BioDare_metadata Version 1
Original BioDare metadata, converted to json format
SEEK ID: https://fairdomhub.org/data_files/8667?version=1
Filename:
BioDare_metadata.json
Format: JSON document
Size: 93.4 KB
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"label": "W: 1*LD 18:00:06:00; 2*LL",
"light_channel": {
"spectrum": "white",
"intensity": "60",
"source": "LED",
"env_conditions": {
"type": "light_complex",
"label": "1*LD 18:00:06:00; 2*LL",
"duration": "3",
"env_day": [
{
"type": "diurnal_light",
"label": "diurnal light",
"duration": "1",
"cycle_length": "24",
"base_value": "0.0",
"second_value": "100.0",
"env_period": {
"start_time": "0:00",
"duration": "18:00"
}
},
{
"type": "constant_light",
"label": "constant light",
"duration": "2",
"cycle_length": "24",
"base_value": "0.0",
"second_value": "100.0",
"env_period": {
"start_time": "0:00",
"duration": "24:00"
}
}
]
}
}
}
},
{
"name": "experiment_edwards_ph6toDD",
"medium": "Agar 2% MS 1 3% Sucrose",
"duration": "3.0",
"temperature_conditions": {
"label": "const. 22.0C",
"env_conditions": {
"type": "constant_temp",
"label": "const. 22.0C",
"duration": "3",
"env_day": {
"type": "constant_temp",
"label": "constant temperature",
"duration": "3",
"cycle_length": "24",
"base_value": "22.0",
"second_value": "22.0"
}
}
},
"light_conditions": {
"label": "W: 1*LD 06:00:18:00; 2*DD",
"light_channel": {
"spectrum": "white",
"intensity": "60",
"source": "LED",
"env_conditions": {
"type": "light_complex",
"label": "1*LD 06:00:18:00; 2*DD",
"duration": "3",
"env_day": [
{
"type": "diurnal_light",
"label": "diurnal light",
"duration": "1",
"cycle_length": "24",
"base_value": "0.0",
"second_value": "100.0",
"env_period": {
"start_time": "0:00",
"duration": "6:00"
}
},
{
"type": "constant_dark",
"label": "constant dark",
"duration": "2",
"cycle_length": "24",
"base_value": "0.0",
"second_value": "0.0"
}
]
}
}
}
},
{
"name": "experiment_edwards_ph12toDD",
"medium": "Agar 2% MS 1 3% Sucrose",
"duration": "3.0",
"temperature_conditions": {
"label": "const. 22.0C",
"env_conditions": {
"type": "constant_temp",
"label": "const. 22.0C",
"duration": "3",
"env_day": {
"type": "constant_temp",
"label": "constant temperature",
"duration": "3",
"cycle_length": "24",
"base_value": "22.0",
"second_value": "22.0"
}
}
},
"light_conditions": {
"label": "W: 1*LD 12:00:12:00; 2*DD",
"light_channel": {
"spectrum": "white",
"intensity": "60",
"source": "LED",
"env_conditions": {
"type": "light_complex",
"label": "1*LD 12:00:12:00; 2*DD",
"duration": "3",
"env_day": [
{
"type": "diurnal_light",
"label": "diurnal light",
"duration": "1",
"cycle_length": "24",
"base_value": "0.0",
"second_value": "100.0",
"env_period": {
"start_time": "0:00",
"duration": "12:00"
}
},
{
"type": "constant_dark",
"label": "constant dark",
"duration": "2",
"cycle_length": "24",
"base_value": "0.0",
"second_value": "0.0"
}
]
}
}
}
},
{
"name": "experiment_edwards_ph18toDD",
"medium": "Agar 2% MS 1 3% Sucrose",
"duration": "3.0",
"temperature_conditions": {
"label": "const. 22.0C",
"env_conditions": {
"type": "constant_temp",
"label": "const. 22.0C",
"duration": "3",
"env_day": {
"type": "constant_temp",
"label": "constant temperature",
"duration": "3",
"cycle_length": "24",
"base_value": "22.0",
"second_value": "22.0"
}
}
},
"light_conditions": {
"label": "W: 1*LD 18:00:06:00; 2*DD",
"light_channel": {
"spectrum": "white",
"intensity": "60",
"source": "LED",
"env_conditions": {
"type": "light_complex",
"label": "1*LD 18:00:06:00; 2*DD",
"duration": "3",
"env_day": [
{
"type": "diurnal_light",
"label": "diurnal light",
"duration": "1",
"cycle_length": "24",
"base_value": "0.0",
"second_value": "100.0",
"env_period": {
"start_time": "0:00",
"duration": "18:00"
}
},
{
"type": "constant_dark",
"label": "constant dark",
"duration": "2",
"cycle_length": "24",
"base_value": "0.0",
"second_value": "0.0"
}
]
}
}
}
}
],
"measurement": {
"technique": "RT-PCR",
"equipment": "Light Cycler 480 (Roche, UK)",
"param": [
{
"@name": "RD error_type",
"@value": "std_err"
},
{
"@name": "RD first_data_col",
"@value": "2"
},
{
"@name": "RD first_data_row",
"@value": "5"
},
{
"@name": "RD time_col",
"@value": "1"
}
]
},
"sample_preparation": {
"method": "RNA was extracted and reverse transcribed as described previously (Locke et al, 2005b). Q-PCR was carried out using SYBR Green JumpStart Taq ReadyMix (Sigma, Gillingham, UK) in technical triplicate."
