BioDare_metadata Version 1
Original BioDare metadata, converted to json format
SEEK ID: https://fairdomhub.org/data_files/8700?version=1
Filename:
BioDare_metadata.json
Format: JSON document
Size: 392 KB
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"comment": "System generated on 17-Oct-2014"
},
"desc": {
"experiment_type": "Luciferase exp",
"id": "13394446996851",
"status": "finished",
"name": "BW-intact_LL-LL_#58",
"purpose": "Testing spatiotemporal pattern of rhythmic gene expression to assay intercellular coupling, and comparing the strength of intercellular coupling in LL with entrainment in LD.",
"description": "Intact leaves of CCA1:LUC grown and imaged under constant light.\nSample number 58 of Table S1 in the 2012 PNAS paper \"Spontaneous spatiotemporal waves of gene expression from biological clocks in the leaf\". The paper is attached as a file to sample #03.",
"comments": "Start date is the date when imaging started.\n\nNumerical data are provided as a 2D x time matrix in Matlab format (.mat), and as a text file with coordinates above each column of data. Please see the attached ReadMe file for notes on the data.",
"provenance": {
"site": "Edinburgh",
"author": "Benedicte Wenden",
"start_date": "2010-02-25"
},
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"medium": "Agar 1.25% MS 0.5",
"incubation": "3 days at 4C",
"growth_space": "Sanyo",
"duration": "11.0",
"temperature_conditions": {
"label": "const. 22.0C",
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"label": "const. 22.0C",
"duration": "11",
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"label": "constant temperature",
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"cycle_length": "24",
"base_value": "22.0",
"second_value": "22.0"
}
}
},
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"intensity": "80",
"source": "tube",
"env_conditions": {
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"label": "LL",
"duration": "11",
"env_day": {
"type": "constant_light",
"label": "constant light",
"duration": "11",
"cycle_length": "24",
"base_value": "0.0",
"second_value": "100.0",
"env_period": {
"start_time": "0:00",
"duration": "24:00"
}
}
}
}
}
},
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"name": "LL",
"medium": "Agar 1.2% MS 0.5",
"growth_space": "Percival + LED",
"duration": "7.0",
"exp_time_zero": "24",
"temperature_conditions": {
"label": "const. 22.0C",
"env_conditions": {
"type": "constant_temp",
"label": "const. 22.0C",
"duration": "7",
"env_day": {
"type": "constant_temp",
"label": "constant temperature",
"duration": "7",
"cycle_length": "24",
"base_value": "22.0",
"second_value": "22.0"
}
}
},
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"label": "B+R: LL",
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{
"spectrum": "red",
"intensity": "20",
"source": "LED",
"env_conditions": {
"type": "constant_light",
"label": "LL",
"duration": "7",
"env_day": {
"type": "constant_light",
"label": "constant light",
"duration": "7",
"cycle_length": "24",
"base_value": "0.0",
"second_value": "100.0",
"env_period": {
"start_time": "0:00",
"duration": "24:00"
}
}
}
},
{
"spectrum": "blue",
"intensity": "20",
"source": "LED",
"env_conditions": {
"type": "constant_light",
"label": "LL",
"duration": "7",
"env_day": {
"type": "constant_light",
"label": "constant light",
"duration": "7",
"cycle_length": "24",
"base_value": "0.0",
"second_value": "100.0",
"env_period": {
"start_time": "0:00",
"duration": "24:00"
}
}
}
}
]
}
},
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"equipment": "HAM 2",
"parameters": "15-minute exposures every 40 minutes. LEDs were switched off 5 mins before each image.",
"description": "As outlined in the PNAS paper."
},
"sample_preparation": {
"method": "11-d-old\nleaves were kept still both horizontally and vertically between\na slide and a coverslip lying on two layers of porous fiber tape\n(Micropore), thus allowing an airflow around the leaves. Horizontal\nmovements were prevented by taping the petiole to the\nslide with a thin piece of porous fiber tape. The rest of the seedling\nwas supported by a second slide and nutrients and water were\nprovided to the root from a liquid Murashige and Skoog (MS)\nmedium (Fig. S1 A and B of PNAS paper).\n\nPlants were sprayed with 5 mM luciferin solution in 0.01% Triton-X100 48h before data collection started. Luciferin was also supplied in the liquid medium to which the roots were transferred 24h before data collection started."
