BioDare_metadata Version 1
Original BioDare metadata, converted to json format
SEEK ID: https://fairdomhub.org/data_files/8611?version=1
Filename:
BioDare_metadata.json
Format: JSON document
Size: 308 KB
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"desc": {
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"id": "12962294335805",
"status": "finished",
"name": "Q-PCR LD (12:12) 17C ELF3",
"purpose": "Experiment carry out to reparameterize the clock off Succrose",
"description": "Seedlings were entrained for 7 days at 22C in 12:12 white light. Then shifted to 17C 12:12 white light. Samples were collected on the 6th day at 17 degrees.",
"comments": "Sample time 24h. 24h sample lost for some genotypes\nPrimer JF260/261 used for this experiment. Primers used in Millar lab and other Robust experiments\nNo data available for Col, prr7-3, prr9-1 or prr7-3/prr9-1",
"provenance": {
"site": "Edinburgh",
"author": "Aurora Pinas-Fernandez",
"start_date": "2010-06-01"
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"name": "Entrainment 22C Diurnal",
"medium": "Agar 1.2% MS 0.5",
"incubation": "3 hours at 4C",
"growth_space": "Sanyo",
"duration": "7.0",
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"env_conditions": {
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"label": "const. 22.0C",
"duration": "7",
"env_day": {
"type": "constant_temp",
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"duration": "7",
"cycle_length": "24",
"base_value": "22.0",
"second_value": "22.0"
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}
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"light_channel": {
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"intensity": "60",
"source": "tube",
"env_conditions": {
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"label": "LD 12:00:12:00",
"duration": "7",
"env_day": {
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"label": "diurnal light",
"duration": "7",
"cycle_length": "24",
"base_value": "0.0",
"second_value": "100.0",
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"duration": "12:00"
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"medium": "Agar 1.2% MS 0.5",
"growth_space": "Binder",
"duration": "6.0",
"exp_time_zero": "72",
"temperature_conditions": {
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"env_conditions": {
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"label": "const. 17.0C",
"duration": "6",
"env_day": {
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"intensity": "60",
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"duration": "6",
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"label": "diurnal light",
"duration": "6",
"cycle_length": "24",
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"second_value": "100.0",
"env_period": {
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"equipment": "Robot + Light Cycler 480",
"parameters": "JF260-ELF3-F & JF261-ELF3-R\nJF588-ELF3-F & JF589-ELF3-F\nCycle: 2 - Roche Parameters-cDNA dil 1/10",
"description": "JF260-ELF3-F: GGAAAGCCATTGCCAATCAA\nJF261-ELF3-R: ATCCGGTGATGCAGCAATAAGT\nJF588-ELF3-F:GGTCATTATATGCCTACACCA\nJF589-ELF3-F: GAAGTAGCCATTACCAGGAG",
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"background": "Wasilewski (WS)",
"genotype": "lhy-21 cca1 gi-11",
"line": "unknown",
"provenance": "Robust Stock"
},
"marker": "ELF3",
"growth_cond_name": "Entrainment 22C Diurnal",
"experiment_cond_name": "17C LD (12:12) Off Sucrose",
"collection_time": "12.00",
"ignored": "false"
},
{
"sample_id": "1427",
"sample_type": "RNA extract",
"origin": "whole seedling",
"growth_stage": "seedling",
"age": "13",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "lhy-21 cca1 gi-11",
"line": "unknown",
"provenance": "Robust Stock"
},
"marker": "ELF3",
"growth_cond_name": "Entrainment 22C Diurnal",
"experiment_cond_name": "17C LD (12:12) Off Sucrose",
"collection_time": "12.00",
"ignored": "false"
},
{
"sample_id": "1428",
"sample_type": "RNA extract",
"origin": "whole seedling",
"growth_stage": "seedling",
"age": "13",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "lhy-21 cca1 gi-11",