},
"samples": {
"sample": [
{
"sample_id": "1",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "0",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "unknown"
},
"marker": "CCA1",
"growth_cond_name": "growth_edwards_ph3",
"experiment_cond_name": "experiment_edwards_ph3toLL",
"ignored": "false"
},
{
"sample_id": "2",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "0",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "unknown"
},
"marker": "CCA1",
"growth_cond_name": "growth_edwards_ph6",
"experiment_cond_name": "experiment_edwards_ph6toLL",
"ignored": "false"
},
{
"sample_id": "3",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "0",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "unknown"
},
"marker": "CCA1",
"growth_cond_name": "growth_edwards_ph9",
"experiment_cond_name": "experiment_edwards_ph9toLL",
"ignored": "false"
},
{
"sample_id": "4",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "0",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "unknown"
},
"marker": "CCA1",
"growth_cond_name": "growth_edwards_ph12",
"experiment_cond_name": "experiment_edwards_ph12toLL",
"ignored": "false"
},
{
"sample_id": "5",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "0",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "unknown"
},
"marker": "CCA1",
"growth_cond_name": "growth_edwards_ph18",
"experiment_cond_name": "experiment_edwards_ph18toLL",
"ignored": "false"
},
{
"sample_id": "6",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "0",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "unknown"
},
"marker": "CCA1",
"growth_cond_name": "growth_edwards_ph6",
"experiment_cond_name": "experiment_edwards_ph6toDD",
"ignored": "false"
},
{
"sample_id": "7",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "0",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "unknown"
},
"marker": "CCA1",
"growth_cond_name": "growth_edwards_ph12",
"experiment_cond_name": "experiment_edwards_ph12toDD",
"ignored": "false"
},
{
"sample_id": "8",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "0",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "unknown"
},
"marker": "CCA1",
"growth_cond_name": "growth_edwards_ph18",
"experiment_cond_name": "experiment_edwards_ph18toDD",
"ignored": "false"
},
{
"sample_id": "9",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "0",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "unknown"
},
"marker": "TOC1",
"growth_cond_name": "growth_edwards_ph3",
"experiment_cond_name": "experiment_edwards_ph3toLL",
"ignored": "false"
},
{
"sample_id": "10",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "0",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "unknown"
},
"marker": "TOC1",
"growth_cond_name": "growth_edwards_ph6",
"experiment_cond_name": "experiment_edwards_ph6toLL",
"ignored": "false"
},
{
"sample_id": "11",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "0",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "unknown"
},
"marker": "TOC1",
"growth_cond_name": "growth_edwards_ph9",
"experiment_cond_name": "experiment_edwards_ph9toLL",
"ignored": "false"
},
{
"sample_id": "12",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "0",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "unknown"
},
"marker": "TOC1",
"growth_cond_name": "growth_edwards_ph12",
"experiment_cond_name": "experiment_edwards_ph12toLL",
"ignored": "false"
},
{
"sample_id": "13",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "0",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "unknown"
},
"marker": "TOC1",
"growth_cond_name": "growth_edwards_ph18",
"experiment_cond_name": "experiment_edwards_ph18toLL",
"ignored": "false"
},
{
"sample_id": "14",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "0",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "unknown"
},
"marker": "TOC1",
"growth_cond_name": "growth_edwards_ph6",
"experiment_cond_name": "experiment_edwards_ph6toDD",
"ignored": "false"
},
{
"sample_id": "15",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "0",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "unknown"
},
"marker": "TOC1",
"growth_cond_name": "growth_edwards_ph12",
"experiment_cond_name": "experiment_edwards_ph12toDD",
"ignored": "false"
