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    "licence": "CC_BY"
  },
  "desc": {
    "experiment_type": "Gen. TS exp",
    "id": "2843",
    "status": "described",
    "name": "TiMet WP1.1 WS seedling vs rosette",
    "purpose": "Compare clock important genes transcript levels in seedlings vs matoure plants.",
    "description": "Ws in biological duplicates, from diurnal cycle (12L/12D) with different plants age: 9 and 20 days. \nNumbers are in transcript copy per cell, obtained assuming 1 g FW contains 25000000 cells.",
    "comments": "The rosette data came from \"TiMet WP1.1 qRT-PCR LD to LL and LD\" experiment",
    "provenance": {
      "site": "Golm",
      "author": "Anna Flis",
      "start_date": "2011-02-01"
    },
    "growth_condition": [
      {
        "name": "LD 20/18C",
        "medium": "Soil",
        "growth_space": "Percivals E-36L",
        "duration": "20.0",
        "comment": "Seeds sown directly in big pots - no pricking (compared to WP1.2A) but thinning to avoid any shading between the seedlings after around 1 week",
        "temperature_conditions": {
          "label": "diurn. 20.0C:18.0C 12:00:12:00",
          "env_conditions": {
            "type": "diurnal_temp",
            "label": "diurn. 20.0C:18.0C 12:00:12:00",
            "duration": "20",
            "env_day": {
              "type": "diurnal_temp",
              "label": "diurnal temp",
              "duration": "20",
              "cycle_length": "24",
              "base_value": "18.0",
              "second_value": "20.0",
              "env_period": {
                "start_time": "0:00",
                "duration": "12:00"
              }
            }
          }
        },
        "light_conditions": {
          "label": "W: LD 12:00:12:00",
          "light_channel": {
            "spectrum": "white",
            "intensity": "160",
            "source": "tube",
            "env_conditions": {
              "type": "diurnal_light",
              "label": "LD 12:00:12:00",
              "duration": "20",
              "env_day": {
                "type": "diurnal_light",
                "label": "diurnal light",
                "duration": "20",
                "cycle_length": "24",
                "base_value": "0.0",
                "second_value": "100.0",
                "env_period": {
                  "start_time": "0:00",
                  "duration": "12:00"
                }
              }
            }
          }
        }
      },
      {
        "name": "LD 20/18C sd",
        "medium": "Agar 1.2% MS 0.5",
        "growth_space": "Percivals E-36L",
        "duration": "9.0",
        "temperature_conditions": {
          "label": "diurn. 20.0C:18.0C 12:00:12:00",
          "env_conditions": {
            "type": "diurnal_temp",
            "label": "diurn. 20.0C:18.0C 12:00:12:00",
            "duration": "9",
            "env_day": {
              "type": "diurnal_temp",
              "label": "diurnal temp",
              "duration": "9",
              "cycle_length": "24",
              "base_value": "18.0",
              "second_value": "20.0",
              "env_period": {
                "start_time": "0:00",
                "duration": "12:00"
              }
            }
          }
        },
        "light_conditions": {
          "label": "W: LD 12:00:12:00",
          "light_channel": {
            "spectrum": "white",
            "intensity": "160",
            "source": "tube",
            "env_conditions": {
              "type": "diurnal_light",
              "label": "LD 12:00:12:00",
              "duration": "9",
              "env_day": {
                "type": "diurnal_light",
                "label": "diurnal light",
                "duration": "9",
                "cycle_length": "24",
                "base_value": "0.0",
                "second_value": "100.0",
                "env_period": {
                  "start_time": "0:00",
                  "duration": "12:00"
                }
              }
            }
          }
        }
      }
    ],
    "experimental_condition": [
      {
        "name": "LD 20/18C sd",
        "medium": "Agar 1.2% MS 0.5",
        "growth_space": "Percivals E-36L",
        "duration": "3.0",
        "temperature_conditions": {
          "label": "diurn. 20.0C:18.0C 12:00:12:00",
          "env_conditions": {
            "type": "diurnal_temp",
            "label": "diurn. 20.0C:18.0C 12:00:12:00",
            "duration": "3",
            "env_day": {
              "type": "diurnal_temp",
              "label": "diurnal temp",
              "duration": "3",
              "cycle_length": "24",
              "base_value": "18.0",
              "second_value": "20.0",
              "env_period": {
                "start_time": "0:00",
                "duration": "12:00"
              }
            }
          }
        },
        "light_conditions": {
          "label": "W: LD 12:00:12:00",
          "light_channel": {
            "spectrum": "white",
            "intensity": "160",
