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    "experiment_type": "Literature data",
    "id": "3488",
    "status": "described",
    "name": "McWatters A.t. Col-0 WT clock RNA timeseries",
    "purpose": "Harriet McWatters study to compare clock gene expression with light and temperature entrainment, published in Flis et al. 2015",
    "description": "Literature data from: 'Defining the robust behaviour of the plant clock gene circuit with absolute RNA timeseries and open infrastructure.'\n\t    by: Harriet G. McWatters.\n\t    \n\t    data are col0 8 d seedlings grown on sucrose in either LD 12:12 at 20 oC or WC 27:12 in LL.\nGene expression normalised on btub4 control RNA in same sample at same time. Each datapoint is mean of two biological replicates (each with three technical replicates).",
    "comments": "Experiment by Harriet McWatters lab in Oxford, perhaps ca. 2007. Published in Flis et al. RS Open Biology 2015.\nPrep details From Knight, Thomson and McWatters PP 2008: \"seedlings were grown on plates containing 1× MS salts with 0.8% to 1% agar and, where indicated, supplemented with 3% (w/v) Suc. In all cases, media pH was corrected to pH 5.8. Unless otherwise stated, seeds were surface-sterilized before being stratified in the dark at 4°C for 48 h prior to transfer to the growth chamber. Plants were grown in Sanyo MLR-350 growth chambers at a constant temperature (20°C). The light level during photoperiods or constant light was 50 μmol m−2 s−1.\"",
    "pubmed_id": "0000",
    "provenance": {
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      "author": "Harriet G. McWatters",
      "start_date": "2015-09-01"
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        "name": "LD12:12",
        "medium": "Agar 1.5% MS 1 3% Sucrose",
        "stratification": "2 days at 4C",
        "growth_space": "Sanyo MLR-350 growth chamber",
        "duration": "7.0",
        "comment": "Actually less agar (0.8-1%) according to the paper",
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          "label": "const. 20.0C",
          "env_conditions": {
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            "label": "const. 20.0C",
            "duration": "7",
            "env_day": {
              "type": "constant_temp",
              "label": "constant temperature",
              "duration": "7",
              "cycle_length": "24",
              "base_value": "20.0",
              "second_value": "20.0"
            }
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          "light_channel": {
            "spectrum": "white",
            "intensity": "50",
            "source": "tube",
            "env_conditions": {
              "type": "diurnal_light",
              "label": "LD 12:00:12:00",
              "duration": "7",
              "env_day": {
                "type": "diurnal_light",
                "label": "diurnal light",
                "duration": "7",
                "cycle_length": "24",
                "base_value": "0.0",
                "second_value": "100.0",
                "env_period": {
                  "start_time": "0:00",
                  "duration": "12:00"
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        "pH": {
          "label": null,
          "env_conditions": {
            "type": "constant",
            "label": "constant",
            "duration": "0",
            "env_day": {
              "type": "constant",
              "label": "constant",
              "duration": "0",
              "cycle_length": "24",
              "base_value": "5.8",
              "second_value": "5.8"
            }
          }
        }
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        "name": "WC 27oC:12oC in LL",
        "medium": "Agar 1.5% MS 1 3% Sucrose",
        "stratification": "2 days at 4C",
        "growth_space": "Sanyo MLR-350 chamber",
        "duration": "7.0",
        "comment": "Actually less agar (0.8-1%) according to the paper",
        "temperature_conditions": {
          "label": "diurn. 27.0C:12.0C 12:00:12:00",
          "env_conditions": {
            "type": "diurnal_temp",
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            "duration": "7",
            "env_day": {
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              "label": "diurnal temp",
              "duration": "7",
              "cycle_length": "24",
              "base_value": "12.0",
              "second_value": "27.0",
              "env_period": {
                "start_time": "0:00",
                "duration": "12:00"
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            }
          }
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          "label": "W: LL",
          "light_channel": {
            "spectrum": "white",
            "intensity": "50",
            "source": "tube",
            "env_conditions": {
              "type": "constant_light",
              "label": "LL",
              "duration": "7",
              "env_day": {
                "type": "constant_light",
                "label": "constant light",
                "duration": "7",
                "cycle_length": "24",
                "base_value": "0.0",
                "second_value": "100.0",
                "env_period": {
                  "start_time": "0:00",
                  "duration": "24:00"
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          }
        },
        "pH": {
          "label": null,
          "env_conditions": {
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            "label": "constant",
            "duration": "0",
            "env_day": {
              "type": "constant",
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              "cycle_length": "24",
              "base_value": "5.8",
              "second_value": "5.8"
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        "name": "LD 12:12",
        "medium": "Agar 1.5% MS 1 3% Sucrose",
