BioDare_metadata Version 1
Original BioDare metadata, converted to json format
SEEK ID: https://fairdomhub.org/data_files/9014?version=1
Filename:
BioDare_metadata.json
Format: JSON document
Size: 270 KB
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"desc": {
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"id": "3188",
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"name": "140515H2",
"purpose": "Control \"dark\" dawn experiment for double dawn experiment based on Virginie and Thiago's design (Stitt Lab).",
"description": "ZT0 lights remain switched off until ZT3. At ZT3 light comes on at 90 umolm-2s-1. Dusk is lights off at ZT 12. Dark dawn cycle is for 4 days then continuous light (first day with dark dawn) for 3 days. ie 9L:15D x4 LLx3.",
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"author": "Sarah Hodge",
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"comment": "4 days of 3 hours dark dawn, 9 hours of bright light 90 umolm-2-s-1, 12 hours dark followed by 3 days constant light, with dark dawn conditions on first dawn. The plates were transferred from entrainment conditions to experimental conditions at ZT4 on day 7.",
"temperature_conditions": {
"label": "const. 22.0C",
"env_conditions": {
"type": "constant_temp",
"label": "const. 22.0C",
"duration": "7",
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"type": "constant_temp",
"label": "constant temperature",
"duration": "7",
"cycle_length": "24",
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"second_value": "22.0"
}
}
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"label": "B+R: 4*DL 03:00-12:00; 1*DL 03:00:21:00; 2*LL",
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{
"spectrum": "red",
"intensity": "55",
"source": "LED",
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"type": "light_complex",
"label": "4*DL 03:00-12:00; 1*DL 03:00:21:00; 2*LL",
"duration": "7",
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{
"type": "diurnal_light",
"label": "diurnal light",
"duration": "4",
"cycle_length": "24",
"base_value": "0.0",
"second_value": "100.0",
"env_period": {
"start_time": "3:00",
"duration": "9:00"
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},
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"type": "diurnal_light",
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"duration": "1",
"cycle_length": "24",
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"second_value": "100.0",
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"start_time": "3:00",
"duration": "21:00"
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},
{
"type": "constant_light",
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"cycle_length": "24",
"base_value": "0.0",
"second_value": "100.0",
"env_period": {
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"duration": "24:00"
}
}
]
}
},
{
"spectrum": "blue",
"intensity": "35",
"source": "LED",
"env_conditions": {
"type": "light_complex",
"label": "4*DL 03:00-12:00; 1*DL 03:00:21:00; 2*LL",
"duration": "7",
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{
"type": "diurnal_light",
"label": "diurnal light",
"duration": "4",
"cycle_length": "24",
"base_value": "0.0",
"second_value": "100.0",
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"duration": "9:00"
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},
{
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"background": "Columbia (Col)",
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},
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},
"pedro": {
"@xmlns:xsi": "http://www.w3.org/2001/XMLSchema-instance",
"@xsi:schemaLocation": "//mpimp-golm/user/Homes/Mengin/PhD/Experiments/EXP-012_Luciferase 3h Double Dawn (Edinburgh Visit Millar's Lab)/DataDescription (Pedro-Biodare)/models/luc/model/newluc_model.xsd",
"id": "will be updated by the system",
"status": "in progress",
"name": "140515H2",
"purpose": "Control \"dark\" dawn experiment for double dawn experiment based on Virginie and Thiago's design (Stitt Lab).",
"description": "ZT0 lights remain switched off until ZT3. At ZT3 light comes on at 90 umolm-2s-1. Dusk is lights off at ZT 12. Dark dawn cycle is for 4 days then continuous light (first day with dark dawn) for 3 days. ie 9L:15D x4 LLx3.",
"comments": "Partner experiment: 140515H1",
"provenance": {
"site": "Edinburgh",
"author": "Sarah Hodge",
"start_date": "2015-05-14"
},
"growth_condition": {
"name": "12L:12D",
"medium": "Agar 1.2% MS 0.5",
"incubation": "6 days at 4C",
"growth_space": "Percival",
"duration": "7",
"comment": "Plants were entrained at light intensity 90 umolm-2s-1 to correspond to the light intensity of the experiment.\nThe plants were entrained for 1 day more than standard conditions due problems with imaging set up.",
"temperature_conditions": {
"constant_temp": {
"cycle_length": "24",
"base_temp": "22"
}
},
"light_conditions": {
"light_channel": {
"spectrum": "white",
"intensity": "90",
"source": "tube",
"diurnal_light": {
"cycle_length": "24",
"start_time": "0",
"duration": "12"
}
}
}
},
"experimental_condition": {
"name": "3D:9L:12Dx3 LLx3",
"medium": "Agar 1.2% MS 0.5",
"growth_space": "Percival + LED",
"duration": "7",