            "source": "tube",
            "env_conditions": {
              "type": "diurnal_light",
              "label": "LD 12:00:12:00",
              "duration": "3",
              "env_day": {
                "type": "diurnal_light",
                "label": "diurnal light",
                "duration": "3",
                "cycle_length": "24",
                "base_value": "0.0",
                "second_value": "100.0",
                "env_period": {
                  "start_time": "0:00",
                  "duration": "12:00"
                }
              }
            }
          }
        }
      },
      {
        "name": "LD 20/18C",
        "medium": "Soil",
        "growth_space": "Percivals E-36L",
        "duration": "3.0",
        "temperature_conditions": {
          "label": "diurn. 20.0C:18.0C 12:00:12:00",
          "env_conditions": {
            "type": "diurnal_temp",
            "label": "diurn. 20.0C:18.0C 12:00:12:00",
            "duration": "3",
            "env_day": {
              "type": "diurnal_temp",
              "label": "diurnal temp",
              "duration": "3",
              "cycle_length": "24",
              "base_value": "18.0",
              "second_value": "20.0",
              "env_period": {
                "start_time": "0:00",
                "duration": "12:00"
              }
            }
          }
        },
        "light_conditions": {
          "label": "W: LD 12:00:12:00",
          "light_channel": {
            "spectrum": "white",
            "intensity": "160",
            "source": "tube",
            "env_conditions": {
              "type": "diurnal_light",
              "label": "LD 12:00:12:00",
              "duration": "3",
              "env_day": {
                "type": "diurnal_light",
                "label": "diurnal light",
                "duration": "3",
                "cycle_length": "24",
                "base_value": "0.0",
                "second_value": "100.0",
                "env_period": {
                  "start_time": "0:00",
                  "duration": "12:00"
                }
              }
            }
          }
        }
      }
    ],
    "measurement": {
      "technique": "RT-PCR",
      "equipment": "PerkinElmer Evolution P3+Applied Biosystems PCR",
      "parameters": "Done by Robot: PerkinElmer Evolution P3 Precision Pipetting Platform with\nApplied Biosystems PCR,\nPRIMERS: first forward then reverse\nLHY\tTGCCTCAAAGCTTTTCGCCTCCT\tGTCTGCAGCACAAGAATCCTGGCT\nCCA1\tTCCAATGCACGCCGCAGTAGAA\tAGGCAATTCGACCCTCGTCAGACA\nPRR9\tAGCTAGCAGAACAACGTCCTCGAGT\tCGTCTGAATTCACGGTTCGCACGA\nPRR7\tAGAGGTGCTTCCGAAAGAAGGTACGA\tACGCACAAATTGGCCTCGCACT\nPRR5\tTGCAATGGCTCCTGCTTCACTCTC\tACTGTACTCATGCGGGCTAACGGA\nTOC1\tTGATGGATCGGGTTTCTCTGCACCA\tTGAGGCATCATGGCTGCTGATTGC\nGI\tTGCGGGCAACTGATGGAATGCT\tTGCTCTTGCCGTGGCTTCAAGT\nLUX\tCAGCGGTAATGTTGGAGTGCCGAT\tTGGCATCTGCATCATCTGTTGCGT\nELF3\tACAACAAGAGATGGGGGAGGAGTGAC\tACTCGCGAGCTTTGCGTTGTGA\nELF4\tAGTTTCTCGTCGGGCTTTCACGGT\tTAAGCTCTAGTTCCGGCAGCACCA",
      "description": "In the first step DNA that may be present in RNA extracts was removed from samples using TURBO DNA-freeTM kit (Applied Biosystems) by following the supplied protocol. The concentration of RNA was determined using Nano-Drop spectrophotometer and 1µg of DNase treated RNA was used for cDNA synthesis.\nThe reaction of reverse transcription was done using the SuperScript III First-Standard Synthesis System Kit (Invitrogen).\n\nOn each 384-well plate with an ABI PRISM 7900 HT sequence detection system (Applied Biosystems Deutschland, Darmstadt, Germany) using PerkinElmer Evolution P3 Precision Pipetting Platform (PerkinElmer Life Science, Rodgau-Jügesheim, Germany) 22 pairs of primers were dispensed (200nM of each primer). PCR mix was prepared by adding 0.5µL of cDNA and 2.5µL of Power SYBR Green PCR Master Mix (Applied Biosystems, Deutschland) to already prepared primers. The qRT-PCR reactions were carried out following the recommended thermal profile: 2 min at 50˚C, 10 min at 95˚C, followed by 40 cycles of 95˚C for 15 s and 60 ˚C for 1 min. The specificity of the amplifications was tested by heating from 60˚C to 95˚C with a speed of 1.9 ˚C min-1, resulting in melting curves. Data analysis was performed using SDS 2.4 software (Applied Biosystems Deutschland).\nAnd all data transformed from copies/g FW to copies / cell assuming 1 g FW contains 25000000 cells"
    },
    "sample_preparation": {
      "method": "Plant material was grinded using Ball-Mill (Retch, Germany). Around 50 mg of material from each sample was aliquoted into 2 µL Eppendorf tubes. RNA was extracted using RNeasy Plant Mini Kit (QIAGEN) by following the manufacturer’s instructions. Briefly, the RLC buffer (500µL) was added to the frozen plant powder and the mixture was homogenised. RNA was eluted from the RNeasy spin column twice, first with 50 µL and then with 30 µL of RNase-free water. The concentration of RNA was determined using the Nano-Drop ND-1000 UV-Vis spectrophotometer (Nano-Drop Technologies)."
