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"security": { "owner": "mengin", "supervisor": "mstitt", "allowedToRead": [ "stitt", "timet" ], "allowedToWrite": [ "stitt", "timet" ] }, "hasTSData": "true", "hasPPAData": "true", "desc": { "experiment_type": "Luciferase exp", "id": "3187", "status": "in progress", "name": "140515H1", "purpose": "Double dawn experiment based on Virginie and Thiago's design (Stitt Lab).", "description": "At ZT0 dawn is dim light (6umolm-2s-1) for 3 hours. At ZT3 light steps up to 90 umolm-2s-1. Dusk is lights off at ZT 12. Double dawn cycle is for 4 days then continuous light (first day with double dawn) for 3 days. ie 12L:12D x4 LLx3.", "comments": "Pedro is not able to record changes in intensity during an experiment, so please refer to the description & experimental conditions comment for true experimental conditions. Partner experiment: 140515H2", "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": "7.0", "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": { "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" } } }, "light_conditions": { "label": "W: LD 12:00:12:00", "light_channel": { "spectrum": "white", "intensity": "90", "source": "tube", "env_conditions": { "type": "diurnal_light", "label": "LD 12:00:12:00", "duration": "7", "env_day": { "type": "diurnal_light", "label": "diurnal light", "duration": "7", "cycle_length": "24", "base_value": "0.0", "second_value": "100.0", "env_period": { "start_time": "0:00", "duration": "12:00" } } } } } }, "experimental_condition": { "name": "3ShL:9L:12Dx4 LLx3", "medium": "Agar 1.2% MS 0.5", "growth_space": "Percival + LED", "duration": "7.0", "comment": "4 days of 3 hours dim light (6 umolm-2s-1), 9 hours of bright light (90 umolm-2-s), 12 hours dark followed by 3 days constant light, with shady conditions on first dawn. The first dawn starts at ZT0 The light intensities are controlled by the arduino. 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", "env_day": { "type": "constant_temp", "label": "constant temperature", "duration": "7", "cycle_length": "24", "base_value": "22.0", "second_value": "22.0" } } }, "light_conditions": { "label": "B+R: 4*LD 12:00:12:00; 3*LL", "light_channel": [ { "spectrum": "blue", "intensity": "35", "source": "LED", "env_conditions": { "type": "light_complex", "label": "4*LD 12:00:12:00; 3*LL", "duration": "7", "env_day": [ { "type": "diurnal_light", "label": "diurnal light", "duration": "4", "cycle_length": "24", "base_value": "0.0", "second_value": "100.0", "env_period": { "start_time": "0:00", "duration": "12:00" } }, { "type": "constant_light", "label": "constant light", "duration": "3", "cycle_length": "24", "base_value": "0.0", "second_value": "100.0", "env_period": { "start_time": "0:00", "duration": "24:00" } } ] } }, { "spectrum": "red", "intensity": "55", "source": "LED", "env_conditions": { "type": "light_complex", "label": "4*LD 12:00:12:00; 3*LL", "duration": "7", "env_day": [ { "type": "diurnal_light", "label": "diurnal light", "duration": "4", "cycle_length": "24", "base_value": "0.0", "second_value": "100.0", "env_period": { "start_time": "0:00", "duration": "12:00" } }, { "type": "constant_light", "label": "constant light", "duration": "3", "cycle_length": "24", "base_value": "0.0", "second_value": "100.0", "env_period": { "start_time": "0:00", "duration": "24:00" } } ] } } ] } }, "measurement": { "technique": "Luciferase luminescence", "equipment": "HAM 1", "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": [ { "sample_id": "1", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "age": "7", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Wasilewski (WS)", "genotype": "Img Background", "line": "empty", "provenance": "Robust stock" }, "marker": "Actin", "growth_cond_name": "12L:12D", "experiment_cond_name": "3ShL:9L:12Dx4 LLx3", "ignored": "false", "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": "12L:12D", "experiment_cond_name": "3ShL:9L:12Dx4 LLx3", "ignored": "false", "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": "12L:12D", "experiment_cond_name": "3ShL:9L:12Dx4 LLx3", "ignored": "false", "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": "12L:12D", "experiment_cond_name": "3ShL:9L:12Dx4 LLx3", "ignored": "false", "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": "12L:12D", "experiment_cond_name": "3ShL:9L:12Dx4 LLx3", "ignored": "false", "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": "12L:12D", "experiment_cond_name": "3ShL:9L:12Dx4 LLx3", "ignored": "false", "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": "12L:12D", "experiment_cond_name": "3ShL:9L:12Dx4 LLx3", "ignored": "false", "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": "12L:12D", "experiment_cond_name": "3ShL:9L:12Dx4 LLx3", "ignored": "false", "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": "12L:12D", "experiment_cond_name": "3ShL:9L:12Dx4 