"line": "unknown",
"provenance": "Robust Stock"
},
"marker": "ELF3",
"growth_cond_name": "Entrainment 22C Diurnal",
"experiment_cond_name": "17C LD (12:12) Off Sucrose",
"collection_time": "12.00",
"ignored": "false"
},
{
"sample_id": "1429",
"sample_type": "RNA extract",
"origin": "whole seedling",
"growth_stage": "seedling",
"age": "13",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "lhy-21 cca1 gi-11",
"line": "unknown",
"provenance": "Robust Stock"
},
"marker": "ELF3",
"growth_cond_name": "Entrainment 22C Diurnal",
"experiment_cond_name": "17C LD (12:12) Off Sucrose",
"collection_time": "14.00",
"ignored": "false"
},
{
"sample_id": "1430",
"sample_type": "RNA extract",
"origin": "whole seedling",
"growth_stage": "seedling",
"age": "13",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "lhy-21 cca1 gi-11",
"line": "unknown",
"provenance": "Robust Stock"
},
"marker": "ELF3",
"growth_cond_name": "Entrainment 22C Diurnal",
"experiment_cond_name": "17C LD (12:12) Off Sucrose",
"collection_time": "14.00",
"ignored": "false"
},
{
"sample_id": "1431",
"sample_type": "RNA extract",
"origin": "whole seedling",
"growth_stage": "seedling",
"age": "13",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "lhy-21 cca1 gi-11",
"line": "unknown",
"provenance": "Robust Stock"
},
"marker": "ELF3",
"growth_cond_name": "Entrainment 22C Diurnal",
"experiment_cond_name": "17C LD (12:12) Off Sucrose",
"collection_time": "14.00",
"ignored": "false"
},
{
"sample_id": "1432",
"sample_type": "RNA extract",
"origin": "whole seedling",
"growth_stage": "seedling",
"age": "13",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "lhy-21 cca1 gi-11",
"line": "unknown",
"provenance": "Robust Stock"
},
"marker": "ELF3",
"growth_cond_name": "Entrainment 22C Diurnal",
"experiment_cond_name": "17C LD (12:12) Off Sucrose",
"collection_time": "16.00",
"ignored": "false"
},
{
"sample_id": "1433",
"sample_type": "RNA extract",
"origin": "whole seedling",
"growth_stage": "seedling",
"age": "13",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "lhy-21 cca1 gi-11",
"line": "unknown",
"provenance": "Robust Stock"
},
"marker": "ELF3",
"growth_cond_name": "Entrainment 22C Diurnal",
"experiment_cond_name": "17C LD (12:12) Off Sucrose",
"collection_time": "16.00",
"ignored": "false"
},
{
"sample_id": "1434",
"sample_type": "RNA extract",
"origin": "whole seedling",
"growth_stage": "seedling",
"age": "13",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "lhy-21 cca1 gi-11",
"line": "unknown",
"provenance": "Robust Stock"
},
"marker": "ELF3",
"growth_cond_name": "Entrainment 22C Diurnal",
"experiment_cond_name": "17C LD (12:12) Off Sucrose",
"collection_time": "16.00",
"ignored": "false"
},
{
"sample_id": "1435",
"sample_type": "RNA extract",
"origin": "whole seedling",
"growth_stage": "seedling",
"age": "13",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "lhy-21 cca1 gi-11",
"line": "unknown",
"provenance": "Robust Stock"
},
"marker": "ELF3",
"growth_cond_name": "Entrainment 22C Diurnal",
"experiment_cond_name": "17C LD (12:12) Off Sucrose",
"collection_time": "18.00",
"ignored": "false"
},
{
"sample_id": "1436",
"sample_type": "RNA extract",
"origin": "whole seedling",
"growth_stage": "seedling",
"age": "13",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "lhy-21 cca1 gi-11",
"line": "unknown",
"provenance": "Robust Stock"
},
"marker": "ELF3",
"growth_cond_name": "Entrainment 22C Diurnal",
"experiment_cond_name": "17C LD (12:12) Off Sucrose",
"collection_time": "18.00",
"ignored": "false"
},
{
"sample_id": "1437",
"sample_type": "RNA extract",
"origin": "whole seedling",
"growth_stage": "seedling",
"age": "13",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "lhy-21 cca1 gi-11",
"line": "unknown",
"provenance": "Robust Stock"
},
"marker": "ELF3",
"growth_cond_name": "Entrainment 22C Diurnal",
"experiment_cond_name": "17C LD (12:12) Off Sucrose",
"collection_time": "18.00",
"ignored": "false"
},
{
"sample_id": "1438",
"sample_type": "RNA extract",
"origin": "whole seedling",
"growth_stage": "seedling",
"age": "13",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "lhy-21 cca1 gi-11",