    },
    "samples": {
      "sample": [
        {
          "sample_id": "1",
          "sample_type": "seedling",
          "origin": "seedling",
          "growth_stage": "seedling",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
            "genotype": "Wild Type",
            "line": "empty"
          },
          "marker": "LHY",
          "data_cathegory": "qRT-PCR",
          "growth_cond_name": "LD 20/18C sd",
          "experiment_cond_name": "LD 20/18C sd",
          "ignored": "false",
          "unit": "copy nr. per cell",
          "param": {
            "@name": "unit",
            "@value": "copy nr. per cell"
          }
        },
        {
          "sample_id": "2",
          "sample_type": "seedling",
          "origin": "seedling",
          "growth_stage": "seedling",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
            "genotype": "Wild Type",
            "line": "empty"
          },
          "marker": "CCA1",
          "data_cathegory": "qRT-PCR",
          "growth_cond_name": "LD 20/18C sd",
          "experiment_cond_name": "LD 20/18C sd",
          "ignored": "false",
          "unit": "copy nr. per cell",
          "param": {
            "@name": "unit",
            "@value": "copy nr. per cell"
          }
        },
        {
          "sample_id": "3",
          "sample_type": "seedling",
          "origin": "seedling",
          "growth_stage": "seedling",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
            "genotype": "Wild Type",
            "line": "empty"
          },
          "marker": "PRR9",
          "data_cathegory": "qRT-PCR",
          "growth_cond_name": "LD 20/18C sd",
          "experiment_cond_name": "LD 20/18C sd",
          "ignored": "false",
          "unit": "copy nr. per cell",
          "param": {
            "@name": "unit",
            "@value": "copy nr. per cell"
          }
        },
        {
          "sample_id": "4",
          "sample_type": "seedling",
          "origin": "seedling",
          "growth_stage": "seedling",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
            "genotype": "Wild Type",
            "line": "empty"
          },
          "marker": "PRR7",
          "data_cathegory": "qRT-PCR",
          "growth_cond_name": "LD 20/18C sd",
          "experiment_cond_name": "LD 20/18C sd",
          "ignored": "false",
          "unit": "copy nr. per cell",
          "param": {
            "@name": "unit",
            "@value": "copy nr. per cell"
          }
        },
        {
          "sample_id": "5",
          "sample_type": "seedling",
          "origin": "seedling",
          "growth_stage": "seedling",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
            "genotype": "Wild Type",
            "line": "empty"
          },
          "marker": "PRR5",
          "data_cathegory": "qRT-PCR",
          "growth_cond_name": "LD 20/18C sd",
          "experiment_cond_name": "LD 20/18C sd",
          "ignored": "false",
          "unit": "copy nr. per cell",
          "param": {
            "@name": "unit",
            "@value": "copy nr. per cell"
          }
        },
        {
          "sample_id": "6",
          "sample_type": "seedling",
          "origin": "seedling",
          "growth_stage": "seedling",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
            "genotype": "Wild Type",
            "line": "empty"
          },
          "marker": "TOC1",
          "data_cathegory": "qRT-PCR",
          "growth_cond_name": "LD 20/18C sd",
          "experiment_cond_name": "LD 20/18C sd",
          "ignored": "false",
          "unit": "copy nr. per cell",
          "param": {
            "@name": "unit",
            "@value": "copy nr. per cell"
          }
        },
        {
          "sample_id": "7",
          "sample_type": "seedling",
          "origin": "seedling",
          "growth_stage": "seedling",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
            "genotype": "Wild Type",
            "line": "empty"
          },
          "marker": "GI",
          "data_cathegory": "qRT-PCR",
          "growth_cond_name": "LD 20/18C sd",
          "experiment_cond_name": "LD 20/18C sd",
          "ignored": "false",
          "unit": "copy nr. per cell",
          "param": {
            "@name": "unit",
            "@value": "copy nr. per cell"
          }
        },
        {
          "sample_id": "8",
          "sample_type": "seedling",
          "origin": "seedling",
          "growth_stage": "seedling",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
            "genotype": "Wild Type",
            "line": "empty"
          },
          "marker": "LUX",
          "data_cathegory": "qRT-PCR",
          "growth_cond_name": "LD 20/18C sd",
          "experiment_cond_name": "LD 20/18C sd",