"comment": "4 days of 3 hours dark dawn, 9 hours of bright light 90 umolm-2-s-1, 12 hours dark followed by 3 days constant light, with dark dawn conditions on first dawn. The plates were transferred from entrainment conditions to experimental conditions at ZT4 on day 7.",
"temperature_conditions": {
"constant_temp": {
"cycle_length": "24",
"base_temp": "22"
}
},
"light_conditions": {
"light_channel": [
{
"spectrum": "red",
"intensity": "55",
"source": "LED",
"light_complex_settings": {
"light_days": [
{
"start_day": "1",
"duration": "4",
"diurnal_light": {
"cycle_length": "24",
"start_time": "3",
"duration": "9"
}
},
{
"start_day": "5",
"duration": "1",
"diurnal_light": {
"cycle_length": "24",
"start_time": "3",
"duration": "21"
}
},
{
"start_day": "6",
"duration": "2",
"constant_light": {
"cycle_length": "24"
}
}
]
}
},
{
"spectrum": "blue",
"intensity": "35",
"source": "LED",
"light_complex_settings": {
"light_days": [
{
"start_day": "1",
"duration": "4",
"diurnal_light": {
"cycle_length": "24",
"start_time": "3",
"duration": "9"
}
},
{
"start_day": "5",
"duration": "1",
"diurnal_light": {
"cycle_length": "24",
"start_time": "3",
"duration": "21"
}
},
{
"start_day": "6",
"duration": "2",
"constant_light": {
"cycle_length": "24"
}
}
]
}
}
]
}
},
"measurement": {
"technique": "Luciferase luminescence",
"equipment": "HAM 2",
"parameters": "Imaging script started 5 minutes before ZT0 55mins wait, 5mins lights off, 30mins capture",
"description": "Seedlings were treated on 6th day with Luciferin. They were then returned to entrainment condition for a further 24h (due to imaging set up problems). Seedlings were transferred to Experimental conditions at ZT4 on d7. Imaging was started on d8."
},
"sample_preparation": {
"method": "Plants sprayed with luciferin on day 6 of growth conditions, returned to entrainment conditions for a further 24hours, they were transferred to experimental conditions at ZT4 on d7. Imaging was started on day 8."
},
"samples": {
"sample": [
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"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
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"background": "Columbia (Col)",
"genotype": "Img Background",
"provenance": "Robust stock"
},
"marker": "Actin",
"growth_cond_name": "12L:12D",
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"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "2",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "M0002",
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},
"marker": "PRR9",
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"param": {
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}
},
{
"sample_id": "3",
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},
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}
},
{
"sample_id": "4",
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"age": "7",
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},
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"param": {
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}
},
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"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "6",
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"line": "M0002",
"provenance": "Robust stock"
},
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},
"biblio": {
"principal": "Mark Stitt",
"institution": "MPIMP - UEDIN",
"author": [
"Sarah Hodge",
"Virginie Mengin",
"Thiago Alexandre Moraes"
]
}
}
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Created: 18th Jun 2026 at 14:47
Last updated: 18th Jun 2026 at 14:48
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Version 1 (earliest) Created 18th Jun 2026 at 14:48 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 Millar Andrew on the original BioDare and automatically transferred to FAIRDOM Hub.
Submitter: Daniel Thedie
Studies: Millar et al. (2015), TiMet double dawns, TiMet shady nights
Assays: 010514H1, 010514H2, 030413H3: 12B-12Dx4 BB3, 030714H1, 030714H2, 060213H3: 12B-12Dx4 BBx3, 060313H1: 5L15Dx4 LLx3 (T-20), 060313H2: 12F-12Dx4 FFx3, 070814H1, 070814H2, 080115H1, 080115H2, 100414H1, 100414H2, 130212H1: 5L15Dx4 LLx3 (T-20), 130213H3: 12R-12Dx4 RRx3, 130313H1: 14L14D x 4 LL x 3 (T-28), 130313H2: 12F-12Dx4 FFx3, 140515H1, 140515H2, 140814H1, 140814H2, 190614H1, 190614H2, 200213H1: 15L5D x4 LL x3 (T-20), 200213H3: 12B-12Dx4 BB3, 200313H2: 7L 21Dx4 LLx3 (T-28), 200313H3: 12L-12Dx4 LLx3, 210814H1, 210814H2, 240414H1, 240414H2, 270213H1: 10L10Dx4 LLx3 (T-20), 270213H3: 12R-12Dx4 RRx3, 270313H1: 21L 7Dx4 LLx3 (T-28), 270313H3: 12L-12Dx4 LLx3, 280814H1, 280814H2, 290313H2: 15L 5Dx4 LLx3, AT0043: 4x 12:12-DD, AT0048 4x 18:6-DD, AT0078: 4x6:18-DD, AT0080: 4x18:6-DD
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140515H2
| Property | Value |
|---|---|
| BioDare ID | 3188 |
| Author | Sarah Hodge |
| Institution | MPIMP - UEDIN |
| License |
Description
ZT0 lights remain switched off until ZT3. At ZT3 light comes on at 90 umolm-2s-1. Dusk is lights off at ZT 12. Dark dawn cycle is for 4 days then continuous light (first day with dark dawn) for 3 days. ie 9L:15D x4 LLx3.
Purpose
Control "dark" dawn experiment for double dawn experiment based on Virginie and Thiago's design ...
Submitter: Daniel Thedie
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Millar Andrew
Study: TiMet double dawns
