BioDare_metadata Version 1
Original BioDare metadata, converted to json format
SEEK ID: https://fairdomhub.org/data_files/8687?version=1
Filename:
BioDare_metadata.json
Format: JSON document
Size: 154 KB
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"genotype": "Wild Type",
"line": "M0024",
"provenance": "Robust stock"
},
"marker": "35S",
"growth_cond_name": "8L:16D",
"experiment_cond_name": "SD to LD",
"ignored": "false",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "87",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "M0024",
"provenance": "Robust stock"
},
"marker": "35S",
"growth_cond_name": "8L:16D",
"experiment_cond_name": "SD to LD",
"ignored": "false",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "88",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "M0024",
"provenance": "Robust stock"
},
"marker": "35S",
"growth_cond_name": "8L:16D",
"experiment_cond_name": "SD to LD",
"ignored": "false",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "89",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "M0024",
"provenance": "Robust stock"
},
"marker": "35S",
"growth_cond_name": "8L:16D",
"experiment_cond_name": "SD to LD",
"ignored": "false",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "90",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "M0024",
"provenance": "Robust stock"
},
"marker": "35S",
"growth_cond_name": "8L:16D",
"experiment_cond_name": "SD to LD",
"ignored": "false",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "91",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "M0024",
"provenance": "Robust stock"
},
"marker": "35S",
"growth_cond_name": "8L:16D",
"experiment_cond_name": "SD to LD",
"ignored": "false",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "92",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "M0024",
"provenance": "Robust stock"
},
"marker": "ELF3",
"growth_cond_name": "8L:16D",
"experiment_cond_name": "SD to LD",
"ignored": "false",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "93",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "M0024",
"provenance": "Robust stock"
},
"marker": "ELF3",
"growth_cond_name": "8L:16D",
"experiment_cond_name": "SD to LD",
"ignored": "false",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "94",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "M0024",
"provenance": "Robust stock"
},
"marker": "ELF3",
"growth_cond_name": "8L:16D",
"experiment_cond_name": "SD to LD",
"ignored": "false",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "95",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "M0024",
"provenance": "Robust stock"
},
"marker": "ELF3",
"growth_cond_name": "8L:16D",
"experiment_cond_name": "SD to LD",
"ignored": "false",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "96",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "M0024",
"provenance": "Robust stock"
},
"marker": "ELF3",
"growth_cond_name": "8L:16D",
"experiment_cond_name": "SD to LD",
"ignored": "false",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "97",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "M0024",
"provenance": "Robust stock"
},
"marker": "ELF3",
"growth_cond_name": "8L:16D",
"experiment_cond_name": "SD to LD",
"ignored": "false",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "98",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "M0024",
"provenance": "Robust stock"
},
"marker": "ELF3",
"growth_cond_name": "8L:16D",
"experiment_cond_name": "SD to LD",
"ignored": "false",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "99",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "M0024",
"provenance": "Robust stock"
},
"marker": "ELF3",
"growth_cond_name": "8L:16D",
"experiment_cond_name": "SD to LD",