          "ignored": "false",
          "unit": "copy nr. per cell",
          "param": {
            "@name": "unit",
            "@value": "copy nr. per cell"
          }
        },
        {
          "sample_id": "9",
          "sample_type": "seedling",
          "origin": "seedling",
          "growth_stage": "seedling",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
            "genotype": "Wild Type",
            "line": "empty"
          },
          "marker": "ELF3",
          "data_cathegory": "qRT-PCR",
          "growth_cond_name": "LD 20/18C sd",
          "experiment_cond_name": "LD 20/18C sd",
          "ignored": "false",
          "unit": "copy nr. per cell",
          "param": {
            "@name": "unit",
            "@value": "copy nr. per cell"
          }
        },
        {
          "sample_id": "10",
          "sample_type": "seedling",
          "origin": "seedling",
          "growth_stage": "seedling",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
            "genotype": "Wild Type",
            "line": "empty"
          },
          "marker": "ELF4",
          "data_cathegory": "qRT-PCR",
          "growth_cond_name": "LD 20/18C sd",
          "experiment_cond_name": "LD 20/18C sd",
          "ignored": "false",
          "unit": "copy nr. per cell",
          "param": {
            "@name": "unit",
            "@value": "copy nr. per cell"
          }
        },
        {
          "sample_id": "11",
          "sample_type": "whole plant",
          "origin": "whole plant",
          "growth_stage": "mid rosette",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
            "genotype": "Wild Type",
            "line": "empty"
          },
          "marker": "LHY",
          "data_cathegory": "qRT-PCR",
          "growth_cond_name": "LD 20/18C",
          "experiment_cond_name": "LD 20/18C",
          "ignored": "false",
          "unit": "copy nr. per cell",
          "param": {
            "@name": "unit",
            "@value": "copy nr. per cell"
          }
        },
        {
          "sample_id": "12",
          "sample_type": "whole plant",
          "origin": "whole plant",
          "growth_stage": "mid rosette",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
            "genotype": "Wild Type",
            "line": "empty"
          },
          "marker": "CCA1",
          "data_cathegory": "qRT-PCR",
          "growth_cond_name": "LD 20/18C",
          "experiment_cond_name": "LD 20/18C",
          "ignored": "false",
          "unit": "copy nr. per cell",
          "param": {
            "@name": "unit",
            "@value": "copy nr. per cell"
          }
        },
        {
          "sample_id": "13",
          "sample_type": "whole plant",
          "origin": "whole plant",
          "growth_stage": "mid rosette",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
            "genotype": "Wild Type",
            "line": "empty"
          },
          "marker": "PRR9",
          "data_cathegory": "qRT-PCR",
          "growth_cond_name": "LD 20/18C",
          "experiment_cond_name": "LD 20/18C",
          "ignored": "false",
          "unit": "copy nr. per cell",
          "param": {
            "@name": "unit",
            "@value": "copy nr. per cell"
          }
        },
        {
          "sample_id": "14",
          "sample_type": "whole plant",
          "origin": "whole plant",
          "growth_stage": "mid rosette",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
            "genotype": "Wild Type",
            "line": "empty"
          },
          "marker": "PRR7",
          "data_cathegory": "qRT-PCR",
          "growth_cond_name": "LD 20/18C",
          "experiment_cond_name": "LD 20/18C",
          "ignored": "false",
          "unit": "copy nr. per cell",
          "param": {
            "@name": "unit",
            "@value": "copy nr. per cell"
          }
        },
        {
          "sample_id": "15",
          "sample_type": "whole plant",
          "origin": "whole plant",
          "growth_stage": "mid rosette",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
            "genotype": "Wild Type",
            "line": "empty"
          },
          "marker": "PRR5",
          "data_cathegory": "qRT-PCR",
          "growth_cond_name": "LD 20/18C",
          "experiment_cond_name": "LD 20/18C",
          "ignored": "false",
          "unit": "copy nr. per cell",
          "param": {
            "@name": "unit",
            "@value": "copy nr. per cell"
          }
        },
        {
          "sample_id": "16",
          "sample_type": "whole plant",
          "origin": "whole plant",
          "growth_stage": "mid rosette",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
            "genotype": "Wild Type",
