BioDare_metadata Version 1
Original BioDare metadata, converted to json format
SEEK ID: https://fairdomhub.org/data_files/9074?version=1
Filename:
BioDare_metadata.json
Format: JSON document
Size: 189 KB
{
"id": "1926",
"status": "in progress",
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{
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"date": "2014-09-15T16:54:01"
},
{
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"date": "2014-09-11T10:02:12"
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"id": "1926",
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"name": "210814H2",
"purpose": "Comparison of Light:Shady night versus standard lights ON/OFF to dissect the role of photoreceptors and photosynthesis in the circadian clock.",
"description": "Experimental conditions (Red and Blue)\n12 hours light : 12 hours dark x7\nlight is at 90umolm-2s-1 (red = 51 umolm-2s-1, blue = 32 umol-2s-1)",
"comments": "Partner experiment: 210814H1",
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"site": "Edinburgh",
"author": "Yvette Wilson",
"start_date": "2014-08-20"
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"duration": "9",
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}
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"duration": "7.0",
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"temperature_conditions": {
"label": "const. 22.0C",
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"duration": "7",
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}
}
},
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{
"spectrum": "blue",
"intensity": "32",
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}
}
}
},
{
"spectrum": "red",
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"duration": "7",
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}
}
}
}
]
}
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"equipment": "HAM 2",
"parameters": "Imaging script started 5 minutes before ZT0\n55mins wait, 5mins lights off, 30mins capture",
"description": "Seedlings were treated on 9th day with Luciferin. They were then transferred Experimental conditions. Imaging was started on d10."
},
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},
"samples": {
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{
"sample_id": "1",
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"age": "7",
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"background": "Columbia (Col)",
"genotype": "Img Background",
"line": "unknown",
"provenance": "Robust stock"
},
"marker": "Actin",
"growth_cond_name": "12L:12D",
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"ignored": "false",
"param": {
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"@value": "Luc"
}
},
{
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"age": "7",
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"background": "Columbia (Col)",
"genotype": "prr7-3 prr9-1",
"line": "G0011",
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},
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}
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}
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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": "142",
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},
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"ignored": "false",
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]
}
},
"pedro": {
"@xmlns:xsi": "http://www.w3.org/2001/XMLSchema-instance",
"@xsi:schemaLocation": "/W:/communal/DataDescription/models/luc/model/newluc_model.xsd",
"id": "will be updated by the system",
"status": "in progress",
"name": "210814H2",
"purpose": "Comparison of Light:Shady night versus standard lights ON/OFF to dissect the role of photoreceptors and photosynthesis in the circadian clock.",
"description": "Experimental conditions (Red and Blue)\n12 hours light : 12 hours dark x7\nlight is at 90umolm-2s-1 (red = 51 umolm-2s-1, blue = 32 umol-2s-1)",
"comments": "Partner experiment: 210814H1",
"provenance": {
"site": "Edinburgh",
"author": "Yvette Wilson",
"start_date": "2014-08-20"
},
"growth_condition": {
"name": "12L:12D",
"medium": "Agar 1.2% MS 0.5",
"incubation": "7 days at 4C",
"growth_space": "Percival",
"duration": "9",
"comment": "Plants were entrained at light intensity 90 umolm-2s-1 to correspond to the light intensity of the experiment.",
"temperature_conditions": {
"constant_temp": {
"cycle_length": "24",
"base_temp": "22"
}
},
"light_conditions": {
"light_channel": {
"spectrum": "white",
"intensity": "90",
"source": "tube",
"diurnal_light": {
"cycle_length": "24",
"start_time": "0",
"duration": "12"
}
}
}
},
"experimental_condition": {
"name": "12L:12Dx7",
"medium": "Agar 1.2% MS 0.5",
"growth_space": "Percival + LED",
"duration": "7",
"comment": "At max light intensity red = 51 umolm-2s-1 and blue light intensity is 32 umol-2s-1.\n\nplants were transferred to experimental condiditons at ZT3",
"temperature_conditions": {
"constant_temp": {
"cycle_length": "24",
"base_temp": "22"
}
},
"light_conditions": {
"light_channel": [
{
"spectrum": "blue",
"intensity": "32",
"source": "LED",
"diurnal_light": {
"cycle_length": "24",
"start_time": "0",
"duration": "12"
}
},
{
"spectrum": "red",
"intensity": "51",
"source": "LED",
"diurnal_light": {
"cycle_length": "24",
"start_time": "0",
"duration": "12"
}
}
]
}
},
"measurement": {
"technique": "Luciferase luminescence",
"equipment": "HAM 2",
"parameters": "Imaging script started 5 minutes before ZT0\n55mins wait, 5mins lights off, 30mins capture",
"description": "Seedlings were treated on 9th day with Luciferin. They were then transferred Experimental conditions. Imaging was started on d10."
},
"sample_preparation": {
"method": "Plants sprayed with luciferin on day 9 of growth conditions and transferred to experimental conditions. Imaging was started on day 10."