"ignored": "false",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "100",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "M0024",
"provenance": "Robust stock"
},
"marker": "ELF3",
"growth_cond_name": "8L:16D",
"experiment_cond_name": "SD to LD",
"ignored": "false",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "101",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "M0024",
"provenance": "Robust stock"
},
"marker": "ELF3",
"growth_cond_name": "8L:16D",
"experiment_cond_name": "SD to LD",
"ignored": "false",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "102",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "M0024",
"provenance": "Robust stock"
},
"marker": "ELF3",
"growth_cond_name": "8L:16D",
"experiment_cond_name": "SD to LD",
"ignored": "false",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "103",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "M0024",
"provenance": "Robust stock"
},
"marker": "ELF3",
"growth_cond_name": "8L:16D",
"experiment_cond_name": "SD to LD",
"ignored": "false",
"param": {
"@name": "TAG",
"@value": "Luc"
}
}
]
}
},
"pedro": {
"@xmlns:xsi": "http://www.w3.org/2001/XMLSchema-instance",
"@xsi:schemaLocation": "/Volumes/cse/biology/ismb/millar/communal/DataDescription/models/luc/model/newluc_model.xsd",
"id": "will be updated by the system",
"status": "finished",
"name": "030810H3 SD-LD",
"purpose": "Re-entrainment dynamics during transition between light:dark cycles with different photoperiods, comparing Arabidopsis thaliana and Ostreococcus tauri. This expt in A. thaliana with transcriptional reporters.",
"description": "Plants entrained in 8L:16D (120umol m-2s-1) for 7 days.\nExperimental Conditions: 2 days 8L:16D, 4 days 16L:8D (red and blue light 60umolm-2s-1)",
"comments": "PARTNER EXPERIMENT : 030810H3 LD-LD",
"provenance": {
"site": "Edinburgh",
"author": "Sarah Hodge",
"start_date": "2010-08-03"
},
"growth_condition": {
"name": "8L:16D",
"medium": "Agar 1.2% MS 0.5",
"incubation": "3 days at 4C",
"growth_space": "Percival",
"duration": "7",
"comment": "Entrainment",
"temperature_conditions": {
"constant_temp": {
"cycle_length": "24",
"base_temp": "22"
}
},
"light_conditions": {
"light_channel": {
"spectrum": "white",
"intensity": "100",
"source": "tube",
"diurnal_light": {
"cycle_length": "24",
"start_time": "0",
"duration": "8"
}
}
}
},
"experimental_condition": {
"name": "SD to LD",
"medium": "Agar 1.2% MS 0.5",
"growth_space": "Percival + LED",
"duration": "7",
"comment": "2 days 8L:16D, 4 days 16L:8D. The light conditions are 60umolm-2s-1 (red and blue).",
"temperature_conditions": {
"constant_temp": {
"cycle_length": "24",
"base_temp": "22"
}
},
"light_conditions": {
"light_channel": [
{
"spectrum": "red",
"intensity": "40",
"source": "LED",
"light_complex_settings": {
"light_days": [
{
"start_day": "1",
"duration": "2",
"diurnal_light": {
"cycle_length": "24",
"start_time": "0",
"duration": "8"
}
},
{
"start_day": "3",
"duration": "4",
"diurnal_light": {
"cycle_length": "24",
"start_time": "0",
"duration": "16"
}
}
]
}
},
{
"spectrum": "blue",
"intensity": "20",
"source": "LED",
"light_complex_settings": {
"light_days": [
{
"start_day": "1",
"duration": "2",
"diurnal_light": {
"cycle_length": "24",
"start_time": "0",
"duration": "8"
}
},
{
"start_day": "3",
"duration": "4",
"diurnal_light": {
"cycle_length": "24",
"start_time": "0",
"duration": "16"
}
}
]
}
}
]
}
},
"measurement": {
"technique": "Luciferase luminescence",
"equipment": "HAM 3",
"parameters": "imaging script starts 5 minutes before required ZT, then 55 minutes interval, 5 minutes light off, 30 minutes capture"
},
"sample_preparation": {
"method": "sprayed on day 6 and returned to entrainment conditions. Plates transferred to experimental conditions at dawn on day 7."