            "line": "empty"
          },
          "marker": "TOC1",
          "data_cathegory": "qRT-PCR",
          "growth_cond_name": "LD 20/18C",
          "experiment_cond_name": "LD 20/18C",
          "ignored": "false",
          "unit": "copy nr. per cell",
          "param": {
            "@name": "unit",
            "@value": "copy nr. per cell"
          }
        },
        {
          "sample_id": "17",
          "sample_type": "whole plant",
          "origin": "whole plant",
          "growth_stage": "mid rosette",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
            "genotype": "Wild Type",
            "line": "empty"
          },
          "marker": "GI",
          "data_cathegory": "qRT-PCR",
          "growth_cond_name": "LD 20/18C",
          "experiment_cond_name": "LD 20/18C",
          "ignored": "false",
          "unit": "copy nr. per cell",
          "param": {
            "@name": "unit",
            "@value": "copy nr. per cell"
          }
        },
        {
          "sample_id": "18",
          "sample_type": "whole plant",
          "origin": "whole plant",
          "growth_stage": "mid rosette",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
            "genotype": "Wild Type",
            "line": "empty"
          },
          "marker": "LUX",
          "data_cathegory": "qRT-PCR",
          "growth_cond_name": "LD 20/18C",
          "experiment_cond_name": "LD 20/18C",
          "ignored": "false",
          "unit": "copy nr. per cell",
          "param": {
            "@name": "unit",
            "@value": "copy nr. per cell"
          }
        },
        {
          "sample_id": "19",
          "sample_type": "whole plant",
          "origin": "whole plant",
          "growth_stage": "mid rosette",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
            "genotype": "Wild Type",
            "line": "empty"
          },
          "marker": "ELF3",
          "data_cathegory": "qRT-PCR",
          "growth_cond_name": "LD 20/18C",
          "experiment_cond_name": "LD 20/18C",
          "ignored": "false",
          "unit": "copy nr. per cell",
          "param": {
            "@name": "unit",
            "@value": "copy nr. per cell"
          }
        },
        {
          "sample_id": "20",
          "sample_type": "whole plant",
          "origin": "whole plant",
          "growth_stage": "mid rosette",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
            "genotype": "Wild Type",
            "line": "empty"
          },
          "marker": "ELF4",
          "data_cathegory": "qRT-PCR",
          "growth_cond_name": "LD 20/18C",
          "experiment_cond_name": "LD 20/18C",
          "ignored": "false",
          "unit": "copy nr. per cell",
          "param": {
            "@name": "unit",
            "@value": "copy nr. per cell"
          }
        }
      ]
    }
  },
  "pedro": {
    "@xmlns:xsi": "http://www.w3.org/2001/XMLSchema-instance",
    "@xsi:schemaLocation": "/D:/Pedro/Customize Pedro/TiMet/models/TiMetExperiment/model/full_general_model.xsd",
    "name": "TiMet WP1.1 WS seedling vs rosette",
    "purpose": "Compare clock important genes transcript levels in seedlings vs matoure plants.",
    "description": "Ws in biological duplicates, from diurnal cycle (12L/12D) with different plants age: 9 and 20 days. \nNumbers are in transcript copy per cell, obtained assuming 1 g FW contains 25000000 cells.",
    "comments": "The rosette data came from \"TiMet WP1.1 qRT-PCR LD to LL and LD\" experiment",
    "provenance": {
      "site": "Golm",
      "author": "Anna Flis",
      "start_date": "2011-02-01"
    },
    "growth_condition": [
      {
        "name": "LD 20/18C",
        "medium": "Soil",
        "growth_space": "Percivals E-36L",
        "duration": "20",
        "comment": "Seeds sown directly in big pots - no pricking (compared to WP1.2A) but thinning to avoid any shading between the seedlings after around 1 week",
        "temperature_conditions": {
          "diurnal_temp": {
            "cycle_length": "24",
            "base_temp": "18",
            "second_temp": "20",
            "start_time": "0",
            "duration": "12"
          }
        },
        "light_conditions": {
          "light_channel": {
            "spectrum": "white",
            "intensity": "160",
            "source": "tube",
            "diurnal_light": {
              "cycle_length": "24",
              "start_time": "0",
              "duration": "12"
            }
          }
        }
      },
      {
        "name": "LD 20/18C sd",
        "medium": "Agar 1.2% MS 0.5",
        "growth_space": "Percivals E-36L",
        "duration": "9",
        "temperature_conditions": {
          "diurnal_temp": {
            "cycle_length": "24",