},
{
"sample_id": "16",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "0",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "unknown"
},
"marker": "TOC1",
"growth_cond_name": "growth_edwards_ph18",
"experiment_cond_name": "experiment_edwards_ph18toDD",
"ignored": "false"
},
{
"sample_id": "17",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "0",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "unknown"
},
"marker": "GI",
"growth_cond_name": "growth_edwards_ph3",
"experiment_cond_name": "experiment_edwards_ph3toLL",
"ignored": "false"
},
{
"sample_id": "18",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "0",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "unknown"
},
"marker": "GI",
"growth_cond_name": "growth_edwards_ph6",
"experiment_cond_name": "experiment_edwards_ph6toLL",
"ignored": "false"
},
{
"sample_id": "19",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "0",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "unknown"
},
"marker": "GI",
"growth_cond_name": "growth_edwards_ph9",
"experiment_cond_name": "experiment_edwards_ph9toLL",
"ignored": "false"
},
{
"sample_id": "20",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "0",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "unknown"
},
"marker": "GI",
"growth_cond_name": "growth_edwards_ph12",
"experiment_cond_name": "experiment_edwards_ph12toLL",
"ignored": "false"
},
{
"sample_id": "21",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "0",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "unknown"
},
"marker": "GI",
"growth_cond_name": "growth_edwards_ph18",
"experiment_cond_name": "experiment_edwards_ph18toLL",
"ignored": "false"
},
{
"sample_id": "22",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "0",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "unknown"
},
"marker": "GI",
"growth_cond_name": "growth_edwards_ph6",
"experiment_cond_name": "experiment_edwards_ph6toDD",
"ignored": "false"
},
{
"sample_id": "23",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "0",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "unknown"
},
"marker": "GI",
"growth_cond_name": "growth_edwards_ph12",
"experiment_cond_name": "experiment_edwards_ph12toDD",
"ignored": "false"
},
{
"sample_id": "24",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "0",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "unknown"
},
"marker": "GI",
"growth_cond_name": "growth_edwards_ph18",
"experiment_cond_name": "experiment_edwards_ph18toDD",
"ignored": "false"
},
{
"sample_id": "25",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "0",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "unknown"
},
"marker": "CO",
"growth_cond_name": "growth_edwards_ph6",
"experiment_cond_name": "experiment_edwards_ph6toLL",
"ignored": "false"
},
{
"sample_id": "26",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "0",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "unknown"
},
"marker": "CO",
"growth_cond_name": "growth_edwards_ph12",
"experiment_cond_name": "experiment_edwards_ph12toLL",
"ignored": "false"
},
{
"sample_id": "27",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "0",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "unknown"
},
"marker": "CO",
"growth_cond_name": "growth_edwards_ph18",
"experiment_cond_name": "experiment_edwards_ph18toLL",
"ignored": "false"
},
{
"sample_id": "28",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "0",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "unknown"
},
"marker": "CO",
"growth_cond_name": "growth_edwards_ph6",
"experiment_cond_name": "experiment_edwards_ph6toDD",
"ignored": "false"
},
{
"sample_id": "29",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "0",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "unknown"
},
"marker": "CO",
"growth_cond_name": "growth_edwards_ph12",
"experiment_cond_name": "experiment_edwards_ph12toDD",
"ignored": "false"
},
{
"sample_id": "30",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "0",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "unknown"
},
"marker": "CO",
"growth_cond_name": "growth_edwards_ph18",
"experiment_cond_name": "experiment_edwards_ph18toDD",
"ignored": "false"
},
{