"line": "unknown",
"provenance": "Robust Stock"
},
"marker": "ELF3",
"growth_cond_name": "Entrainment 22C Diurnal",
"experiment_cond_name": "17C LD (12:12) Off Sucrose",
"collection_time": "20.00",
"ignored": "false"
},
{
"sample_id": "1439",
"sample_type": "RNA extract",
"origin": "whole seedling",
"growth_stage": "seedling",
"age": "13",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "lhy-21 cca1 gi-11",
"line": "unknown",
"provenance": "Robust Stock"
},
"marker": "ELF3",
"growth_cond_name": "Entrainment 22C Diurnal",
"experiment_cond_name": "17C LD (12:12) Off Sucrose",
"collection_time": "20.00",
"ignored": "false"
},
{
"sample_id": "1440",
"sample_type": "RNA extract",
"origin": "whole seedling",
"growth_stage": "seedling",
"age": "13",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "lhy-21 cca1 gi-11",
"line": "unknown",
"provenance": "Robust Stock"
},
"marker": "ELF3",
"growth_cond_name": "Entrainment 22C Diurnal",
"experiment_cond_name": "17C LD (12:12) Off Sucrose",
"collection_time": "20.00",
"ignored": "false"
},
{
"sample_id": "1441",
"sample_type": "RNA extract",
"origin": "whole seedling",
"growth_stage": "seedling",
"age": "13",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "lhy-21 cca1 gi-11",
"line": "unknown",
"provenance": "Robust Stock"
},
"marker": "ELF3",
"growth_cond_name": "Entrainment 22C Diurnal",
"experiment_cond_name": "17C LD (12:12) Off Sucrose",
"collection_time": "22.00",
"ignored": "false"
},
{
"sample_id": "1442",
"sample_type": "RNA extract",
"origin": "whole seedling",
"growth_stage": "seedling",
"age": "13",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "lhy-21 cca1 gi-11",
"line": "unknown",
"provenance": "Robust Stock"
},
"marker": "ELF3",
"growth_cond_name": "Entrainment 22C Diurnal",
"experiment_cond_name": "17C LD (12:12) Off Sucrose",
"collection_time": "22.00",
"ignored": "false"
},
{
"sample_id": "1443",
"sample_type": "RNA extract",
"origin": "whole seedling",
"growth_stage": "seedling",
"age": "13",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "lhy-21 cca1 gi-11",
"line": "unknown",
"provenance": "Robust Stock"
},
"marker": "ELF3",
"growth_cond_name": "Entrainment 22C Diurnal",
"experiment_cond_name": "17C LD (12:12) Off Sucrose",
"collection_time": "22.00",
"ignored": "false"
},
{
"sample_id": "1444",
"sample_type": "RNA extract",
"origin": "whole seedling",
"growth_stage": "seedling",
"age": "13",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "lhy-21 cca1 gi-11",
"line": "unknown",
"provenance": "Robust Stock"
},
"marker": "ELF3",
"growth_cond_name": "Entrainment 22C Diurnal",
"experiment_cond_name": "17C LD (12:12) Off Sucrose",
"collection_time": "24.00",
"ignored": "false"
},
{
"sample_id": "1445",
"sample_type": "RNA extract",
"origin": "whole seedling",
"growth_stage": "seedling",
"age": "13",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "lhy-21 cca1 gi-11",
"line": "unknown",
"provenance": "Robust Stock"
},
"marker": "ELF3",
"growth_cond_name": "Entrainment 22C Diurnal",
"experiment_cond_name": "17C LD (12:12) Off Sucrose",
"collection_time": "24.00",
"ignored": "false"
},
{
"sample_id": "1446",
"sample_type": "RNA extract",
"origin": "whole seedling",
"growth_stage": "seedling",
"age": "13",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "lhy-21 cca1 gi-11",
"line": "unknown",
"provenance": "Robust Stock"
},
"marker": "ELF3",
"growth_cond_name": "Entrainment 22C Diurnal",
"experiment_cond_name": "17C LD (12:12) Off Sucrose",
"collection_time": "24.00",
"ignored": "false"
}
]
}
},
"pedro": {
"@xmlns:xsi": "http://www.w3.org/2001/XMLSchema-instance",
"@xsi:schemaLocation": "/W:/ROBuST/DataDescription/models/pcr/model/pcr_model.xsd",
"status": "finished",
"name": "Q-PCR LD (12:12) 17C ELF3",
"purpose": "Experiment carry out to reparameterize the clock off Succrose",
"description": "Seedlings were entrained for 7 days at 22C in 12:12 white light. Then shifted to 17C 12:12 white light. Samples were collected on the 6th day at 17 degrees.",