            "base_temp": "18",
            "second_temp": "20",
            "start_time": "0",
            "duration": "12"
          }
        },
        "light_conditions": {
          "light_channel": {
            "spectrum": "white",
            "intensity": "160",
            "source": "tube",
            "diurnal_light": {
              "cycle_length": "24",
              "start_time": "0",
              "duration": "12"
            }
          }
        }
      }
    ],
    "experimental_condition": [
      {
        "name": "LD 20/18C sd",
        "medium": "Agar 1.2% MS 0.5",
        "growth_space": "Percivals E-36L",
        "duration": "3",
        "temperature_conditions": {
          "diurnal_temp": {
            "cycle_length": "24",
            "base_temp": "18",
            "second_temp": "20",
            "start_time": "0",
            "duration": "12"
          }
        },
        "light_conditions": {
          "light_channel": {
            "spectrum": "white",
            "intensity": "160",
            "source": "tube",
            "diurnal_light": {
              "cycle_length": "24",
              "start_time": "0",
              "duration": "12"
            }
          }
        }
      },
      {
        "name": "LD 20/18C",
        "medium": "Soil",
        "growth_space": "Percivals E-36L",
        "duration": "3",
        "temperature_conditions": {
          "diurnal_temp": {
            "cycle_length": "24",
            "base_temp": "18",
            "second_temp": "20",
            "start_time": "0",
            "duration": "12"
          }
        },
        "light_conditions": {
          "light_channel": {
            "spectrum": "white",
            "intensity": "160",
            "source": "tube",
            "diurnal_light": {
              "cycle_length": "24",
              "start_time": "0",
              "duration": "12"
            }
          }
        }
      }
    ],
    "measurement": {
      "technique": "RT-PCR",
      "equipment": "PerkinElmer Evolution P3+Applied Biosystems PCR",
      "parameters": "Done by Robot: PerkinElmer Evolution P3 Precision Pipetting Platform with\nApplied Biosystems PCR,\nPRIMERS: first forward then reverse\nLHY\tTGCCTCAAAGCTTTTCGCCTCCT\tGTCTGCAGCACAAGAATCCTGGCT\nCCA1\tTCCAATGCACGCCGCAGTAGAA\tAGGCAATTCGACCCTCGTCAGACA\nPRR9\tAGCTAGCAGAACAACGTCCTCGAGT\tCGTCTGAATTCACGGTTCGCACGA\nPRR7\tAGAGGTGCTTCCGAAAGAAGGTACGA\tACGCACAAATTGGCCTCGCACT\nPRR5\tTGCAATGGCTCCTGCTTCACTCTC\tACTGTACTCATGCGGGCTAACGGA\nTOC1\tTGATGGATCGGGTTTCTCTGCACCA\tTGAGGCATCATGGCTGCTGATTGC\nGI\tTGCGGGCAACTGATGGAATGCT\tTGCTCTTGCCGTGGCTTCAAGT\nLUX\tCAGCGGTAATGTTGGAGTGCCGAT\tTGGCATCTGCATCATCTGTTGCGT\nELF3\tACAACAAGAGATGGGGGAGGAGTGAC\tACTCGCGAGCTTTGCGTTGTGA\nELF4\tAGTTTCTCGTCGGGCTTTCACGGT\tTAAGCTCTAGTTCCGGCAGCACCA",
      "description": "In the first step DNA that may be present in RNA extracts was removed from samples using TURBO DNA-freeTM kit (Applied Biosystems) by following the supplied protocol. The concentration of RNA was determined using Nano-Drop spectrophotometer and 1µg of DNase treated RNA was used for cDNA synthesis.\nThe reaction of reverse transcription was done using the SuperScript III First-Standard Synthesis System Kit (Invitrogen).\n\nOn each 384-well plate with an ABI PRISM 7900 HT sequence detection system (Applied Biosystems Deutschland, Darmstadt, Germany) using PerkinElmer Evolution P3 Precision Pipetting Platform (PerkinElmer Life Science, Rodgau-Jügesheim, Germany) 22 pairs of primers were dispensed (200nM of each primer). PCR mix was prepared by adding 0.5µL of cDNA and 2.5µL of Power SYBR Green PCR Master Mix (Applied Biosystems, Deutschland) to already prepared primers. The qRT-PCR reactions were carried out following the recommended thermal profile: 2 min at 50˚C, 10 min at 95˚C, followed by 40 cycles of 95˚C for 15 s and 60 ˚C for 1 min. The specificity of the amplifications was tested by heating from 60˚C to 95˚C with a speed of 1.9 ˚C min-1, resulting in melting curves. Data analysis was performed using SDS 2.4 software (Applied Biosystems Deutschland).\nAnd all data transformed from copies/g FW to copies / cell assuming 1 g FW contains 25000000 cells"
    },
    "sample_preparation": {
      "method": "Plant material was grinded using Ball-Mill (Retch, Germany). Around 50 mg of material from each sample was aliquoted into 2 µL Eppendorf tubes. RNA was extracted using RNeasy Plant Mini Kit (QIAGEN) by following the manufacturer’s instructions. Briefly, the RLC buffer (500µL) was added to the frozen plant powder and the mixture was homogenised. RNA was eluted from the RNeasy spin column twice, first with 50 µL and then with 30 µL of RNase-free water. The concentration of RNA was determined using the Nano-Drop ND-1000 UV-Vis spectrophotometer (Nano-Drop Technologies)."
