{
  "id": "2842",
  "status": "described",
  "provenance": {
    "desc_version": "2",
    "data_version": "1",
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      "by": "Tomasz Zielinski",
      "date": "2015-02-22T18:47:37",
      "version": "1.0"
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    "modified": [
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        "by": "Andrew Millar",
        "date": "2015-10-08T01:03:38",
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        "date": "2015-09-07T18:30:01",
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        "date": "2015-02-22T18:57:28",
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        "date": "2015-02-22T18:48:58",
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      "file_type": "description file",
      "content_type": "text/xml",
      "original_name": "description file",
      "local_name": "2842_dsc.xml",
      "local_path": "/localdisk/data/biodare/biodare3_prod/Robust/Storage/2842/2842_dsc.xml",
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      "original_name": "TiMetUpWP1.1 PCR ELF3 LD.xml",
      "local_name": "TiMetUpWP1.1 PCR ELF3 LD.xml",
      "local_path": "/localdisk/data/biodare/biodare3_prod/Robust/Storage/2842/TiMetUpWP1.1 PCR ELF3 LD.xml",
      "uploaded": {
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      "content_type": "text/plain",
      "original_name": "2842_bibl.xml",
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      "local_path": "/localdisk/data/biodare/biodare3_prod/Robust/Storage/2842/2842_bibl.xml",
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        "date": "2015-02-22T18:57:28",
        "version": "2"
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    }
  },
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    "file_type": "data file",
    "original_name": "RNA ELF3 LD.xlsx",
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      "file_type": "data file",
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      "original_name": "RNA ELF3 LD.xlsx",
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        "date": "2015-02-22T18:48:46",
        "version": "1"
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      "parameter": [
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          "value": "time_in_hours"
        },
        {
          "name": "first_err_col",
          "value": "36"
        },
        {
          "name": "error_type",
          "value": "std. dev."
        },
        {
          "name": "time_offset",
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        },
        {
          "name": "interval",
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        },
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          "value": "5"
        },
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          "name": "time_col",
          "value": "1"
        },
        {
          "name": "format",
          "value": "EXCEL_TBL_ERR"
        }
      ]
    }
  },
  "user_file": {
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    "original_name": "Primers_TiMet_AnnaFlis2013.xlsx",
    "version": {
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      "original_name": "Primers_TiMet_AnnaFlis2013.xlsx",
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      "uploaded": {
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        "date": "2015-09-07T18:30:01",
        "version": "1"
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  "security": {
    "owner": "tomasz",
    "supervisor": "andrew",
    "allowedToRead": [
      "millar",
      "timet",
      "public"
    ],
    "allowedToWrite": [
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      "timet"
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  },
  "hasTSData": "true",
  "open_access_info": {
    "grantedBy": "andrew",
    "grantedOn": "2015-10-08T01:03:38",
    "licence": "CC_BY"
  },
  "desc": {
    "experiment_type": "Gen. TS exp",
    "id": "2842",
    "status": "described",
    "name": "TiMet WP1.1 qRT-PCR elf3 LD",
    "purpose": "TiMet focuses on an important and general biological problem – how  are plant metabolism \nand growth regulated and orchestrated in a daily-changing environment?",
    "description": "WT and elf3-4 mutants, in biological duplicates, diurnal light, harvest every 2 hours\nNumbers are in transcript copy per cell, obtained assuming 1 g FW contains 25000000 cells.",
    "comments": "The elf3 mutant was harvested at 13 day not at 21 as the rest due to its early flowering phenotype. This experiment is partenr to \"TiMet WP1.1 qRT-PCR LD to LL and LD\"",
    "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": "12.0",
      "comment": "ELF3 was gorwth for shorter than other mutants to avoid bolting",
      "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": "12",
          "env_day": {
            "type": "diurnal_temp",
            "label": "diurnal temp",
            "duration": "12",
            "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": "12",
            "env_day": {
              "type": "diurnal_light",
              "label": "diurnal light",
              "duration": "12",
              "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",
      "medium": "Soil",
      "growth_space": "Percivals E-36L",
      "duration": "2.0",
      "comment": "Continuation of the growth conditions, harvested only 1 day",
      "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": "2",
          "env_day": {
            "type": "diurnal_temp",
            "label": "diurnal temp",
            "duration": "2",
            "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": "2",
            "env_day": {
              "type": "diurnal_light",
              "label": "diurnal light",
              "duration": "2",
              "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)."