"comments": "Sample time 24h. 24h sample lost for some genotypes\nPrimer JF260/261 used for this experiment. Primers used in Millar lab and other Robust experiments\nNo data available for Col, prr7-3, prr9-1 or prr7-3/prr9-1",
"provenance": {
"site": "Edinburgh",
"author": "Aurora Pinas-Fernandez",
"start_date": "2010-06-01"
},
"growth_condition": {
"name": "Entrainment 22C Diurnal",
"medium": "Agar 1.2% MS 0.5",
"incubation": "3 hours at 4C",
"growth_space": "Sanyo",
"duration": "7",
"temperature_conditions": {
"constant_temp": {
"cycle_length": "24",
"base_temp": "22"
}
},
"light_conditions": {
"light_channel": {
"spectrum": "white",
"intensity": "60",
"source": "tube",
"diurnal_light": {
"cycle_length": "24",
"start_time": "0",
"duration": "12"
}
}
}
},
"experimental_condition": {
"name": "17C LD (12:12) Off Sucrose",
"medium": "Agar 1.2% MS 0.5",
"growth_space": "Binder",
"duration": "6",
"exp_time_zero": "72",
"temperature_conditions": {
"constant_temp": {
"cycle_length": "24",
"base_temp": "17"
}
},
"light_conditions": {
"light_channel": {
"spectrum": "white",
"intensity": "60",
"source": "tube",
"diurnal_light": {
"cycle_length": "24",
"start_time": "0",
"duration": "12"
}
}
}
},
"measurement": {
"technique": "RT-PCR",
"equipment": "Robot + Light Cycler 480",
"parameters": "JF260-ELF3-F & JF261-ELF3-R\nJF588-ELF3-F & JF589-ELF3-F\nCycle: 2 - Roche Parameters-cDNA dil 1/10",
"description": "JF260-ELF3-F: GGAAAGCCATTGCCAATCAA\nJF261-ELF3-R: ATCCGGTGATGCAGCAATAAGT\nJF588-ELF3-F:GGTCATTATATGCCTACACCA\nJF589-ELF3-F: GAAGTAGCCATTACCAGGAG"
},
"sample_preparation": {
"method": "Samples were harvested and keeped on RNAlader for some weeks, at 4C and -20C. RNa extraction was done following protocol of GE Health Care-illustra RNAspin 96RNA Isolation kit. Samples were spect with Nanodrop. cDNA synthesis was done with Super Script Vilo kit( Invitrogene) from 1ugr RNA."
},
"samples": {
"sample": [
{
"sample_id": "1166",
"sample_type": "RNA extract",
"origin": "whole seedling",
"growth_stage": "seedling",
"age": "13",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"provenance": "Robust Stock"
},
"marker": "ELF3",
"growth_cond_name": "Entrainment 22C Diurnal",
"experiment_cond_name": "17C LD (12:12) Off Sucrose",
"collection_time": "0.00"
},
{
"sample_id": "1167",
"sample_type": "RNA extract",
"origin": "whole seedling",
"growth_stage": "seedling",
"age": "13",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"provenance": "Robust Stock"
},
"marker": "ELF3",
"growth_cond_name": "Entrainment 22C Diurnal",
"experiment_cond_name": "17C LD (12:12) Off Sucrose",
"collection_time": "0.00"
},
{
"sample_id": "1168",
"sample_type": "RNA extract",
"origin": "whole seedling",
"growth_stage": "seedling",
"age": "13",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"provenance": "Robust Stock"
},
"marker": "ELF3",
"growth_cond_name": "Entrainment 22C Diurnal",
"experiment_cond_name": "17C LD (12:12) Off Sucrose",
"collection_time": "0.00"
},
{
"sample_id": "1169",
"sample_type": "RNA extract",
"origin": "whole seedling",
"growth_stage": "seedling",
"age": "13",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"provenance": "Robust Stock"
},
"marker": "ELF3",
"growth_cond_name": "Entrainment 22C Diurnal",
"experiment_cond_name": "17C LD (12:12) Off Sucrose",
"collection_time": "2.00"
},
{
"sample_id": "1170",
"sample_type": "RNA extract",
"origin": "whole seedling",
"growth_stage": "seedling",
"age": "13",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"provenance": "Robust Stock"
},
"marker": "ELF3",
"growth_cond_name": "Entrainment 22C Diurnal",
"experiment_cond_name": "17C LD (12:12) Off Sucrose",
"collection_time": "2.00"
},
{
"sample_id": "1171",
"sample_type": "RNA extract",
"origin": "whole seedling",
"growth_stage": "seedling",
"age": "13",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"provenance": "Robust Stock"
},
"marker": "ELF3",
"growth_cond_name": "Entrainment 22C Diurnal",
"experiment_cond_name": "17C LD (12:12) Off Sucrose",
"collection_time": "2.00"
},
{
"sample_id": "1172",
"sample_type": "RNA extract",
"origin": "whole seedling",
"growth_stage": "seedling",
"age": "13",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"provenance": "Robust Stock"