"sample_id": "31",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "0",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "unknown"
},
"marker": "DPE2",
"growth_cond_name": "growth_edwards_ph6",
"experiment_cond_name": "experiment_edwards_ph6toLL",
"ignored": "false"
},
{
"sample_id": "32",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "0",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "unknown"
},
"marker": "DPE2",
"growth_cond_name": "growth_edwards_ph12",
"experiment_cond_name": "experiment_edwards_ph12toLL",
"ignored": "false"
},
{
"sample_id": "33",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "0",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "unknown"
},
"marker": "DPE2",
"growth_cond_name": "growth_edwards_ph18",
"experiment_cond_name": "experiment_edwards_ph18toLL",
"ignored": "false"
},
{
"sample_id": "34",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "0",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "unknown"
},
"marker": "DPE2",
"growth_cond_name": "growth_edwards_ph6",
"experiment_cond_name": "experiment_edwards_ph6toDD",
"ignored": "false"
},
{
"sample_id": "35",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "0",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "unknown"
},
"marker": "DPE2",
"growth_cond_name": "growth_edwards_ph12",
"experiment_cond_name": "experiment_edwards_ph12toDD",
"ignored": "false"
},
{
"sample_id": "36",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "0",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "unknown"
},
"marker": "DPE2",
"growth_cond_name": "growth_edwards_ph18",
"experiment_cond_name": "experiment_edwards_ph18toDD",
"ignored": "false"
},
{
"sample_id": "37",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "0",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "unknown"
},
"marker": "FKF1",
"growth_cond_name": "growth_edwards_ph6",
"experiment_cond_name": "experiment_edwards_ph6toLL",
"ignored": "false"
},
{
"sample_id": "38",
"sample_type": "seedling",
"origin": "seedling",
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"age": "0",
"genetic_info": {
"species": "Arabidopsis thaliana",
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"genotype": "Wild Type",
"line": "unknown"
},
"marker": "FKF1",
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"ignored": "false"
},
{
"sample_id": "39",
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"origin": "seedling",
"growth_stage": "seedling",
"age": "0",
"genetic_info": {
"species": "Arabidopsis thaliana",
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"genotype": "Wild Type",
"line": "unknown"
},
"marker": "FKF1",
"growth_cond_name": "growth_edwards_ph18",
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"ignored": "false"
},
{
"sample_id": "40",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "0",
"genetic_info": {
"species": "Arabidopsis thaliana",
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"genotype": "Wild Type",
"line": "unknown"
},
"marker": "FKF1",
"growth_cond_name": "growth_edwards_ph6",
"experiment_cond_name": "experiment_edwards_ph6toDD",
"ignored": "false"
},
{
"sample_id": "41",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "0",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "unknown"
},
"marker": "FKF1",
"growth_cond_name": "growth_edwards_ph12",
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"ignored": "false"
},
{
"sample_id": "42",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "0",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "unknown"
},
"marker": "FKF1",
"growth_cond_name": "growth_edwards_ph18",
"experiment_cond_name": "experiment_edwards_ph18toDD",
"ignored": "false"
},
{
"sample_id": "43",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "0",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "unknown"
},
"marker": "SEX4",
"growth_cond_name": "growth_edwards_ph6",
"experiment_cond_name": "experiment_edwards_ph6toLL",
"ignored": "false"
},
{
"sample_id": "45",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "0",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "unknown"
},
"marker": "SEX4",
"growth_cond_name": "growth_edwards_ph12",
"experiment_cond_name": "experiment_edwards_ph12toLL",
"ignored": "false"
},