    },
    "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": "whole plant",
          "origin": "whole plant",
          "growth_stage": "mid rosette",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
            "genotype": "elf3-4",
            "line": "empty"
          },
          "marker": "ACT2 155",
          "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": "2",
          "sample_type": "whole plant",
          "origin": "whole plant",
          "growth_stage": "mid rosette",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
            "genotype": "elf3-4",
            "line": "empty"
          },
          "marker": "ACT2 633",
          "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": "3",
          "sample_type": "whole plant",
          "origin": "whole plant",
          "growth_stage": "mid rosette",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
            "genotype": "elf3-4",
            "line": "empty"
          },
          "marker": "GAPDH3'",
          "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": "4",
          "sample_type": "whole plant",
          "origin": "whole plant",
          "growth_stage": "mid rosette",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
            "genotype": "elf3-4",
            "line": "empty"
          },
          "marker": "GAPDH5'",
          "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": "5",
          "sample_type": "whole plant",
          "origin": "whole plant",
          "growth_stage": "mid rosette",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
            "genotype": "elf3-4",
            "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": "6",
          "sample_type": "whole plant",
          "origin": "whole plant",
          "growth_stage": "mid rosette",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
            "genotype": "elf3-4",
            "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": "7",
          "sample_type": "whole plant",
          "origin": "whole plant",
          "growth_stage": "mid rosette",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
            "genotype": "elf3-4",
            "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": "8",
          "sample_type": "whole plant",
          "origin": "whole plant",
          "growth_stage": "mid rosette",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
            "genotype": "elf3-4",
            "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": "9",
          "sample_type": "whole plant",
          "origin": "whole plant",
          "growth_stage": "mid rosette",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
            "genotype": "elf3-4",
            "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": "10",
          "sample_type": "whole plant",
          "origin": "whole plant",
          "growth_stage": "mid rosette",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
            "genotype": "elf3-4",
            "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": "11",
          "sample_type": "whole plant",
          "origin": "whole plant",
          "growth_stage": "mid rosette",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
            "genotype": "elf3-4",
            "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": "12",
          "sample_type": "whole plant",
          "origin": "whole plant",
          "growth_stage": "mid rosette",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
            "genotype": "elf3-4",
            "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": "13",
          "sample_type": "whole plant",
          "origin": "whole plant",
          "growth_stage": "mid rosette",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
            "genotype": "elf3-4",
            "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"
          }
        },
        {
          "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": "elf3-4",
            "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": "15",
          "sample_type": "whole plant",
          "origin": "whole plant",
          "growth_stage": "mid rosette",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
            "genotype": "elf3-4",
            "line": "empty"
          },
          "marker": "PIF4",
          "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": "elf3-4",
            "line": "empty"
          },
          "marker": "PIF5",
          "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": "ACT2 155",
          "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": "ACT2 633",
          "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": "GAPDH3'",
          "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": "GAPDH5'",
          "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": "21",
          "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": "22",
          "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": "23",
          "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": "24",
          "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": "25",
          "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": "26",
          "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": "27",
          "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": "28",
          "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": "29",
          "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"
          }
        },
        {
          "sample_id": "30",
          "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": "31",
          "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": "PIF4",
          "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": "32",
          "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": "PIF5",
          "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 qRT-PCR elf3 LD",
    "purpose": "TiMet focuses on an important and general biological problem – how  are plant metabolism \nand growth regulated and orchestrated in a daily-changing environment?",
    "description": "WT and elf3-4 mutants, in biological duplicates, diurnal light, harvest every 2 hours\nNumbers are in transcript copy per cell, obtained assuming 1 g FW contains 25000000 cells.",
    "comments": "The elf3 mutant was harvested at 13 day not at 21 as the rest due to its early flowering phenotype. This experiment is partenr to \"TiMet WP1.1 qRT-PCR LD to LL and LD\"",
    "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": "12",
      "comment": "ELF3 was gorwth for shorter than other mutants to avoid bolting",
      "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",
      "medium": "Soil",
      "growth_space": "Percivals E-36L",
      "duration": "2",
      "comment": "Continuation of the growth conditions, harvested only 1 day",
      "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)."