},
"samples": {
"sample": [
{
"sample_id": "1",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "Img Background",
"provenance": "Robust stock"
},
"marker": "Actin",
"growth_cond_name": "12L:12D",
"experiment_cond_name": "12L:12Dx7",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "2",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "prr7-3 prr9-1",
"line": "G0011",
"provenance": "Robust stock"
},
"marker": "CCR2",
"growth_cond_name": "12L:12D",
"experiment_cond_name": "12L:12Dx7",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "3",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "prr7-3 prr9-1",
"line": "G0011",
"provenance": "Robust stock"
},
"marker": "CCR2",
"growth_cond_name": "12L:12D",
"experiment_cond_name": "12L:12Dx7",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "4",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "prr7-3 prr9-1",
"line": "G0011",
"provenance": "Robust stock"
},
"marker": "CCR2",
"growth_cond_name": "12L:12D",
"experiment_cond_name": "12L:12Dx7",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "5",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "prr7-3 prr9-1",
"line": "G0011",
"provenance": "Robust stock"
},
"marker": "CCR2",
"growth_cond_name": "12L:12D",
"experiment_cond_name": "12L:12Dx7",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "6",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "prr7-3 prr9-1",
"line": "G0011",
"provenance": "Robust stock"
},
"marker": "CCR2",
"growth_cond_name": "12L:12D",
"experiment_cond_name": "12L:12Dx7",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "7",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "prr7-3 prr9-1",
"line": "G0011",
"provenance": "Robust stock"
},
"marker": "CCR2",
"growth_cond_name": "12L:12D",
"experiment_cond_name": "12L:12Dx7",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "8",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "prr7-3 prr9-1",
"line": "G0011",
"provenance": "Robust stock"
},
"marker": "CCR2",
"growth_cond_name": "12L:12D",
"experiment_cond_name": "12L:12Dx7",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "9",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "prr7-3 prr9-1",
"line": "G0011",
"provenance": "Robust stock"
},
"marker": "CCR2",
"growth_cond_name": "12L:12D",
"experiment_cond_name": "12L:12Dx7",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "10",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "prr7-3 prr9-1",
"line": "G0011",
"provenance": "Robust stock"
},
"marker": "CCR2",
"growth_cond_name": "12L:12D",
"experiment_cond_name": "12L:12Dx7",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "11",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "prr7-3 prr9-1",
"line": "G0011",
"provenance": "Robust stock"
},
"marker": "CCR2",
"growth_cond_name": "12L:12D",
"experiment_cond_name": "12L:12Dx7",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "12",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "prr7-3 prr9-1",
"line": "G0011",
"provenance": "Robust stock"
},
"marker": "CCR2",
"growth_cond_name": "12L:12D",
"experiment_cond_name": "12L:12Dx7",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "13",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "prr7-3 prr9-1",
"line": "G0011",
"provenance": "Robust stock"
},
"marker": "CCR2",
"growth_cond_name": "12L:12D",
"experiment_cond_name": "12L:12Dx7",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "14",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "prr7-3 prr9-1",
"line": "G0011",
"provenance": "Robust stock"
},
"marker": "CCR2",
"growth_cond_name": "12L:12D",
"experiment_cond_name": "12L:12Dx7",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "15",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "prr7-3 prr9-1",
"line": "G0011",
"provenance": "Robust stock"
},
"marker": "CCR2",
"growth_cond_name": "12L:12D",
"experiment_cond_name": "12L:12Dx7",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "16",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "prr7-3 prr9-1",
"line": "G0011",
"provenance": "Robust stock"
},
"marker": "CCR2",
"growth_cond_name": "12L:12D",
"experiment_cond_name": "12L:12Dx7",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "17",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
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"line": "G0010",
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},
"marker": "CCR2",
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"experiment_cond_name": "12L:12Dx7",
"param": {
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"@value": "Luc"
}
},
{
"sample_id": "18",
"sample_type": "seedling",
"origin": "seedling",
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"age": "7",
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},
"marker": "CCR2",
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"experiment_cond_name": "12L:12Dx7",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "19",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "Wild Type",
"line": "G0010",
"provenance": "Robust stock"
},
"marker": "CCR2",
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"experiment_cond_name": "12L:12Dx7",
"param": {
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"@value": "Luc"
}
},
{
"sample_id": "20",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "Wild Type",
"line": "G0010",
"provenance": "Robust stock"
},
"marker": "CCR2",
"growth_cond_name": "12L:12D",
"experiment_cond_name": "12L:12Dx7",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "21",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "Wild Type",
"line": "G0010",
"provenance": "Robust stock"
},
"marker": "CCR2",
"growth_cond_name": "12L:12D",
"experiment_cond_name": "12L:12Dx7",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "22",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "Wild Type",
"line": "G0010",
"provenance": "Robust stock"
},
"marker": "CCR2",
"growth_cond_name": "12L:12D",
"experiment_cond_name": "12L:12Dx7",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "23",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
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"line": "G0010",
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},
"marker": "CCR2",
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"experiment_cond_name": "12L:12Dx7",
"param": {
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}
},
{
"sample_id": "24",
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"age": "7",
"genetic_info": {
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"genotype": "Wild Type",
"line": "G0010",
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},
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"experiment_cond_name": "12L:12Dx7",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "25",
