BioDare_metadata Version 1
Original BioDare metadata, converted to json format
SEEK ID: https://fairdomhub.org/data_files/9145?version=1
Filename:
BioDare_metadata.json
Format: JSON document
Size: 63 KB
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},
{
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},
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"experiment_cond_name": "FR experimental conditions",
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},
{
"sample_id": "26",
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},
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},
{
"sample_id": "27",
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},
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},
{
"sample_id": "28",
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},
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},
{
"sample_id": "29",
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},
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},
{
"sample_id": "30",
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},
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},
{
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},
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},
{
"sample_id": "32",
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},
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},
{
"sample_id": "33",
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},
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},
{
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},
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},
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},
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},
{
"sample_id": "36",
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"species": "Arabidopsis thaliana",
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},
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},
{
"sample_id": "37",
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},
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},
{
"sample_id": "38",
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},
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},
{
"sample_id": "39",
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},
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},
{
"sample_id": "40",
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"species": "Arabidopsis thaliana",
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"genotype": "elf3-4",
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},
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},
{
"sample_id": "41",
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},
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},
{
"sample_id": "42",
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"species": "Arabidopsis thaliana",
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},
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"ignored": "false"
},
{
"sample_id": "43",
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"species": "Arabidopsis thaliana",
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},
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},
{
"sample_id": "44",
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},
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},
{
"sample_id": "45",
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},
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},
{
"sample_id": "46",
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"species": "Arabidopsis thaliana",
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},
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}
]
}
},
"pedro": {
"@xmlns:xsi": "http://www.w3.org/2001/XMLSchema-instance",
"@xsi:schemaLocation": "/Z:/communal/DataDescription/models/aluc_model/model/luc_model.xsd",
"id": "12730680847492",
"status": "terminated",
"name": "Clock genes under Far Red light - 6",
"purpose": "Analysis of CCA1 and CCR2 in phyb, elf3-4, elf4-1 and toc1-4 mutants under strict FR light treatment",
"description": "Seedlings receive 3hrs of white light to germinate, then are entrained under 12/12 FR/D cycles for 3 days, sprayed, and imaged 24hrs after under 1 FR/D cycle, 3 days of continuous FR and 48h of DD",
"comments": "Extremely bad contamination (fungus and bacteria)",
"provenance": {
"site": "Edinburgh",
"author": "Benedicte Wenden",
"start_date": "2009-03-13"
},
"growth_condition": {
"name": "FR growth conditions",
"medium": "Agar 1.2% MS 0.5;Agar 1.5% MS 1 3% Sucrose",
"incubation": "4 days at 4C",
"growth_space": "Percival + LED",
"duration": "4",
"temperature_conditions": {
"constant_temp": {
"cycle_length": "24",
"base_temp": "22"
}
},
"light_conditions": {
"light_channel": [
{
"spectrum": "infra red",
"intensity": "2",
"source": "LED",
"light_complex_settings": {
"light_days": [
{
"start_day": "1",
"duration": "1",
"constant_dark": {
"cycle_length": "24"
}
},
{
"start_day": "2",
"duration": "3",
"diurnal_light": {
"cycle_length": "24",
"start_time": "0",
"duration": "12"
}
}
]
}
},
{
"spectrum": "white",
"intensity": "80",
"source": "LED",
"light_complex_settings": {
"light_days": [
{
"start_day": "1",
"duration": "1",
"diurnal_light": {
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"start_time": "0",
"duration": "3"
}
},
{
"start_day": "2",
"duration": "3",
"constant_dark": {
"cycle_length": "24"
}
}
]
}
}
]
}
},
"experimental_condition": {
"name": "FR experimental conditions",
"medium": "Agar 1.2% MS 0.5;Agar 1.5% MS 1 3% Sucrose",
"growth_space": "Percival + LED",
"duration": "6",
"exp_time_zero": "0",
"temperature_conditions": {
"constant_temp": {
"cycle_length": "24",
"base_temp": "22"
}
},
"light_conditions": {
"light_channel": {
"spectrum": "infra red",
"intensity": "2",
"source": "LED",
"light_complex_settings": {
"light_days": [
{
"start_day": "1",
"duration": "1",
"diurnal_light": {
"cycle_length": "24",
"start_time": "0",
"duration": "12"
}
},
{
"start_day": "2",
"duration": "3",
"constant_light": {
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}
},
{
"start_day": "5",
"duration": "2",
"constant_dark": {
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}
}
]
}
}
}
},
"measurement": {
"technique": "Luciferase luminescence",
"equipment": "HAM 3",
"description": "A picture every 1.5 hr"
},
"sample_preparation": {
"method": "Plates were sprayed with luciferin 24 hrs before measurement"
},
"samples": {
"sample": [
{
"sample_id": "1",
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"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
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"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Img Background",
"line": "1",
"provenance": "Robust Stock"
},
"marker": "ARR3"
},
{
"sample_id": "2",
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"growth_stage": "seedling",
"age": "7",
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"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "W1",
"provenance": "Robust Stock"
},
"marker": "CCA1"
},
{
"sample_id": "3",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "W1",
"provenance": "Robust Stock"
},
"marker": "CCA1"
},
{
"sample_id": "4",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
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"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "W1",
"provenance": "Robust Stock"
},
"marker": "CCA1"
},
{
"sample_id": "5",
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},
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},
{
"sample_id": "6",
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"growth_stage": "seedling",