{
"sample_id": "46",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "0",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "unknown"
},
"marker": "SEX4",
"growth_cond_name": "growth_edwards_ph18",
"experiment_cond_name": "experiment_edwards_ph18toLL",
"ignored": "false"
},
{
"sample_id": "47",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "0",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "unknown"
},
"marker": "SEX4",
"growth_cond_name": "growth_edwards_ph6",
"experiment_cond_name": "experiment_edwards_ph6toDD",
"ignored": "false"
},
{
"sample_id": "48",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "0",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "unknown"
},
"marker": "SEX4",
"growth_cond_name": "growth_edwards_ph12",
"experiment_cond_name": "experiment_edwards_ph12toDD",
"ignored": "false"
},
{
"sample_id": "49",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "0",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "unknown"
},
"marker": "SEX4",
"growth_cond_name": "growth_edwards_ph18",
"experiment_cond_name": "experiment_edwards_ph18toDD",
"ignored": "false"
}
]
}
},
"pedro": {
"@xmlns:xsi": "http://www.w3.org/2001/XMLSchema-instance",
"@xsi:schemaLocation": "/Z:/communal/DataDescription/models/literature/model/full_literature.xsd",
"name": "Edwards et al. (2010); WT in different light conditions.",
"purpose": "To investigate the dusk-sensing of clock genes and compare the results to mathematical models of the circadian clock.",
"description": "Theory suggested that multiple loops contribute the flexibility for molecular rhythms to track multiple phases of the external cycle. Clear dawn- and dusk-tracking rhythms illustrate the flexibility of timing in Ipomoea nil. Molecular clock components in Arabidopsis thaliana showed complex, photoperiod-dependent regulation.",
"pubmed_id": "21045818",
"provenance": {
"pub_title": "Quantitative analysis of regulatory flexibility under changing environmental conditions.",
"first_author": "Edwards, K.D.",
"group": "Millar",
"pub_date": "2010-11-02"
},
"growth_condition": [
{
"name": "growth_edwards_ph3",
"medium": "Agar 2% MS 1 3% Sucrose",
"stratification": "3 days at 4C",
"duration": "7",
"temperature_conditions": {
"constant_temp": {
"cycle_length": "24",
"base_temp": "22"
}
},
"light_conditions": {
"light_channel": {
"spectrum": "white",
"intensity": "60",
"source": "LED",
"diurnal_light": {
"cycle_length": "24",
"start_time": "0",
"duration": "3"
}
}
}
},
{
"name": "growth_edwards_ph6",
"medium": "Agar 2% MS 1 3% Sucrose",
"stratification": "3 days at 4C",
"duration": "7",
"temperature_conditions": {
"constant_temp": {
"cycle_length": "24",
"base_temp": "22"
}
},
"light_conditions": {
"light_channel": {
"spectrum": "white",
"intensity": "60",
"source": "LED",
"diurnal_light": {
"cycle_length": "24",
"start_time": "0",
"duration": "6"
}
}
}
},
{
"name": "growth_edwards_ph9",
"medium": "Agar 2% MS 1 3% Sucrose",
"stratification": "3 days at 4C",
"duration": "7",
"temperature_conditions": {
"constant_temp": {
"cycle_length": "24",
"base_temp": "22"
}
},
"light_conditions": {
"light_channel": {
"spectrum": "white",
"intensity": "60",
"source": "LED",
"diurnal_light": {
"cycle_length": "24",
"start_time": "0",
"duration": "9"
}
}
}
},
{
"name": "growth_edwards_ph12",
"medium": "Agar 2% MS 1 3% Sucrose",
"stratification": "3 days at 4C",
"duration": "7",
"temperature_conditions": {
"constant_temp": {
"cycle_length": "24",
"base_temp": "22"
}
},
"light_conditions": {
"light_channel": {
"spectrum": "white",
"intensity": "60",
"source": "LED",
"diurnal_light": {
"cycle_length": "24",
"start_time": "0",
"duration": "12"
}
}
}
},
{
"name": "growth_edwards_ph18",
"medium": "Agar 2% MS 1 3% Sucrose",
"stratification": "3 days at 4C",
"duration": "7",
"temperature_conditions": {
"constant_temp": {
"cycle_length": "24",
"base_temp": "22"
}
},
"light_conditions": {
"light_channel": {
"spectrum": "white",
"intensity": "60",
"source": "LED",
"diurnal_light": {
"cycle_length": "24",
"start_time": "0",
"duration": "18"
}
}
}
}
],
"experimental_condition": [
{
"name": "experiment_edwards_ph3toLL",
"medium": "Agar 2% MS 1 3% Sucrose",
"duration": "3",
"temperature_conditions": {