LLx3", "ignored": "false", "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": "12L:12D", "experiment_cond_name": "3ShL:9L:12Dx4 LLx3", "ignored": "false", "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": "12L:12D", "experiment_cond_name": "3ShL:9L:12Dx4 LLx3", "ignored": "false", "param": { "@name": "TAG", "@value": "Luc" } }, { "sample_id": "12", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "age": "7", "genetic_info": { "species": "Arabidopsis 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"seedling", "origin": "seedling", "growth_stage": "seedling", "age": "7", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "prr9-1", "line": "G0169 (T4 H5-1)", "provenance": "Robust stock" }, "marker": "TOC1", "growth_cond_name": "12L:12D", "experiment_cond_name": "3ShL:9L:12Dx4 LLx3", "ignored": "false", "param": { "@name": "TAG", "@value": "Luc" } }, { "sample_id": "176", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "age": "7", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "prr9-1", "line": "G0169 (T4 H5-1)", "provenance": "Robust stock" }, "marker": "TOC1", "growth_cond_name": "12L:12D", "experiment_cond_name": "3ShL:9L:12Dx4 LLx3", "ignored": "false", "param": { "@name": "TAG", "@value": "Luc" } }, { "sample_id": "177", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "age": "7", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "prr9-1", "line": "G0169 (T4 H5-1)", "provenance": "Robust stock" }, "marker": "TOC1", "growth_cond_name": "12L:12D", "experiment_cond_name": "3ShL:9L:12Dx4 LLx3", "ignored": "false", "param": { "@name": "TAG", "@value": "Luc" } }, { "sample_id": "178", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "age": "7", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Columbia (Col)", "genotype": "prr9-1", "line": "G0169 (T4 H5-1)", "provenance": "Robust stock" }, "marker": "TOC1", "growth_cond_name": "12L:12D", "experiment_cond_name": "3ShL:9L:12Dx4 LLx3", "ignored": "false", "param": { "@name": "TAG", "@value": "Luc" } } ] } }, "pedro": { "@xmlns:xsi": "http://www.w3.org/2001/XMLSchema-instance", "@xsi:schemaLocation": "/H:/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": "140515H1", "purpose": "Double dawn experiment based on Virginie and Thiago's design (Stitt Lab).", "description": "At ZT0 dawn is dim light (6umolm-2s-1) for 3 hours. At ZT3 light steps up to 90 umolm-2s-1. Dusk is lights off at ZT 12. Double dawn cycle is for 4 days then continuous light (first day with double dawn) for 3 days. ie 12L:12D x4 LLx3.", "comments": "Pedro is not able to record changes in intensity during an experiment, so please refer to the description & experimental conditions comment for true experimental conditions. Partner experiment: 140515H2", "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": "3ShL:9L:12Dx4 LLx3", "medium": "Agar 1.2% MS 0.5", "growth_space": "Percival + LED", "duration": "7", "comment": "4 days of 3 hours dim light (6 umolm-2s-1), 9 hours of bright light (90 umolm-2-s), 12 hours dark followed by 3 days constant light, with shady conditions on first dawn. The first dawn starts at ZT0 The light intensities are controlled by the arduino. 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": "blue", "intensity": "35", "source": "LED", "light_complex_settings": { "light_days": [ { "start_day": "1", "duration": "4", "diurnal_light": { "cycle_length": "24", "start_time": "0", "duration": "12" } }, { "start_day": "5", "duration": "3", "constant_light": { "cycle_length": "24" } } ] } }, { "spectrum": "red", "intensity": "55", "source": "LED", "light_complex_settings": { "light_days": [ { "start_day": "1", "duration": "4", "diurnal_light": { "cycle_length": "24", "start_time": "0", "duration": "12" } }, { "start_day": "5", "duration": "3", "constant_light": { "cycle_length": "24" } } ] } } ] } }, "measurement": { "technique": "Luciferase luminescence", "equipment": "HAM 1", "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": [ { "sample_id": "1", "sample_type": "seedling", "origin": "seedling", "growth_stage": "seedling", "age": "7", "genetic_info": { "species": "Arabidopsis thaliana", "background": "Wasilewski (WS)", "genotype": "Img Background", "provenance": "Robust stock" }, "marker": "Actin", "growth_cond_name": "12L:12D", "experiment_cond_name": "3ShL:9L:12Dx4 LLx3", "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": "12L:12D", "experiment_cond_name": "3ShL:9L:12Dx4 LLx3", "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": "12L:12D", "experiment_cond_name": "3ShL:9L:12Dx4 LLx3", "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": "12L:12D", "experiment_cond_name": "3ShL:9L:12Dx4 LLx3", "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", 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"experiment_cond_name": "3ShL:9L:12Dx4 LLx3", "param": { "@name": "TAG", "@value": "Luc" } } ] } }, "biblio": { "principal": "Mark Stitt", "institution": "MPIMP - UEDIN", "author": [ "Sarah Hodge", "Virginie Mengin", "Thiago Alexandre Moraes" ] } }