},
"marker": "ELF3",
"growth_cond_name": "Entrainment 22C Diurnal",
"experiment_cond_name": "17C LD (12:12) Off Sucrose",
"collection_time": "4.00"
},
{
"sample_id": "1173",
"sample_type": "RNA extract",
"origin": "whole seedling",
"growth_stage": "seedling",
"age": "13",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"provenance": "Robust Stock"
},
"marker": "ELF3",
"growth_cond_name": "Entrainment 22C Diurnal",
"experiment_cond_name": "17C LD (12:12) Off Sucrose",
"collection_time": "4.00"
},
{
"sample_id": "1174",
"sample_type": "RNA extract",
"origin": "whole seedling",
"growth_stage": "seedling",
"age": "13",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"provenance": "Robust Stock"
},
"marker": "ELF3",
"growth_cond_name": "Entrainment 22C Diurnal",
"experiment_cond_name": "17C LD (12:12) Off Sucrose",
"collection_time": "4.00"
},
{
"sample_id": "1175",
"sample_type": "RNA extract",
"origin": "whole seedling",
"growth_stage": "seedling",
"age": "13",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"provenance": "Robust Stock"
},
"marker": "ELF3",
"growth_cond_name": "Entrainment 22C Diurnal",
"experiment_cond_name": "17C LD (12:12) Off Sucrose",
"collection_time": "6.00"
},
{
"sample_id": "1176",
"sample_type": "RNA extract",
"origin": "whole seedling",
"growth_stage": "seedling",
"age": "13",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"provenance": "Robust Stock"
},
"marker": "ELF3",
"growth_cond_name": "Entrainment 22C Diurnal",
"experiment_cond_name": "17C LD (12:12) Off Sucrose",
"collection_time": "6.00"
},
{
"sample_id": "1177",
"sample_type": "RNA extract",
"origin": "whole seedling",
"growth_stage": "seedling",
"age": "13",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"provenance": "Robust Stock"
},
"marker": "ELF3",
"growth_cond_name": "Entrainment 22C Diurnal",
"experiment_cond_name": "17C LD (12:12) Off Sucrose",
"collection_time": "6.00"
},
{
"sample_id": "1178",
"sample_type": "RNA extract",
"origin": "whole seedling",
"growth_stage": "seedling",
"age": "13",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"provenance": "Robust Stock"
},
"marker": "ELF3",
"growth_cond_name": "Entrainment 22C Diurnal",
"experiment_cond_name": "17C LD (12:12) Off Sucrose",
"collection_time": "8.00"
},
{
"sample_id": "1179",
"sample_type": "RNA extract",
"origin": "whole seedling",
"growth_stage": "seedling",
"age": "13",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"provenance": "Robust Stock"
},
"marker": "ELF3",
"growth_cond_name": "Entrainment 22C Diurnal",
"experiment_cond_name": "17C LD (12:12) Off Sucrose",
"collection_time": "8.00"
},
{
"sample_id": "1180",
"sample_type": "RNA extract",
"origin": "whole seedling",
"growth_stage": "seedling",
"age": "13",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"provenance": "Robust Stock"
},
"marker": "ELF3",
"growth_cond_name": "Entrainment 22C Diurnal",
"experiment_cond_name": "17C LD (12:12) Off Sucrose",
"collection_time": "8.00"
},
{
"sample_id": "1181",
"sample_type": "RNA extract",
"origin": "whole seedling",
"growth_stage": "seedling",
"age": "13",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"provenance": "Robust Stock"
},
"marker": "ELF3",
"growth_cond_name": "Entrainment 22C Diurnal",
"experiment_cond_name": "17C LD (12:12) Off Sucrose",
"collection_time": "10.00"
},
{
"sample_id": "1182",
"sample_type": "RNA extract",
"origin": "whole seedling",
"growth_stage": "seedling",
"age": "13",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"provenance": "Robust Stock"
},
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},
"biblio": {
"principal": "Karen Halliday",
"institution": "University of Edinburgh",
"author": "Aurora Pinas-Fernandez",
"curator": [
"Julia Foreman",
"Andrew Millar"
]
}
}
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Created: 18th Jun 2026 at 12:28
Last updated: 18th Jun 2026 at 12:29
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Version 1 (earliest) Created 18th Jun 2026 at 12:28 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 Flis Anna on the original BioDare and automatically transferred to FAIRDOM Hub.
