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BioDare_metadata.json
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},
"light_conditions": {
"light_channel": {
"spectrum": "white",
"intensity": "50",
"source": "tube",
"diurnal_light": {
"cycle_length": "24",
"start_time": "0",
"duration": "12"
}
}
},
"pH": {
"settings": {
"const": {
"base_value": "5.8"
}
}
}
},
{
"name": "WC 27oC:12oC in LL",
"medium": "Agar 1.5% MS 1 3% Sucrose",
"stratification": "2 days at 4C",
"growth_space": "Sanyo MLR-350 chamber",
"duration": "7",
"comment": "Actually less agar (0.8-1%) according to the paper",
"temperature_conditions": {
"diurnal_temp": {
"cycle_length": "24",
"base_temp": "12",
"second_temp": "27",
"start_time": "0",
"duration": "12"
}
},
"light_conditions": {
"light_channel": {
"spectrum": "white",
"intensity": "50",
"source": "tube",
"constant_light": {
"cycle_length": "24"
}
}
},
"pH": {
"settings": {
"const": {
"base_value": "5.8"
}
}
}
}
],
"experimental_condition": [
{
"name": "LD 12:12",
"medium": "Agar 1.5% MS 1 3% Sucrose",
"growth_space": "Sanyo MLR-350",
"duration": "1",
"comment": "same as entraining condition",
"temperature_conditions": {
"constant_temp": {
"cycle_length": "24",
"base_temp": "20"
}
},
"light_conditions": {
"light_channel": {
"spectrum": "white",
"intensity": "50",
"source": "tube",
"diurnal_light": {
"cycle_length": "24",
"start_time": "0",
"duration": "12"
}
}
},
"pH": {
"settings": {
"const": {
"base_value": "5.8"
}
}
}
},
{
"name": "WC 27oC:12oC in LL",
"medium": "Agar 1.5% MS 1 3% Sucrose",
"duration": "1",
"comment": "same as entraining condition",
"temperature_conditions": {
"diurnal_temp": {
"cycle_length": "24",
"base_temp": "12",
"second_temp": "27",
"start_time": "0",
"duration": "12"
}
},
"light_conditions": {
"light_channel": {
"spectrum": "white",
"intensity": "50",
"source": "tube",
"constant_light": {
"cycle_length": "24"
}
}
},
"pH": {
"settings": {
"const": {
"base_value": "5.8"
}
}
}
}
],
"measurement": {
"technique": "RT-PCR",
"equipment": "SYBR Green PCR Master mix (Applied Biosystems [4309155]) using an Applied Biosystems Prism-7300.",
"description": "From Knight et al. 2008: Samples of 20 to 30 seedlings were collected every 3 h and snap-frozen in liquid nitrogen; the first sample was collected at subjective dawn on day 14, after 24 h in LL. Similarly, for analysis of flowering time gene expression, seedlings were grown on plates as described above in LD 16:8 photoperiods for 13 d and sampled every 2 h on day 14 in a free-running cycle. RNA was extracted (RNeasy kit, Qiagen [74904] with additional DNAse digestion) from each sample and cDNA synthesized (Taq-Man, Applied Biosystems [N808-0234] reverse transcriptase kit) for each time point. Real-time reverse transcription (RT)-PCR was carried out in triplicate with SYBR Green PCR Master mix (Applied Biosystems [4309155]) using an Applied Biosystems Prism-7300. Levels of specific mRNA and βTUBULIN4 (βTUB4) controls were calculated by the standard curve method (Applied Biosystems user bulletin 2); the relative expression (arbitrary units) of each gene of interest was obtained by dividing by contemporaneous βTUB4 expression. No-RT and no-template controls were included as negative controls for each set of reactions. Two or three independent biological repeats gave similar results."
},
"sample_preparation": {
"method": "From Knight et al. 2008: Samples of 20 to 30 seedlings were collected every 3 h and snap-frozen in liquid nitrogen; the first sample was collected at subjective dawn on day 14, after 24 h in LL. Similarly, for analysis of flowering time gene expression, seedlings were grown on plates as described above in LD 16:8 photoperiods for 13 d and sampled every 2 h on day 14 in a free-running cycle. RNA was extracted (RNeasy kit, Qiagen [74904] with additional DNAse digestion) from each sample and cDNA synthesized (Taq-Man, Applied Biosystems [N808-0234] reverse transcriptase kit) for each time point."
