE, Sample_list
Snapshots: No snapshots
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)
Organisms: Arabidopsis thaliana
SOPs: No SOPs
Data files: 17C-LD-OS-lhyccagi, 17C-LD-OS-prr7-3, 17C-LD-OS-wt-cca1, 17C-LD-OS-wt-lhy21, 17C-LD-OS-wt-prr-gi-lc-toc.1, 2011-12 TOC1 LD, BioDare_metadata, Plt15&16-TOC-200710-Prog.1, Plt15&16-TOC-200710-Prog.1, Plt17-TOC-260710-Prog, Plt18-TOC-280710-Prog, Plt19&20-TOC-090810-Prog, Plt21-TOC-180810-Prog, Readme, STANDARD_DATAFILE, STANDARD_RAWDATAFILE, Sample_list
Snapshots: No snapshots
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)
Organisms: Arabidopsis thaliana
SOPs: No SOPs
Data files: 17C-LD-OS-lhyccagi, 17C-LD-OS-prr7-3, 17C-LD-OS-wt-cca1, 17C-LD-OS-wt-lhy21, 17C-LD-OS-wt-prr-gi-lc-toc.1, 2011-12 GI LD.2, BioDare_metadata, Plate15&16-GI-200710-Prog, Plate17-GI-260710-Prog, Plate18-GI-280710-Prog, Plate19&21-GI-090810-Prog, Plate21-GI-180810-Prog, Readme, STANDARD_DATAFILE.2, STANDARD_RAWDATAFILE.2, Sample_list
Snapshots: No snapshots
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)
Organisms: Arabidopsis thaliana
SOPs: No SOPs
Data files: 17C-LD-OS-lhyccagi, 17C-LD-OS-prr7-3, 17C-LD-OS-wt-cca1, 17C-LD-OS-wt-lhy21, 17C-LD-OS-wt-prr-gi-lc-toc.1, 2011-12 LUX LD.1, BioDare_metadata, Plt15&16-lux-200710-Prog, Plt17-lux-260710-Prog, Plt18-lux-280710-Prog, Plt19&20-lux-120810-Prog, Plt21-lux-190810-Prog, Readme, STANDARD_DATAFILE.1, STANDARD_RAWDATAFILE.1, Sample_list
Snapshots: No snapshots
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)
Organisms: Arabidopsis thaliana
SOPs: No SOPs
Data files: 2011-12 CAB2 LD, BioDare_metadata, Readme, STANDARD_DATAFILE, STANDARD_RAWDATAFILE, Sample_list
Snapshots: No snapshots
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)
Organisms: Arabidopsis thaliana
SOPs: No SOPs
Data files: 17C-LD-OffSuc-ELF4, 2011-12 ELF4 LD, BioDare_metadata, Readme, STANDARD_DATAFILE, STANDARD_RAWDATAFILE, Sample_list
Snapshots: No snapshots
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)
Organisms: Arabidopsis thaliana
SOPs: No SOPs
Data files: 17C-LD-OffSuc-ELF3(JF261-262), 17C-LD-OffSuc-ELF3(JF588-589), 2011-12 ELF3 LD Primers 260-261.1, BioDare_metadata, Readme, STANDARD_DATAFILE.1, STANDARD_RAWDATAFILE.1, Sample_list
Snapshots: No snapshots
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)
Organisms: Arabidopsis thaliana
SOPs: No SOPs
Data files: 7.7 timecourse 1&2 reformatted for BioDare 2 De..., BioDare_metadata, Expt1 for BioDare upload.2, MMS qRT-PCR primers and toc1-2 control, Readme, STANDARD_DATAFILE.2, STANDARD_RAWDATAFILE.2, Sample_list
Snapshots: No snapshots
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)
Organisms: Arabidopsis thaliana
SOPs: No SOPs
Data files: BioDare_metadata, Expt2 for BioDare upload.1, MMS qRT-PCR primers and toc1-2 control, Readme, STANDARD_DATAFILE.1, STANDARD_RAWDATAFILE.1, Sample_list
Snapshots: No snapshots
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)
Organisms: Arabidopsis thaliana
SOPs: No SOPs
Data files: BioDare_metadata, Expt3 for BioDare upload.1, MMS qRT-PCR primers and toc1-2 control, Readme, STANDARD_DATAFILE.1, STANDARD_RAWDATAFILE.1, Sample_list
Snapshots: No snapshots
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)
Organisms: Arabidopsis thaliana
SOPs: No SOPs
Data files: BioDare_metadata, Expt4 for BioDare upload, MMS qRT-PCR primers and toc1-2 control, Readme, STANDARD_DATAFILE, STANDARD_RAWDATAFILE, Sample_list
Snapshots: No snapshots
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)
Organisms: Arabidopsis thaliana
SOPs: No SOPs
Data files: BioDare_metadata, McWatters RNA data, McWatters RNA data.1, Readme, Sample_list
Snapshots: No snapshots
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)
Organisms: Arabidopsis thaliana
SOPs: No SOPs
Data files: 17C-LD-0Suc LHY by Aurora, Andrew's edit, 17C-LD-0Suc LHY by Aurora, Andrew's edit for Bi..., BioDare_metadata, Readme, Sample_list
Snapshots: No snapshots
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)
Organisms: Arabidopsis thaliana
SOPs: No SOPs
Data files: BioDare_metadata, Readme, Sample_list, TiMet 1.2 - Photoperiod exp - transcripts AJMv2...