},
"samples": {
"sample": [
{
"sample_id": "1",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Columbia (Col)",
"genotype": "Img Background",
"provenance": "Robust stock"
},
"marker": "Actin",
"growth_cond_name": "8L:16D",
"experiment_cond_name": "SD to LD",
"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",
"provenance": "Robust stock"
},
"marker": "PRR9",
"growth_cond_name": "8L:16D",
"experiment_cond_name": "SD to LD",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "3",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "M0002",
"provenance": "Robust stock"
},
"marker": "PRR9",
"growth_cond_name": "8L:16D",
"experiment_cond_name": "SD to LD",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "4",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "M0002",
"provenance": "Robust stock"
},
"marker": "PRR9",
"growth_cond_name": "8L:16D",
"experiment_cond_name": "SD to LD",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "5",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "M0002",
"provenance": "Robust stock"
},
"marker": "PRR9",
"growth_cond_name": "8L:16D",
"experiment_cond_name": "SD to LD",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "6",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "M0002",
"provenance": "Robust stock"
},
"marker": "PRR9",
"growth_cond_name": "8L:16D",
"experiment_cond_name": "SD to LD",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "7",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "M0002",
"provenance": "Robust stock"
},
"marker": "PRR9",
"growth_cond_name": "8L:16D",
"experiment_cond_name": "SD to LD",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "8",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "M0002",
"provenance": "Robust stock"
},
"marker": "PRR9",
"growth_cond_name": "8L:16D",
"experiment_cond_name": "SD to LD",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "9",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "M0002",
"provenance": "Robust stock"
},
"marker": "PRR9",
"growth_cond_name": "8L:16D",
"experiment_cond_name": "SD to LD",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "10",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "M0002",
"provenance": "Robust stock"
},
"marker": "PRR9",
"growth_cond_name": "8L:16D",
"experiment_cond_name": "SD to LD",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "11",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "M0002",
"provenance": "Robust stock"
},
"marker": "PRR9",
"growth_cond_name": "8L:16D",
"experiment_cond_name": "SD to LD",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "12",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "M0002",
"provenance": "Robust stock"
},
"marker": "PRR9",
"growth_cond_name": "8L:16D",
"experiment_cond_name": "SD to LD",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "13",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "M0002",
"provenance": "Robust stock"
},
"marker": "PRR9",
"growth_cond_name": "8L:16D",
"experiment_cond_name": "SD to LD",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "14",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "M0002",
"provenance": "Robust stock"
},
"marker": "PRR9",
"growth_cond_name": "8L:16D",
"experiment_cond_name": "SD to LD",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "15",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "M0002",
"provenance": "Robust stock"
},
"marker": "PRR9",
"growth_cond_name": "8L:16D",
"experiment_cond_name": "SD to LD",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "16",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "M0006",
"provenance": "Robust stock"
},
"marker": "TOC1",
"growth_cond_name": "8L:16D",
"experiment_cond_name": "SD to LD",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "17",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "M0006",
"provenance": "Robust stock"
},
"marker": "TOC1",
"growth_cond_name": "8L:16D",
"experiment_cond_name": "SD to LD",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "18",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "M0006",
"provenance": "Robust stock"
},
"marker": "TOC1",
"growth_cond_name": "8L:16D",
"experiment_cond_name": "SD to LD",
"param": {
"@name": "TAG",
"@value": "Luc"
}
},
{
"sample_id": "19",
"sample_type": "seedling",
"origin": "seedling",
"growth_stage": "seedling",
"age": "7",
"genetic_info": {
"species": "Arabidopsis thaliana",
"background": "Wasilewski (WS)",
"genotype": "Wild Type",
"line": "M0006",
"provenance": "Robust stock"
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},
"biblio": {
"principal": "Andrew Millar",
"institution": "University of Edinburgh",
"author": "Sarah Hodge"
}
}
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Created: 18th Jun 2026 at 12:59
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Version 1 (earliest) Created 18th Jun 2026 at 12:59 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 Dixon Laura on the original BioDare and automatically transferred to FAIRDOM Hub.
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Light and circadian regulation of clock components aids flexible responses to environmental signals
Dixon et al. (2014)
DOI: 10.1111/nph.12853
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030810H3 SD-LD
| Property | Value |
|---|---|
| BioDare ID | 13982027442235 |
| Author | Sarah Hodge |
| Institution | University of Edinburgh |
| License | CC_BY |
Description
Plants entrained in 8L:16D (120umol m-2s-1) for 7 days. Experimental Conditions: 2 days 8L:16D, 4 days 16L:8D (red and blue light 60umolm-2s-1)
Purpose
Re-entrainment dynamics during transition between light:dark cycles with different photoperiods, comparing Arabidopsis thaliana and ...
Submitter: Daniel Thedie
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: Dixon Laura
Study: Dixon et al. (2014)