},
"samples": {
"sample": [
{
"sample_id": "1",
"sample_type": "group of seedlings",
"origin": "group of seedlings",
"growth_stage": "seedling",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "Wild Type"
},
"marker": "CCA1",
"growth_cond_name": "LD12:12",
"experiment_cond_name": "LD 12:12"
},
{
"sample_id": "2",
"sample_type": "group of seedlings",
"origin": "group of seedlings",
"growth_stage": "seedling",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "Wild Type"
},
"marker": "CCA1",
"growth_cond_name": "LD12:12",
"experiment_cond_name": "LD 12:12"
},
{
"sample_id": "3",
"sample_type": "group of seedlings",
"origin": "group of seedlings",
"growth_stage": "seedling",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "Wild Type"
},
"marker": "TOC1",
"growth_cond_name": "LD12:12",
"experiment_cond_name": "LD 12:12"
},
{
"sample_id": "4",
"sample_type": "group of seedlings",
"origin": "group of seedlings",
"growth_stage": "seedling",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "Wild Type"
},
"marker": "TOC1",
"growth_cond_name": "LD12:12",
"experiment_cond_name": "LD 12:12"
},
{
"sample_id": "5",
"sample_type": "group of seedlings",
"origin": "group of seedlings",
"growth_stage": "seedling",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "Wild Type"
},
"marker": "CCA1",
"growth_cond_name": "WC 27oC:12oC in LL",
"experiment_cond_name": "WC 27oC:12oC in LL"
},
{
"sample_id": "6",
"sample_type": "group of seedlings",
"origin": "group of seedlings",
"growth_stage": "seedling",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "Wild Type"
},
"marker": "CCA1",
"growth_cond_name": "WC 27oC:12oC in LL",
"experiment_cond_name": "WC 27oC:12oC in LL"
},
{
"sample_id": "7",
"sample_type": "group of seedlings",
"origin": "group of seedlings",
"growth_stage": "seedling",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "Wild Type"
},
"marker": "TOC1",
"growth_cond_name": "WC 27oC:12oC in LL",
"experiment_cond_name": "WC 27oC:12oC in LL"
},
{
"sample_id": "8",
"sample_type": "group of seedlings",
"origin": "group of seedlings",
"growth_stage": "seedling",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "Wild Type"
},
"marker": "TOC1",
"growth_cond_name": "WC 27oC:12oC in LL",
"experiment_cond_name": "WC 27oC:12oC in LL"
}
]
}
},
"biblio": {
"principal": "Harriet G. McWatters",
"institution": "University of Oxford",
"curator": "Andrew J. Millar"
}
}
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Created: 18th Jun 2026 at 12:46
Last updated: 18th Jun 2026 at 12:46
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Version 1 (earliest) Created 18th Jun 2026 at 12:46 by Daniel Thedie
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https://orcid.org/0000-0002-1352-7245Research Software Engineer in the Biological Research Data Management team (BioRDM) at the University of Edinburgh.
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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
Advanced Projects list for this Data file with search and filtering
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
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Collection of experiments created by Flis Anna on the original BioDare and automatically transferred to FAIRDOM Hub.
Submitter: Daniel Thedie
Studies: Flis et al. (2015), Flis et al. (2016), Unpublished
Assays: Clock gene RNAs under RD-RR in clock mutants, expt 1, Clock gene RNAs under RD-RR in clock mutants, expt 2, Clock gene RNAs under RD-RR in clock mutants, expt 3, Clock gene RNAs under RD-RR in clock mutants, expt 4, Flis et al. TiMet clock gene comparison across photoperiods, McWatters A.t. Col-0 WT clock RNA timeseries, Q-PCR LD (12:12) 17C CAB2, Q-PCR LD (12:12) 17C CCA1, Q-PCR LD (12:12) 17C ELF3, Q-PCR LD (12:12) 17C ELF4, Q-PCR LD (12:12) 17C GI, Q-PCR LD (12:12) 17C LHY, Q-PCR LD (12:12) 17C LUX, Q-PCR LD (12:12) 17C PRR5, Q-PCR LD (12:12) 17C PRR7, Q-PCR LD (12:12) 17C PRR9, Q-PCR LD (12:12) 17C TOC1, TiMet WP1.1 WS seedling vs rosette, TiMet WP1.1 qRT-PCR LD to LL and LD, TiMet WP1.1 qRT-PCR elf3 LD
Advanced Studies list for this Data file with search and filtering
Defining the robust behaviour of the plant clock gene circuit with absolute RNA timeseries and open infrastructure
Flis et al. (2015)
DOI: 10.1098/rsob.150042
Submitter: Daniel Thedie
Investigation: Flis Anna
Assays: Clock gene RNAs under RD-RR in clock mutants, expt 1, Clock gene RNAs under RD-RR in clock mutants, expt 2, Clock gene RNAs under RD-RR in clock mutants, expt 3, Clock gene RNAs under RD-RR in clock mutants, expt 4, McWatters A.t. Col-0 WT clock RNA timeseries, Q-PCR LD (12:12) 17C CAB2, Q-PCR LD (12:12) 17C CCA1, Q-PCR LD (12:12) 17C ELF3, Q-PCR LD (12:12) 17C ELF4, Q-PCR LD (12:12) 17C GI, Q-PCR LD (12:12) 17C LHY, Q-PCR LD (12:12) 17C LUX, Q-PCR LD (12:12) 17C PRR5, Q-PCR LD (12:12) 17C PRR7, Q-PCR LD (12:12) 17C PRR9, Q-PCR LD (12:12) 17C TOC1, TiMet WP1.1 WS seedling vs rosette, TiMet WP1.1 qRT-PCR LD to LL and LD, TiMet WP1.1 qRT-PCR elf3 LD
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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)