    },
    "samples": {
      "sample": [
        {
          "sample_id": "1",
          "sample_type": "seedling",
          "origin": "seedling",
          "growth_stage": "seedling",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
            "genotype": "Wild Type"
          },
          "marker": "LHY",
          "data_cathegory": "qRT-PCR",
          "growth_cond_name": "LD 20/18C sd",
          "experiment_cond_name": "LD 20/18C sd",
          "param": {
            "@name": "unit",
            "@value": "copy nr. per cell"
          }
        },
        {
          "sample_id": "2",
          "sample_type": "seedling",
          "origin": "seedling",
          "growth_stage": "seedling",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
            "genotype": "Wild Type"
          },
          "marker": "CCA1",
          "data_cathegory": "qRT-PCR",
          "growth_cond_name": "LD 20/18C sd",
          "experiment_cond_name": "LD 20/18C sd",
          "param": {
            "@name": "unit",
            "@value": "copy nr. per cell"
          }
        },
        {
          "sample_id": "3",
          "sample_type": "seedling",
          "origin": "seedling",
          "growth_stage": "seedling",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
            "genotype": "Wild Type"
          },
          "marker": "PRR9",
          "data_cathegory": "qRT-PCR",
          "growth_cond_name": "LD 20/18C sd",
          "experiment_cond_name": "LD 20/18C sd",
          "param": {
            "@name": "unit",
            "@value": "copy nr. per cell"
          }
        },
        {
          "sample_id": "4",
          "sample_type": "seedling",
          "origin": "seedling",
          "growth_stage": "seedling",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
            "genotype": "Wild Type"
          },
          "marker": "PRR7",
          "data_cathegory": "qRT-PCR",
          "growth_cond_name": "LD 20/18C sd",
          "experiment_cond_name": "LD 20/18C sd",
          "param": {
            "@name": "unit",
            "@value": "copy nr. per cell"
          }
        },
        {
          "sample_id": "5",
          "sample_type": "seedling",
          "origin": "seedling",
          "growth_stage": "seedling",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
            "genotype": "Wild Type"
          },
          "marker": "PRR5",
          "data_cathegory": "qRT-PCR",
          "growth_cond_name": "LD 20/18C sd",
          "experiment_cond_name": "LD 20/18C sd",
          "param": {
            "@name": "unit",
            "@value": "copy nr. per cell"
          }
        },
        {
          "sample_id": "6",
          "sample_type": "seedling",
          "origin": "seedling",
          "growth_stage": "seedling",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
            "genotype": "Wild Type"
          },
          "marker": "TOC1",
          "data_cathegory": "qRT-PCR",
          "growth_cond_name": "LD 20/18C sd",
          "experiment_cond_name": "LD 20/18C sd",
          "param": {
            "@name": "unit",
            "@value": "copy nr. per cell"
          }
        },
        {
          "sample_id": "7",
          "sample_type": "seedling",
          "origin": "seedling",
          "growth_stage": "seedling",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
            "genotype": "Wild Type"
          },
          "marker": "GI",
          "data_cathegory": "qRT-PCR",
          "growth_cond_name": "LD 20/18C sd",
          "experiment_cond_name": "LD 20/18C sd",
          "param": {
            "@name": "unit",
            "@value": "copy nr. per cell"
          }
        },
        {
          "sample_id": "8",
          "sample_type": "seedling",
          "origin": "seedling",
          "growth_stage": "seedling",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
            "genotype": "Wild Type"
          },
          "marker": "LUX",
          "data_cathegory": "qRT-PCR",
          "growth_cond_name": "LD 20/18C sd",
          "experiment_cond_name": "LD 20/18C sd",
          "param": {
            "@name": "unit",
            "@value": "copy nr. per cell"
          }
        },
        {
          "sample_id": "9",
          "sample_type": "seedling",
          "origin": "seedling",
          "growth_stage": "seedling",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
            "genotype": "Wild Type"
          },
          "marker": "ELF3",
          "data_cathegory": "qRT-PCR",
          "growth_cond_name": "LD 20/18C sd",
          "experiment_cond_name": "LD 20/18C sd",
          "param": {
            "@name": "unit",
            "@value": "copy nr. per cell"
          }
        },
        {
          "sample_id": "10",
          "sample_type": "seedling",
          "origin": "seedling",
          "growth_stage": "seedling",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
            "genotype": "Wild Type"
          },
          "marker": "ELF4",
          "data_cathegory": "qRT-PCR",
          "growth_cond_name": "LD 20/18C sd",
          "experiment_cond_name": "LD 20/18C sd",
          "param": {
            "@name": "unit",
            "@value": "copy nr. per cell"
          }
        },
        {
          "sample_id": "11",
          "sample_type": "whole plant",
          "origin": "whole plant",