"constant_temp": {
"cycle_length": "24",
"base_temp": "22"
}
},
"light_conditions": {
"light_channel": {
"spectrum": "white",
"intensity": "60",
"source": "LED",
"light_complex_settings": {
"light_days": [
{
"start_day": "1",
"duration": "1",
"diurnal_light": {
"cycle_length": "24",
"start_time": "0",
"duration": "3"
}
},
{
"start_day": "2",
"duration": "2",
"constant_light": {
"cycle_length": "24"
}
}
]
}
}
}
},
{
"name": "experiment_edwards_ph6toLL",
"medium": "Agar 2% MS 1 3% Sucrose",
"duration": "3",
"temperature_conditions": {
"constant_temp": {
"cycle_length": "24",
"base_temp": "22"
}
},
"light_conditions": {
"light_channel": {
"spectrum": "white",
"intensity": "60",
"source": "LED",
"light_complex_settings": {
"light_days": [
{
"start_day": "1",
"duration": "1",
"diurnal_light": {
"cycle_length": "24",
"start_time": "0",
"duration": "6"
}
},
{
"start_day": "2",
"duration": "2",
"constant_light": {
"cycle_length": "24"
}
}
]
}
}
}
},
{
"name": "experiment_edwards_ph9toLL",
"medium": "Agar 2% MS 1 3% Sucrose",
"duration": "3",
"temperature_conditions": {
"constant_temp": {
"cycle_length": "24",
"base_temp": "22"
}
},
"light_conditions": {
"light_channel": {
"spectrum": "white",
"intensity": "60",
"source": "LED",
"light_complex_settings": {
"light_days": [
{
"start_day": "1",
"duration": "1",
"diurnal_light": {
"cycle_length": "24",
"start_time": "0",
"duration": "9"
}
},
{
"start_day": "2",
"duration": "2",
"constant_light": {
"cycle_length": "24"
}
}
]
}
}
}
},
{
"name": "experiment_edwards_ph12toLL",
"medium": "Agar 2% MS 1 3% Sucrose",
"duration": "3",
"temperature_conditions": {
"constant_temp": {
"cycle_length": "24",
"base_temp": "22"
}
},
"light_conditions": {
"light_channel": {
"spectrum": "white",
"intensity": "60",
"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": "2",
"constant_light": {
"cycle_length": "24"
}
}
]
}
}
}
},
{
"name": "experiment_edwards_ph18toLL",
"medium": "Agar 2% MS 1 3% Sucrose",
"duration": "3",
"temperature_conditions": {
"constant_temp": {
"cycle_length": "24",
"base_temp": "22"
}
},
"light_conditions": {
"light_channel": {
"spectrum": "white",
"intensity": "60",
"source": "LED",
"light_complex_settings": {
"light_days": [
{
"start_day": "1",
"duration": "1",
"diurnal_light": {
"cycle_length": "24",
"start_time": "0",
"duration": "18"
}
},
{
"start_day": "2",
"duration": "2",
"constant_light": {
"cycle_length": "24"
}
}
]
}
}
}
},
{
"name": "experiment_edwards_ph6toDD",
"medium": "Agar 2% MS 1 3% Sucrose",
"duration": "3",
"temperature_conditions": {
"constant_temp": {
"cycle_length": "24",
"base_temp": "22"
}
},
"light_conditions": {
"light_channel": {
"spectrum": "white",
"intensity": "60",
"source": "LED",
"light_complex_settings": {
"light_days": [
{
"start_day": "1",
"duration": "1",
"diurnal_light": {
"cycle_length": "24",
"start_time": "0",
"duration": "6"
}
},
{
"start_day": "2",
"duration": "2",
"constant_dark": {
"cycle_length": "24"
}
}
]
}
}
}
},
{
"name": "experiment_edwards_ph12toDD",
"medium": "Agar 2% MS 1 3% Sucrose",
"duration": "3",
"temperature_conditions": {
"constant_temp": {
"cycle_length": "24",
"base_temp": "22"
}
},
"light_conditions": {
"light_channel": {
"spectrum": "white",
"intensity": "60",
"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": "2",
"constant_dark": {
"cycle_length": "24"
}
}
]
}
}
}
},
{
"name": "experiment_edwards_ph18toDD",
"medium": "Agar 2% MS 1 3% Sucrose",
"duration": "3",
"temperature_conditions": {
"constant_temp": {
"cycle_length": "24",
"base_temp": "22"
}
},
"light_conditions": {
"light_channel": {
"spectrum": "white",
"intensity": "60",
"source": "LED",
"light_complex_settings": {
"light_days": [
{
"start_day": "1",
"duration": "1",
"diurnal_light": {
"cycle_length": "24",
"start_time": "0",
"duration": "18"
}
},
{
"start_day": "2",
"duration": "2",
"constant_dark": {
"cycle_length": "24"
}
}
]
}
}
}
}
],
"measurement": {
"technique": "RT-PCR",
"equipment": "Light Cycler 480 (Roche, UK)"
},
"sample_preparation": {
"method": "RNA was extracted and reverse transcribed as described previously (Locke et al, 2005b). Q-PCR was carried out using SYBR Green JumpStart Taq ReadyMix (Sigma, Gillingham, UK) in technical triplicate."