    },
    "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": "whole plant",
          "origin": "whole plant",
          "growth_stage": "mid rosette",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
            "genotype": "elf3-4"
          },
          "marker": "ACT2 155",
          "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": "2",
          "sample_type": "whole plant",
          "origin": "whole plant",
          "growth_stage": "mid rosette",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
            "genotype": "elf3-4"
          },
          "marker": "ACT2 633",
          "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": "3",
          "sample_type": "whole plant",
          "origin": "whole plant",
          "growth_stage": "mid rosette",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
            "genotype": "elf3-4"
          },
          "marker": "GAPDH3'",
          "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": "4",
          "sample_type": "whole plant",
          "origin": "whole plant",
          "growth_stage": "mid rosette",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
            "genotype": "elf3-4"
          },
          "marker": "GAPDH5'",
          "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": "5",
          "sample_type": "whole plant",
          "origin": "whole plant",
          "growth_stage": "mid rosette",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
            "genotype": "elf3-4"
          },
          "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": "6",
          "sample_type": "whole plant",
          "origin": "whole plant",
          "growth_stage": "mid rosette",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
            "genotype": "elf3-4"
          },
          "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": "7",
          "sample_type": "whole plant",
          "origin": "whole plant",
          "growth_stage": "mid rosette",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
            "genotype": "elf3-4"
          },
          "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": "8",
          "sample_type": "whole plant",
          "origin": "whole plant",
          "growth_stage": "mid rosette",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
            "genotype": "elf3-4"
          },
          "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": "9",
          "sample_type": "whole plant",
          "origin": "whole plant",
          "growth_stage": "mid rosette",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
            "genotype": "elf3-4"
          },
          "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": "10",
          "sample_type": "whole plant",
          "origin": "whole plant",
          "growth_stage": "mid rosette",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
            "genotype": "elf3-4"
          },
          "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": "11",
          "sample_type": "whole plant",
          "origin": "whole plant",
          "growth_stage": "mid rosette",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
            "genotype": "elf3-4"
          },
          "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": "12",
          "sample_type": "whole plant",
          "origin": "whole plant",
          "growth_stage": "mid rosette",
          "age": "20",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Wasilewski (WS)",
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          }
        },
        {
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          }
        },
        {
          "sample_id": "15",
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          },
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          }
        },
        {
          "sample_id": "16",
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          "age": "20",
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          },
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          }
        },
        {
          "sample_id": "18",
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          }
        },
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          }
        },
        {
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          },
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          }
        },
        {
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          },
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          "experiment_cond_name": "LD 20/18C",
          "param": {
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          }
        },
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          "growth_stage": "mid rosette",
          "age": "20",
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          },
          "marker": "PRR9",
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          "experiment_cond_name": "LD 20/18C",
          "param": {
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          }
        },
        {
          "sample_id": "24",
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          }
        },
        {
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        },
        {
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          "experiment_cond_name": "LD 20/18C",
          "param": {
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          }
        },
        {
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          },
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          "experiment_cond_name": "LD 20/18C",
          "param": {
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            "@value": "copy nr. per cell"
          }
        },
        {
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          "origin": "whole plant",
          "growth_stage": "mid rosette",
          "age": "20",
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            "genotype": "Wild Type"
          },
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          "data_cathegory": "qRT-PCR",
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          "experiment_cond_name": "LD 20/18C",
          "param": {
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            "@value": "copy nr. per cell"
          }
        },
        {
          "sample_id": "31",
          "sample_type": "whole plant",
          "origin": "whole plant",
          "growth_stage": "mid rosette",
          "age": "20",
          "genetic_info": {
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            "background": "Wasilewski (WS)",
            "genotype": "Wild Type"
          },
          "marker": "PIF4",
          "data_cathegory": "qRT-PCR",
          "growth_cond_name": "LD 20/18C",
          "experiment_cond_name": "LD 20/18C",
          "param": {
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            "@value": "copy nr. per cell"
          }
        },
        {
          "sample_id": "32",
          "sample_type": "whole plant",
          "origin": "whole plant",
          "growth_stage": "mid rosette",
          "age": "20",
          "genetic_info": {
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            "background": "Wasilewski (WS)",
            "genotype": "Wild Type"
          },
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          "data_cathegory": "qRT-PCR",
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          "param": {
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          }
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      ]
    }
  },
  "biblio": {
    "principal": "Mark Stitt",
    "institution": "MPI of Molecular Plant Physiology",
    "author": [
      "Anna Flis",
      "Ronan Sulpice"
    ],
    "curator": "Tomasz Zielinski"
  }
}