"age": "7",
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"species": "Arabidopsis thaliana",
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"line": "W1",
"provenance": "Robust Stock"
},
"marker": "CCA1"
},
{
"sample_id": "7",
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"age": "7",
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"species": "Arabidopsis thaliana",
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},
"marker": "CCA1"
},
{
"sample_id": "8",
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"growth_stage": "seedling",
"age": "7",
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"species": "Arabidopsis thaliana",
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"genotype": "Wild Type",
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"provenance": "Robust Stock"
},
"marker": "CCA1"
},
{
"sample_id": "9",
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"species": "Arabidopsis thaliana",
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},
"marker": "CCA1"
},
{
"sample_id": "10",
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"age": "7",
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"species": "Arabidopsis thaliana",
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},
"marker": "CCA1"
},
{
"sample_id": "11",
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"origin": "seedling",
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"age": "7",
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"species": "Arabidopsis thaliana",
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"genotype": "Wild Type",
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},
"marker": "CCA1"
},
{
"sample_id": "12",
"sample_type": "seedling",
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"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "W1",
"provenance": "Robust Stock"
},
"marker": "CCA1"
},
{
"sample_id": "13",
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"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
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"species": "Arabidopsis thaliana",
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"line": "W1",
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},
"marker": "CCA1"
},
{
"sample_id": "14",
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"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
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"species": "Arabidopsis thaliana",
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"genotype": "Wild Type",
"line": "W1",
"provenance": "Robust Stock"
},
"marker": "CCA1"
},
{
"sample_id": "15",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "W1",
"provenance": "Robust Stock"
},
"marker": "CCA1"
},
{
"sample_id": "16",
"sample_type": "group of seedlings",
"origin": "group of seedlings",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "W1",
"provenance": "Robust Stock"
},
"marker": "CCA1",
"parameter": "40"
},
{
"sample_id": "17",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
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"species": "Arabidopsis thaliana",
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},
"marker": "CCR2"
},
{
"sample_id": "18",
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"growth_stage": "seedling",
"age": "7",
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"species": "Arabidopsis thaliana",
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"line": "W1",
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},
"marker": "CCR2"
},
{
"sample_id": "19",
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"age": "7",
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"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
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"line": "W1",
"provenance": "Robust Stock"
},
"marker": "CCR2"
},
{
"sample_id": "20",
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"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "W1",
"provenance": "Robust Stock"
},
"marker": "CCR2"
},
{
"sample_id": "21",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "W1",
"provenance": "Robust Stock"
},
"marker": "CCR2"
},
{
"sample_id": "22",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
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"genotype": "Wild Type",
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"provenance": "Robust Stock"
},
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},
{
"sample_id": "23",
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"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
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"species": "Arabidopsis thaliana",
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"genotype": "Wild Type",
"line": "W1",
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},
"marker": "CCR2"
},
{
"sample_id": "24",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "W1",
"provenance": "Robust Stock"
},
"marker": "CCR2"
},
{
"sample_id": "25",
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{
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{
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{
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},
"marker": "CCR2"
},
{
"sample_id": "45",
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{
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},
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}
]
}
},
"biblio": {
"principal": "Andrew Millar",
"institution": "University of Edinburgh",
"author": "Benedicte Wenden"
}
}
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Views: 44 Downloads: 1
Created: 19th Jun 2026 at 09:56
Last updated: 19th Jun 2026 at 09:56
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Version 1 (earliest) Created 19th Jun 2026 at 09:56 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
Advanced Investigations list for this Data file with search and filtering
Collection of experiments created by Wenden Benedicte on the original BioDare and automatically transferred to FAIRDOM Hub.
Submitter: Daniel Thedie
Studies: Unpublished, Wenden et al. (2012)
Assays: BW-detached_LD-LL_#03, BW-detached_LD-LL_#06, BW-detached_LL-LL_#14, BW-detached_LL-LL_#16, BW-detached_LL-LL_#20, BW-intact_LD-LL_#23, BW-intact_LL-LD_#31, BW-intact_LL-LL_#37, BW-intact_LL-LL_#46, BW-intact_LL-LL_#56, BW-intact_LL-LL_#58, CCA1 and CCR2 markers in elf4 mutant under Far Red light, Clock genes under Far Red light - 3, Clock genes under Far Red light - 5, Clock genes under Far Red light - 6, Wenden_qPCR_clock_cFR, WT and elf4, Wenden_qPCR_clock_cFR, WT and phyA
Advanced Studies list for this Data file with search and filtering
Unpublished
DOI: none
Submitter: Daniel Thedie
Investigation: Wenden Benedicte
Assays: CCA1 and CCR2 markers in elf4 mutant under Far Red light, Clock genes under Far Red light - 3, Clock genes under Far Red light - 5, Clock genes under Far Red light - 6, Wenden_qPCR_clock_cFR, WT and elf4, Wenden_qPCR_clock_cFR, WT and phyA
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Clock genes under Far Red light - 6
| Property | Value |
|---|---|
| BioDare ID | 12730680847492 |
| Author | Benedicte Wenden |
| Institution | University of Edinburgh |
| License | CC_BY |
Description
Seedlings receive 3hrs of white light to germinate, then are entrained under 12/12 FR/D cycles for 3 days, sprayed, and imaged 24hrs after under 1 FR/D cycle, 3 days of continuous FR and 48h of DD
Purpose
Analysis of CCA1 and CCR2 in phyb, elf3-4, elf4-1 and ...
Submitter: Daniel Thedie
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Wenden Benedicte
Study: Unpublished