},
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"sample": [
{
"sample_id": "1",
"sample_type": "tissue",
"origin": "leaf",
"growth_stage": "seedling",
"age": "11",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "W1",
"provenance": "Robust stock"
},
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"ignored": "false"
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"genotype": "Wild Type",
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},
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},
{
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"growth_stage": "seedling",
"age": "11",
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},
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"sample_type": "tissue",
"origin": "leaf",
"growth_stage": "seedling",
"age": "11",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "W1",
"provenance": "Robust stock"
},
"marker": "CCA1",
"growth_cond_name": "LL growth",
"experiment_cond_name": "LL",
"ignored": "false"
},
{
"sample_id": "326",
"sample_type": "tissue",
"origin": "leaf",
"growth_stage": "seedling",
"age": "11",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "W1",
"provenance": "Robust stock"
},
"marker": "CCA1",
"growth_cond_name": "LL growth",
"experiment_cond_name": "LL",
"ignored": "false"
},
{
"sample_id": "327",
"sample_type": "tissue",
"origin": "leaf",
"growth_stage": "seedling",
"age": "11",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "W1",
"provenance": "Robust stock"
},
"marker": "CCA1",
"growth_cond_name": "LL growth",
"experiment_cond_name": "LL",
"ignored": "false"
},
{
"sample_id": "328",
"sample_type": "tissue",
"origin": "leaf",
"growth_stage": "seedling",
"age": "11",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "W1",
"provenance": "Robust stock"
},
"marker": "CCA1",
"growth_cond_name": "LL growth",
"experiment_cond_name": "LL",
"ignored": "false"
},
{
"sample_id": "329",
"sample_type": "tissue",
"origin": "leaf",
"growth_stage": "seedling",
"age": "11",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "W1",
"provenance": "Robust stock"
},
"marker": "CCA1",
"growth_cond_name": "LL growth",
"experiment_cond_name": "LL",
"ignored": "false"
},
{
"sample_id": "330",
"sample_type": "tissue",
"origin": "leaf",
"growth_stage": "seedling",
"age": "11",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "W1",
"provenance": "Robust stock"
},
"marker": "CCA1",
"growth_cond_name": "LL growth",
"experiment_cond_name": "LL",
"ignored": "false"
},
{
"sample_id": "331",
"sample_type": "tissue",
"origin": "leaf",
"growth_stage": "seedling",
"age": "11",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "W1",
"provenance": "Robust stock"
},
"marker": "CCA1",
"growth_cond_name": "LL growth",
"experiment_cond_name": "LL",
"ignored": "false"
},
{
"sample_id": "332",
"sample_type": "tissue",
"origin": "leaf",
"growth_stage": "seedling",
"age": "11",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "W1",
"provenance": "Robust stock"
},
"marker": "CCA1",
"growth_cond_name": "LL growth",
"experiment_cond_name": "LL",
"ignored": "false"
},
{
"sample_id": "333",
"sample_type": "tissue",
"origin": "leaf",
"growth_stage": "seedling",
"age": "11",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "W1",
"provenance": "Robust stock"
},
"marker": "CCA1",
"growth_cond_name": "LL growth",
"experiment_cond_name": "LL",
"ignored": "false"
},
{
"sample_id": "334",
"sample_type": "tissue",
"origin": "leaf",
"growth_stage": "seedling",
"age": "11",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "W1",
"provenance": "Robust stock"
},
"marker": "CCA1",
"growth_cond_name": "LL growth",
"experiment_cond_name": "LL",
"ignored": "false"
},
{
"sample_id": "335",
"sample_type": "tissue",
"origin": "leaf",
"growth_stage": "seedling",
"age": "11",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "W1",
"provenance": "Robust stock"
},
"marker": "CCA1",
"growth_cond_name": "LL growth",
"experiment_cond_name": "LL",
"ignored": "false"
},
{
"sample_id": "336",
"sample_type": "tissue",
"origin": "leaf",
"growth_stage": "seedling",
"age": "11",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "W1",
"provenance": "Robust stock"
},
"marker": "CCA1",
"growth_cond_name": "LL growth",
"experiment_cond_name": "LL",
"ignored": "false"
},
{
"sample_id": "337",
"sample_type": "tissue",
"origin": "leaf",
"growth_stage": "seedling",
"age": "11",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "W1",
"provenance": "Robust stock"
},
"marker": "CCA1",
"growth_cond_name": "LL growth",