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},
"marker": "CCR2",
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"experiment_cond_name": "12L:12Dx7",
"param": {
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}
},
{
"sample_id": "26",
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},
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"param": {
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}
},
{
"sample_id": "27",
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"age": "7",
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"line": "G0010",
"provenance": "Robust stock"
},
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"experiment_cond_name": "12L:12Dx7",
"param": {
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}
},
{
"sample_id": "28",
"sample_type": "seedling",
"origin": "seedling",
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"genetic_info": {
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},
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"experiment_cond_name": "12L:12Dx7",
"param": {
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}
},
{
"sample_id": "29",
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},
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"param": {
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}
},
{
"sample_id": "30",
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},
"marker": "CCR2",
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"experiment_cond_name": "12L:12Dx7",
"param": {
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}
},
{
"sample_id": "31",
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"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "Wild Type",
"line": "G0010",
"provenance": "Robust stock"
},
"marker": "CCR2",
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"experiment_cond_name": "12L:12Dx7",
"param": {
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"@value": "Luc"
}
},
{
"sample_id": "32",
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"origin": "seedling",
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"age": "7",
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"line": "G0010",
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},
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"growth_cond_name": "12L:12D",
"experiment_cond_name": "12L:12Dx7",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "33",
"sample_type": "seedling",
"origin": "seedling",
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"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "Wild Type",
"line": "G0010",
"provenance": "Robust stock"
},
"marker": "CCR2",
"growth_cond_name": "12L:12D",
"experiment_cond_name": "12L:12Dx7",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "34",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "cca1;lhy",
"line": "G0060",
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},
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"experiment_cond_name": "12L:12Dx7",
"param": {
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}
},
{
"sample_id": "35",
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},
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"experiment_cond_name": "12L:12Dx7",
"param": {
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"@value": "Luc"
}
},
{
"sample_id": "36",
"sample_type": "seedling",
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},
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"experiment_cond_name": "12L:12Dx7",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "37",
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},
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"param": {
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}
},
{
"sample_id": "38",
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},
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"experiment_cond_name": "12L:12Dx7",
"param": {
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"@value": "Luc"
}
},
{
"sample_id": "39",
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"species": "Arabidopsis thaliana",
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"provenance": "Robust stock"
},
"marker": "CAB",
"growth_cond_name": "12L:12D",
"experiment_cond_name": "12L:12Dx7",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "40",
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},
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"param": {
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}
},
{
"sample_id": "41",
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},
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"param": {
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}
},
{
"sample_id": "42",
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]
}
},
"biblio": {}
}
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Views: 55 Downloads: 2
Created: 18th Jun 2026 at 15:07
Last updated: 18th Jun 2026 at 15:08
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Version 1 (earliest) Created 18th Jun 2026 at 15:08 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
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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 Millar Andrew on the original BioDare and automatically transferred to FAIRDOM Hub.
Submitter: Daniel Thedie
Studies: Millar et al. (2015), TiMet double dawns, TiMet shady nights
Assays: 010514H1, 010514H2, 030413H3: 12B-12Dx4 BB3, 030714H1, 030714H2, 060213H3: 12B-12Dx4 BBx3, 060313H1: 5L15Dx4 LLx3 (T-20), 060313H2: 12F-12Dx4 FFx3, 070814H1, 070814H2, 080115H1, 080115H2, 100414H1, 100414H2, 130212H1: 5L15Dx4 LLx3 (T-20), 130213H3: 12R-12Dx4 RRx3, 130313H1: 14L14D x 4 LL x 3 (T-28), 130313H2: 12F-12Dx4 FFx3, 140515H1, 140515H2, 140814H1, 140814H2, 190614H1, 190614H2, 200213H1: 15L5D x4 LL x3 (T-20), 200213H3: 12B-12Dx4 BB3, 200313H2: 7L 21Dx4 LLx3 (T-28), 200313H3: 12L-12Dx4 LLx3, 210814H1, 210814H2, 240414H1, 240414H2, 270213H1: 10L10Dx4 LLx3 (T-20), 270213H3: 12R-12Dx4 RRx3, 270313H1: 21L 7Dx4 LLx3 (T-28), 270313H3: 12L-12Dx4 LLx3, 280814H1, 280814H2, 290313H2: 15L 5Dx4 LLx3, AT0043: 4x 12:12-DD, AT0048 4x 18:6-DD, AT0078: 4x6:18-DD, AT0080: 4x18:6-DD
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210814H2
| Property | Value |
|---|---|
| BioDare ID | 1926 |
| Author | Yvette Wilson |
| Institution | |
| License |
Description
Experimental conditions (Red and Blue) 12 hours light : 12 hours dark x7 light is at 90umolm-2s-1 (red = 51 umolm-2s-1, blue = 32 umol-2s-1)
Purpose
Comparison of Light:Shady night versus standard lights ON/OFF to dissect the role of photoreceptors and photosynthesis in the circadian clock.
Comments
Partner experiment: 210814H1
Submitter: Daniel Thedie
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Millar Andrew
Study: TiMet shady nights