Submitter: Daniel Thedie
Studies: Flis et al. (2015), Flis et al. (2016), Unpublished
Assays: Clock gene RNAs under RD-RR in clock mutants, expt 1, Clock gene RNAs under RD-RR in clock mutants, expt 2, Clock gene RNAs under RD-RR in clock mutants, expt 3, Clock gene RNAs under RD-RR in clock mutants, expt 4, Flis et al. TiMet clock gene comparison across photoperiods, McWatters A.t. Col-0 WT clock RNA timeseries, Q-PCR LD (12:12) 17C CAB2, Q-PCR LD (12:12) 17C CCA1, Q-PCR LD (12:12) 17C ELF3, Q-PCR LD (12:12) 17C ELF4, Q-PCR LD (12:12) 17C GI, Q-PCR LD (12:12) 17C LHY, Q-PCR LD (12:12) 17C LUX, Q-PCR LD (12:12) 17C PRR5, Q-PCR LD (12:12) 17C PRR7, Q-PCR LD (12:12) 17C PRR9, Q-PCR LD (12:12) 17C TOC1, TiMet WP1.1 WS seedling vs rosette, TiMet WP1.1 qRT-PCR LD to LL and LD, TiMet WP1.1 qRT-PCR elf3 LD
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Defining the robust behaviour of the plant clock gene circuit with absolute RNA timeseries and open infrastructure
Flis et al. (2015)
DOI: 10.1098/rsob.150042
Submitter: Daniel Thedie
Investigation: Flis Anna
Assays: Clock gene RNAs under RD-RR in clock mutants, expt 1, Clock gene RNAs under RD-RR in clock mutants, expt 2, Clock gene RNAs under RD-RR in clock mutants, expt 3, Clock gene RNAs under RD-RR in clock mutants, expt 4, McWatters A.t. Col-0 WT clock RNA timeseries, Q-PCR LD (12:12) 17C CAB2, Q-PCR LD (12:12) 17C CCA1, Q-PCR LD (12:12) 17C ELF3, Q-PCR LD (12:12) 17C ELF4, Q-PCR LD (12:12) 17C GI, Q-PCR LD (12:12) 17C LHY, Q-PCR LD (12:12) 17C LUX, Q-PCR LD (12:12) 17C PRR5, Q-PCR LD (12:12) 17C PRR7, Q-PCR LD (12:12) 17C PRR9, Q-PCR LD (12:12) 17C TOC1, TiMet WP1.1 WS seedling vs rosette, TiMet WP1.1 qRT-PCR LD to LL and LD, TiMet WP1.1 qRT-PCR elf3 LD
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Q-PCR LD (12:12) 17C ELF3
| Property | Value |
|---|---|
| BioDare ID | 12962294335805 |
| Author | Aurora Pinas-Fernandez |
| Institution | University of Edinburgh |
| License |
Description
Seedlings were entrained for 7 days at 22C in 12:12 white light. Then shifted to 17C 12:12 white light. Samples were collected on the 6th day at 17 degrees.
Purpose
Experiment carry out to reparameterize the clock off Succrose
Comments
Sample time 24h. 24h sample ...
Submitter: Daniel Thedie
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Flis Anna
Study: Flis et al. (2015)