"experiment_cond_name": "LL",
"ignored": "false"
},
{
"sample_id": "338",
"sample_type": "tissue",
"origin": "leaf",
"growth_stage": "seedling",
"age": "11",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "W1",
"provenance": "Robust stock"
},
"marker": "CCA1",
"growth_cond_name": "LL growth",
"experiment_cond_name": "LL",
"ignored": "false"
},
{
"sample_id": "339",
"sample_type": "tissue",
"origin": "leaf",
"growth_stage": "seedling",
"age": "11",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "W1",
"provenance": "Robust stock"
},
"marker": "CCA1",
"growth_cond_name": "LL growth",
"experiment_cond_name": "LL",
"ignored": "false"
},
{
"sample_id": "340",
"sample_type": "tissue",
"origin": "leaf",
"growth_stage": "seedling",
"age": "11",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "W1",
"provenance": "Robust stock"
},
"marker": "CCA1",
"growth_cond_name": "LL growth",
"experiment_cond_name": "LL",
"ignored": "false"
},
{
"sample_id": "341",
"sample_type": "tissue",
"origin": "leaf",
"growth_stage": "seedling",
"age": "11",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "W1",
"provenance": "Robust stock"
},
"marker": "CCA1",
"growth_cond_name": "LL growth",
"experiment_cond_name": "LL",
"ignored": "false"
},
{
"sample_id": "342",
"sample_type": "tissue",
"origin": "leaf",
"growth_stage": "seedling",
"age": "11",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "W1",
"provenance": "Robust stock"
},
"marker": "CCA1",
"growth_cond_name": "LL growth",
"experiment_cond_name": "LL",
"ignored": "false"
},
{
"sample_id": "343",
"sample_type": "tissue",
"origin": "leaf",
"growth_stage": "seedling",
"age": "11",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "W1",
"provenance": "Robust stock"
},
"marker": "CCA1",
"growth_cond_name": "LL growth",
"experiment_cond_name": "LL",
"ignored": "false"
},
{
"sample_id": "344",
"sample_type": "tissue",
"origin": "leaf",
"growth_stage": "seedling",
"age": "11",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "W1",
"provenance": "Robust stock"
},
"marker": "CCA1",
"growth_cond_name": "LL growth",
"experiment_cond_name": "LL",
"ignored": "false"
},
{
"sample_id": "345",
"sample_type": "tissue",
"origin": "leaf",
"growth_stage": "seedling",
"age": "11",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "W1",
"provenance": "Robust stock"
},
"marker": "CCA1",
"growth_cond_name": "LL growth",
"experiment_cond_name": "LL",
"ignored": "false"
},
{
"sample_id": "346",
"sample_type": "tissue",
"origin": "leaf",
"growth_stage": "seedling",
"age": "11",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "W1",
"provenance": "Robust stock"
},
"marker": "CCA1",
"growth_cond_name": "LL growth",
"experiment_cond_name": "LL",
"ignored": "false"
},
{
"sample_id": "347",
"sample_type": "tissue",
"origin": "leaf",
"growth_stage": "seedling",
"age": "11",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "W1",
"provenance": "Robust stock"
},
"marker": "CCA1",
"growth_cond_name": "LL growth",
"experiment_cond_name": "LL",
"ignored": "false"
},
{
"sample_id": "348",
"sample_type": "tissue",
"origin": "leaf",
"growth_stage": "seedling",
"age": "11",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "W1",
"provenance": "Robust stock"
},
"marker": "CCA1",
"growth_cond_name": "LL growth",
"experiment_cond_name": "LL",
"ignored": "false"
},
{
"sample_id": "349",
"sample_type": "tissue",
"origin": "leaf",
"growth_stage": "seedling",
"age": "11",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "W1",
"provenance": "Robust stock"
},
"marker": "CCA1",
"growth_cond_name": "LL growth",
"experiment_cond_name": "LL",
"ignored": "false"
},
{
"sample_id": "350",
"sample_type": "tissue",
"origin": "leaf",
"growth_stage": "seedling",
"age": "11",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "W1",
"provenance": "Robust stock"
},
"marker": "CCA1",
"growth_cond_name": "LL growth",
"experiment_cond_name": "LL",
"ignored": "false"
},
{
"sample_id": "351",
"sample_type": "tissue",
"origin": "leaf",
"growth_stage": "seedling",
"age": "11",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "W1",
"provenance": "Robust stock"
},
"marker": "CCA1",
"growth_cond_name": "LL growth",
"experiment_cond_name": "LL",
"ignored": "false"
},
{
"sample_id": "352",
"sample_type": "tissue",
"origin": "leaf",
"growth_stage": "seedling",
"age": "11",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "W1",
"provenance": "Robust stock"
},
"marker": "CCA1",
"growth_cond_name": "LL growth",
"experiment_cond_name": "LL",
"ignored": "false"
},
{
"sample_id": "353",