          "growth_stage": "mid rosette",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
            "genotype": "Wild Type"
          },
          "marker": "LHY",
          "data_cathegory": "qRT-PCR",
          "growth_cond_name": "LD 20/18C",
          "experiment_cond_name": "LD 20/18C",
          "param": {
            "@name": "unit",
            "@value": "copy nr. per cell"
          }
        },
        {
          "sample_id": "12",
          "sample_type": "whole plant",
          "origin": "whole plant",
          "growth_stage": "mid rosette",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
            "genotype": "Wild Type"
          },
          "marker": "CCA1",
          "data_cathegory": "qRT-PCR",
          "growth_cond_name": "LD 20/18C",
          "experiment_cond_name": "LD 20/18C",
          "param": {
            "@name": "unit",
            "@value": "copy nr. per cell"
          }
        },
        {
          "sample_id": "13",
          "sample_type": "whole plant",
          "origin": "whole plant",
          "growth_stage": "mid rosette",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
            "genotype": "Wild Type"
          },
          "marker": "PRR9",
          "data_cathegory": "qRT-PCR",
          "growth_cond_name": "LD 20/18C",
          "experiment_cond_name": "LD 20/18C",
          "param": {
            "@name": "unit",
            "@value": "copy nr. per cell"
          }
        },
        {
          "sample_id": "14",
          "sample_type": "whole plant",
          "origin": "whole plant",
          "growth_stage": "mid rosette",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
            "genotype": "Wild Type"
          },
          "marker": "PRR7",
          "data_cathegory": "qRT-PCR",
          "growth_cond_name": "LD 20/18C",
          "experiment_cond_name": "LD 20/18C",
          "param": {
            "@name": "unit",
            "@value": "copy nr. per cell"
          }
        },
        {
          "sample_id": "15",
          "sample_type": "whole plant",
          "origin": "whole plant",
          "growth_stage": "mid rosette",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
            "genotype": "Wild Type"
          },
          "marker": "PRR5",
          "data_cathegory": "qRT-PCR",
          "growth_cond_name": "LD 20/18C",
          "experiment_cond_name": "LD 20/18C",
          "param": {
            "@name": "unit",
            "@value": "copy nr. per cell"
          }
        },
        {
          "sample_id": "16",
          "sample_type": "whole plant",
          "origin": "whole plant",
          "growth_stage": "mid rosette",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
            "genotype": "Wild Type"
          },
          "marker": "TOC1",
          "data_cathegory": "qRT-PCR",
          "growth_cond_name": "LD 20/18C",
          "experiment_cond_name": "LD 20/18C",
          "param": {
            "@name": "unit",
            "@value": "copy nr. per cell"
          }
        },
        {
          "sample_id": "17",
          "sample_type": "whole plant",
          "origin": "whole plant",
          "growth_stage": "mid rosette",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
            "genotype": "Wild Type"
          },
          "marker": "GI",
          "data_cathegory": "qRT-PCR",
          "growth_cond_name": "LD 20/18C",
          "experiment_cond_name": "LD 20/18C",
          "param": {
            "@name": "unit",
            "@value": "copy nr. per cell"
          }
        },
        {
          "sample_id": "18",
          "sample_type": "whole plant",
          "origin": "whole plant",
          "growth_stage": "mid rosette",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
            "genotype": "Wild Type"
          },
          "marker": "LUX",
          "data_cathegory": "qRT-PCR",
          "growth_cond_name": "LD 20/18C",
          "experiment_cond_name": "LD 20/18C",
          "param": {
            "@name": "unit",
            "@value": "copy nr. per cell"
          }
        },
        {
          "sample_id": "19",
          "sample_type": "whole plant",
          "origin": "whole plant",
          "growth_stage": "mid rosette",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
            "genotype": "Wild Type"
          },
          "marker": "ELF3",
          "data_cathegory": "qRT-PCR",
          "growth_cond_name": "LD 20/18C",
          "experiment_cond_name": "LD 20/18C",
          "param": {
            "@name": "unit",
            "@value": "copy nr. per cell"
          }
        },
        {
          "sample_id": "20",
          "sample_type": "whole plant",
          "origin": "whole plant",
          "growth_stage": "mid rosette",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
            "genotype": "Wild Type"
          },
          "marker": "ELF4",
          "data_cathegory": "qRT-PCR",
          "growth_cond_name": "LD 20/18C",
          "experiment_cond_name": "LD 20/18C",
          "param": {
            "@name": "unit",
            "@value": "copy nr. per cell"
          }
        }
      ]
    }
  },
  "biblio": {
    "principal": "Mark Stitt",
    "institution": "MPI of Molecular Plant Physiology",
    "author": [
      "Anna Flis",
      "Ronan Sulpice"
    ],
    "curator": "Tomasz Zielinski"
  }
}