Snapshots: No snapshots
Plate1118 #1-CCR2 for BioDare (from BioDare)
Creator: Victoria Hibberd
Submitter: Daniel Thedie
List of samples used in the assay (extracted from original BioDare metadata and converted to csv)
Creator: Victoria Hibberd
Submitter: Daniel Thedie
Original BioDare metadata, converted to json format
Creator: Victoria Hibberd
Submitter: Daniel Thedie
Readme file
Creator: Victoria Hibberd
Submitter: Daniel Thedie
Plate1117 #1-CAB2 for BioDare (from BioDare)
Creator: Victoria Hibberd
Submitter: Daniel Thedie
List of samples used in the assay (extracted from original BioDare metadata and converted to csv)
Creator: Victoria Hibberd
Submitter: Daniel Thedie
Original BioDare metadata, converted to json format
Creator: Victoria Hibberd
Submitter: Daniel Thedie
Readme file
Creator: Victoria Hibberd
Submitter: Daniel Thedie
Plate1116 #1-CCA1 for BioDare.1 (from BioDare)
Creator: Victoria Hibberd
Submitter: Daniel Thedie
List of samples used in the assay (extracted from original BioDare metadata and converted to csv)
Creator: Victoria Hibberd
Submitter: Daniel Thedie
Original BioDare metadata, converted to json format
Creator: Victoria Hibberd
Submitter: Daniel Thedie
Readme file
Creator: Victoria Hibberd
Submitter: Daniel Thedie
Kim_Nature07_suppl_tex (from BioDare)
Creator: Kim WY
Submitter: Daniel Thedie
Kim_Nature07 (from BioDare)
Creator: Kim WY
Submitter: Daniel Thedie
STANDARD_DATAFILE (from BioDare)
Creator: Kim WY
Submitter: Daniel Thedie
STANDARD_RAWDATAFILE (from BioDare)
Creator: Kim WY
Submitter: Daniel Thedie
Kim2007_wt_LD_TOC1_GI_ZTL_proteins (from BioDare)
Creator: Kim WY
Submitter: Daniel Thedie
List of samples used in the assay (extracted from original BioDare metadata and converted to csv)
Creator: Kim WY
Submitter: Daniel Thedie
Original BioDare metadata, converted to json format
Creator: Kim WY
Submitter: Daniel Thedie
Readme file
Creator: Kim WY
Submitter: Daniel Thedie
Abstract (Expand)
Authors: Yin Hoon Chew, Daniel D Seaton, Virginie Mengin, Anna Flis, Sam T Mugford, Gavin M George, Michael Moulin, Alastair Hume, Samuel C Zeeman, Teresa B Fitzpatrick, Alison M Smith, Mark Stitt, Andrew J Millar
Date Published: 30th May 2022
Publication Type: Journal Article
DOI: 10.1093/insilicoplants/diac010
Citation: in silico Plants 4(2):diac010.
Abstract (Expand)
Authors: Anna Flis, Ronan Sulpice, Daniel D. Seaton, Alexander A. Ivakov, Magda Liput, Christin Abel, Andrew J. Millar, Mark Stitt
Date Published: 15th Jul 2016
Publication Type: Journal Article
DOI: 10.1111/pce.12754
Citation: Plant Cell & Environment 39(9):1955-1981.
Abstract (Expand)
Authors: Andrew J. Millar, Jamie T. Carrington, Wei Ven Tee, Sarah K. Hodge
Date Published: 17th Dec 2015
Publication Type: Preprint
DOI: 10.1101/034629
Citation: Preprint. https://doi.org/10.1101/034629
Abstract (Expand)
Authors: Laura E. Dixon, Sarah K. Hodge, Gerben van Ooijen, Carl Troein, Ozgur E. Akman, Andrew J. Millar
Date Published: 20th May 2014
Publication Type: Journal Article
DOI: 10.1111/nph.12853
Citation: New Phytologist 203(2):568-577.
Abstract (Expand)
Authors: Bénédicte Wenden, David L. K. Toner, Sarah K. Hodge, Ramon Grima, Andrew J. Millar
Date Published: 10th Apr 2012
Publication Type: Journal Article
Citation: Proc. Natl. Acad. Sci. U.S.A. 109(17):6757-6762.
Abstract
Authors: Kieron D Edwards, Ozgur E Akman, Kirsten Knox, Peter J Lumsden, Adrian W Thomson, Paul E Brown, Alexandra Pokhilko, Laszlo Kozma‐Bognar, Ferenc Nagy, David A Rand, Andrew J Millar
Date Published: 2nd Nov 2010
Publication Type: Journal Article
DOI: 10.1038/msb.2010.81
Citation: Mol Syst Biol 6(1):MSB201081.
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