"sample_type": "tissue",
"origin": "leaf",
"growth_stage": "seedling",
"age": "11",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "W1",
"provenance": "Robust stock"
},
"marker": "CCA1",
"growth_cond_name": "LL growth",
"experiment_cond_name": "LL",
"ignored": "false"
},
{
"sample_id": "354",
"sample_type": "tissue",
"origin": "leaf",
"growth_stage": "seedling",
"age": "11",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "W1",
"provenance": "Robust stock"
},
"marker": "CCA1",
"growth_cond_name": "LL growth",
"experiment_cond_name": "LL",
"ignored": "false"
},
{
"sample_id": "355",
"sample_type": "tissue",
"origin": "leaf",
"growth_stage": "seedling",
"age": "11",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "W1",
"provenance": "Robust stock"
},
"marker": "CCA1",
"growth_cond_name": "LL growth",
"experiment_cond_name": "LL",
"ignored": "false"
},
{
"sample_id": "356",
"sample_type": "tissue",
"origin": "leaf",
"growth_stage": "seedling",
"age": "11",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "W1",
"provenance": "Robust stock"
},
"marker": "CCA1",
"growth_cond_name": "LL growth",
"experiment_cond_name": "LL",
"ignored": "false"
},
{
"sample_id": "357",
"sample_type": "tissue",
"origin": "leaf",
"growth_stage": "seedling",
"age": "11",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "W1",
"provenance": "Robust stock"
},
"marker": "CCA1",
"growth_cond_name": "LL growth",
"experiment_cond_name": "LL",
"ignored": "false"
},
{
"sample_id": "358",
"sample_type": "tissue",
"origin": "leaf",
"growth_stage": "seedling",
"age": "11",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "W1",
"provenance": "Robust stock"
},
"marker": "CCA1",
"growth_cond_name": "LL growth",
"experiment_cond_name": "LL",
"ignored": "false"
},
{
"sample_id": "359",
"sample_type": "tissue",
"origin": "leaf",
"growth_stage": "seedling",
"age": "11",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "W1",
"provenance": "Robust stock"
},
"marker": "CCA1",
"growth_cond_name": "LL growth",
"experiment_cond_name": "LL",
"ignored": "false"
},
{
"sample_id": "360",
"sample_type": "tissue",
"origin": "leaf",
"growth_stage": "seedling",
"age": "11",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "W1",
"provenance": "Robust stock"
},
"marker": "CCA1",
"growth_cond_name": "LL growth",
"experiment_cond_name": "LL",
"ignored": "false"
}
]
}
},
"pedro": {
"@xmlns:xsi": "http://www.w3.org/2001/XMLSchema-instance",
"@xsi:schemaLocation": "/O:/communal/DataDescription/models/luc/model/newluc_model.xsd",
"id": "will be updated by the system",
"status": "finished",
"name": "BW-intact_LL-LL_#58",
"purpose": "Testing spatiotemporal pattern of rhythmic gene expression to assay intercellular coupling, and comparing the strength of intercellular coupling in LL with entrainment in LD.",
"description": "Intact leaves of CCA1:LUC grown and imaged under constant light.\nSample number 58 of Table S1 in the 2012 PNAS paper \"Spontaneous spatiotemporal waves of gene expression from biological clocks in the leaf\". The paper is attached as a file to sample #03.",
"comments": "Start date is the date when imaging started.\n\nNumerical data are provided as a 2D x time matrix in Matlab format (.mat), and as a text file with coordinates above each column of data. Please see the attached ReadMe file for notes on the data.",
"provenance": {
"site": "Edinburgh",
"author": "Benedicte Wenden",
"start_date": "2010-02-25"
},
"growth_condition": {
"name": "LL growth",
"medium": "Agar 1.25% MS 0.5",
"incubation": "3 days at 4C",
"growth_space": "Sanyo",
"duration": "11",
"temperature_conditions": {
"constant_temp": {
"cycle_length": "24",
"base_temp": "22"
}
},
"light_conditions": {
"light_channel": {
"spectrum": "white",
"intensity": "80",
"source": "tube",
"constant_light": {
"cycle_length": "24"
}
}
}
},
"experimental_condition": {
"name": "LL",
"medium": "Agar 1.2% MS 0.5",
"growth_space": "Percival + LED",
"duration": "7",
"exp_time_zero": "24",
"temperature_conditions": {
"constant_temp": {
"cycle_length": "24",
"base_temp": "22"
}
},
"light_conditions": {
"light_channel": [
{
"spectrum": "red",
"intensity": "20",
"source": "LED",
"constant_light": {
"cycle_length": "24"
}
},
{
"spectrum": "blue",
"intensity": "20",
"source": "LED",
"constant_light": {
"cycle_length": "24"
}
}
]
}
},
"measurement": {
"technique": "Luciferase luminescence",
"equipment": "HAM 2",
"parameters": "15-minute exposures every 40 minutes. LEDs were switched off 5 mins before each image.",
"description": "As outlined in the PNAS paper."