},
"samples": {
"sample": [
{
"sample_id": "1",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type"
},
"marker": "CCA1",
"growth_cond_name": "growth_edwards_ph3",
"experiment_cond_name": "experiment_edwards_ph3toLL"
},
{
"sample_id": "2",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type"
},
"marker": "CCA1",
"growth_cond_name": "growth_edwards_ph6",
"experiment_cond_name": "experiment_edwards_ph6toLL"
},
{
"sample_id": "3",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type"
},
"marker": "CCA1",
"growth_cond_name": "growth_edwards_ph9",
"experiment_cond_name": "experiment_edwards_ph9toLL"
},
{
"sample_id": "4",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type"
},
"marker": "CCA1",
"growth_cond_name": "growth_edwards_ph12",
"experiment_cond_name": "experiment_edwards_ph12toLL"
},
{
"sample_id": "5",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type"
},
"marker": "CCA1",
"growth_cond_name": "growth_edwards_ph18",
"experiment_cond_name": "experiment_edwards_ph18toLL"
},
{
"sample_id": "6",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type"
},
"marker": "CCA1",
"growth_cond_name": "growth_edwards_ph6",
"experiment_cond_name": "experiment_edwards_ph6toDD"
},
{
"sample_id": "7",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type"
},
"marker": "CCA1",
"growth_cond_name": "growth_edwards_ph12",
"experiment_cond_name": "experiment_edwards_ph12toDD"
},
{
"sample_id": "8",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type"
},
"marker": "CCA1",
"growth_cond_name": "growth_edwards_ph18",
"experiment_cond_name": "experiment_edwards_ph18toDD"
},
{
"sample_id": "9",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type"
},
"marker": "TOC1",
"growth_cond_name": "growth_edwards_ph3",
"experiment_cond_name": "experiment_edwards_ph3toLL"
},
{
"sample_id": "10",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type"
},
"marker": "TOC1",
"growth_cond_name": "growth_edwards_ph6",
"experiment_cond_name": "experiment_edwards_ph6toLL"
},
{
"sample_id": "11",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type"
},
"marker": "TOC1",
"growth_cond_name": "growth_edwards_ph9",
"experiment_cond_name": "experiment_edwards_ph9toLL"
},
{
"sample_id": "12",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type"
},
"marker": "TOC1",
"growth_cond_name": "growth_edwards_ph12",
"experiment_cond_name": "experiment_edwards_ph12toLL"
},
{
"sample_id": "13",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type"
},
"marker": "TOC1",
"growth_cond_name": "growth_edwards_ph18",
"experiment_cond_name": "experiment_edwards_ph18toLL"
},
{
"sample_id": "14",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type"
},
"marker": "TOC1",
"growth_cond_name": "growth_edwards_ph6",
"experiment_cond_name": "experiment_edwards_ph6toDD"
},
{
"sample_id": "15",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type"
},
"marker": "TOC1",
"growth_cond_name": "growth_edwards_ph12",
"experiment_cond_name": "experiment_edwards_ph12toDD"
},
{
"sample_id": "16",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type"
},
"marker": "TOC1",
"growth_cond_name": "growth_edwards_ph18",
"experiment_cond_name": "experiment_edwards_ph18toDD"
},
{
"sample_id": "17",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type"
},
"marker": "GI",
"growth_cond_name": "growth_edwards_ph3",
"experiment_cond_name": "experiment_edwards_ph3toLL"
},
{
"sample_id": "18",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type"
},
"marker": "GI",
"growth_cond_name": "growth_edwards_ph6",
"experiment_cond_name": "experiment_edwards_ph6toLL"
},
{
"sample_id": "19",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type"
},
"marker": "GI",
"growth_cond_name": "growth_edwards_ph9",
"experiment_cond_name": "experiment_edwards_ph9toLL"
},
{
"sample_id": "20",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type"
},
"marker": "GI",
"growth_cond_name": "growth_edwards_ph12",
"experiment_cond_name": "experiment_edwards_ph12toLL"
},
{
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]
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},
"biblio": {
"principal": "Andrew J. Millar",
"institution": "University of Edinburgh",
"author": "Kieron D. Edwards"
}
}
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Created: 18th Jun 2026 at 12:53
Last updated: 18th Jun 2026 at 12:53
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Version 1 (earliest) Created 18th Jun 2026 at 12:53 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 Kieron D Edwards on the original BioDare and automatically transferred to FAIRDOM Hub.
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Quantitative analysis of regulatory flexibility under changing environmental conditions
Edwards et al. (2010)
DOI: 10.1038/msb.2010.81
Submitter: Daniel Thedie
Investigation: Kieron D Edwards
Assays: Edwards et al. (2010); WT in different light conditions.
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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)