},
"sample_preparation": {
"method": "11-d-old\nleaves were kept still both horizontally and vertically between\na slide and a coverslip lying on two layers of porous fiber tape\n(Micropore), thus allowing an airflow around the leaves. Horizontal\nmovements were prevented by taping the petiole to the\nslide with a thin piece of porous fiber tape. The rest of the seedling\nwas supported by a second slide and nutrients and water were\nprovided to the root from a liquid Murashige and Skoog (MS)\nmedium (Fig. S1 A and B of PNAS paper).\n\nPlants were sprayed with 5 mM luciferin solution in 0.01% Triton-X100 48h before data collection started. Luciferin was also supplied in the liquid medium to which the roots were transferred 24h before data collection started."
},
"samples": {
"sample": [
{
"sample_id": "1",
"sample_type": "tissue",
"origin": "leaf",
"growth_stage": "seedling",
"age": "11",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "W1",
"provenance": "Robust stock"
},
"marker": "CCA1",
"growth_cond_name": "LL growth",
"experiment_cond_name": "LL"
},
{
"sample_id": "2",
"sample_type": "tissue",
"origin": "leaf",
"growth_stage": "seedling",
"age": "11",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "W1",
"provenance": "Robust stock"
},
"marker": "CCA1",
"growth_cond_name": "LL growth",
"experiment_cond_name": "LL"
},
{
"sample_id": "3",
"sample_type": "tissue",
"origin": "leaf",
"growth_stage": "seedling",
"age": "11",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "W1",
"provenance": "Robust stock"
},
"marker": "CCA1",
"growth_cond_name": "LL growth",
"experiment_cond_name": "LL"
},
{
"sample_id": "4",
"sample_type": "tissue",
"origin": "leaf",
"growth_stage": "seedling",
"age": "11",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "W1",
"provenance": "Robust stock"
},
"marker": "CCA1",
"growth_cond_name": "LL growth",
"experiment_cond_name": "LL"
},
{
"sample_id": "5",
"sample_type": "tissue",
"origin": "leaf",
"growth_stage": "seedling",
"age": "11",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "W1",
"provenance": "Robust stock"
},
"marker": "CCA1",
"growth_cond_name": "LL growth",
"experiment_cond_name": "LL"
},
{
"sample_id": "6",
"sample_type": "tissue",
"origin": "leaf",
"growth_stage": "seedling",
"age": "11",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "W1",
"provenance": "Robust stock"
},
"marker": "CCA1",
"growth_cond_name": "LL growth",
"experiment_cond_name": "LL"
},
{
"sample_id": "7",
"sample_type": "tissue",
"origin": "leaf",
"growth_stage": "seedling",
"age": "11",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "W1",
"provenance": "Robust stock"
},
"marker": "CCA1",
"growth_cond_name": "LL growth",
"experiment_cond_name": "LL"
},
{
"sample_id": "8",
"sample_type": "tissue",
"origin": "leaf",
"growth_stage": "seedling",
"age": "11",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "W1",
"provenance": "Robust stock"
},
"marker": "CCA1",
"growth_cond_name": "LL growth",
"experiment_cond_name": "LL"
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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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Created: 18th Jun 2026 at 13:03
Last updated: 18th Jun 2026 at 13:04
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Version 1 (earliest) Created 18th Jun 2026 at 13:04 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 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
Spontaneous spatiotemporal waves of gene expression from biological clocks in the leaf
Wenden et al. (2012)
DOI: 10.1073/pnas.1118814109
Submitter: Daniel Thedie
Investigation: Wenden Benedicte
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
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BW-intact_LL-LL_#58
| Property | Value |
|---|---|
| BioDare ID | 13394446996851 |
| Author | Benedicte Wenden |
| Institution | University of Edinburgh |
| License | CC_BY |
Description
Intact leaves of CCA1:LUC grown and imaged under constant light. Sample number 58 of Table S1 in the 2012 PNAS paper "Spontaneous spatiotemporal waves of gene expression from biological clocks in the leaf". The paper is attached as a file to sample #03.
Purpose
Testing ...
Submitter: Daniel Thedie
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Wenden Benedicte
Study: Wenden et al. (2012)