        "growth_space": "Sanyo MLR-350",
        "duration": "1.0",
        "comment": "same as entraining condition",
        "temperature_conditions": {
          "label": "const. 20.0C",
          "env_conditions": {
            "type": "constant_temp",
            "label": "const. 20.0C",
            "duration": "1",
            "env_day": {
              "type": "constant_temp",
              "label": "constant temperature",
              "duration": "1",
              "cycle_length": "24",
              "base_value": "20.0",
              "second_value": "20.0"
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            "spectrum": "white",
            "intensity": "50",
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            "env_conditions": {
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              "label": "LD 12:00:12:00",
              "duration": "1",
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                "duration": "1",
                "cycle_length": "24",
                "base_value": "0.0",
                "second_value": "100.0",
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        "pH": {
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              "cycle_length": "24",
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        "name": "WC 27oC:12oC in LL",
        "medium": "Agar 1.5% MS 1 3% Sucrose",
        "duration": "1.0",
        "comment": "same as entraining condition",
        "temperature_conditions": {
          "label": "diurn. 27.0C:12.0C 12:00:12:00",
          "env_conditions": {
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            "label": "diurn. 27.0C:12.0C 12:00:12:00",
            "duration": "1",
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              "label": "diurnal temp",
              "duration": "1",
              "cycle_length": "24",
              "base_value": "12.0",
              "second_value": "27.0",
              "env_period": {
                "start_time": "0:00",
                "duration": "12:00"
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          }
        },
        "light_conditions": {
          "label": "W: LL",
          "light_channel": {
            "spectrum": "white",
            "intensity": "50",
            "source": "tube",
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              "label": "LL",
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              "env_day": {
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                "label": "constant light",
                "duration": "1",
                "cycle_length": "24",
                "base_value": "0.0",
                "second_value": "100.0",
                "env_period": {
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                  "duration": "24:00"
                }
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          "label": null,
          "env_conditions": {
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            "label": "constant",
            "duration": "0",
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              "cycle_length": "24",
              "base_value": "5.8",
              "second_value": "5.8"
            }
          }
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    ],
    "measurement": {
      "technique": "RT-PCR",
      "equipment": "SYBR Green PCR Master mix (Applied Biosystems [4309155]) using an Applied Biosystems Prism-7300.",
      "description": "Literature data from: ''\n\t    by: .\n\t    \n\t    From Knight et al. 2008: Samples of 20 to 30 seedlings were collected every 3 h and snap-frozen in liquid nitrogen; the first sample was collected at subjective dawn on day 14, after 24 h in LL. Similarly, for analysis of flowering time gene expression, seedlings were grown on plates as described above in LD 16:8 photoperiods for 13 d and sampled every 2 h on day 14 in a free-running cycle. RNA was extracted (RNeasy kit, Qiagen [74904] with additional DNAse digestion) from each sample and cDNA synthesized (Taq-Man, Applied Biosystems [N808-0234] reverse transcriptase kit) for each time point. Real-time reverse transcription (RT)-PCR was carried out in triplicate with SYBR Green PCR Master mix (Applied Biosystems [4309155]) using an Applied Biosystems Prism-7300. Levels of specific mRNA and βTUBULIN4 (βTUB4) controls were calculated by the standard curve method (Applied Biosystems user bulletin 2); the relative expression (arbitrary units) of each gene of interest was obtained by dividing by contemporaneous βTUB4 expression. No-RT and no-template controls were included as negative controls for each set of reactions. Two or three independent biological repeats gave similar results."
    },
    "sample_preparation": {
      "method": "From Knight et al. 2008: Samples of 20 to 30 seedlings were collected every 3 h and snap-frozen in liquid nitrogen; the first sample was collected at subjective dawn on day 14, after 24 h in LL. Similarly, for analysis of flowering time gene expression, seedlings were grown on plates as described above in LD 16:8 photoperiods for 13 d and sampled every 2 h on day 14 in a free-running cycle. RNA was extracted (RNeasy kit, Qiagen [74904] with additional DNAse digestion) from each sample and cDNA synthesized (Taq-Man, Applied Biosystems [N808-0234] reverse transcriptase kit) for each time point."
    },
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          "sample_id": "1",
          "sample_type": "group of seedlings",
          "origin": "group of seedlings",
          "growth_stage": "seedling",
          "genetic_info": {
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            "background": "Columbia (Col)",
            "genotype": "Wild Type",
            "line": "empty"
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          "growth_cond_name": "LD12:12",
          "experiment_cond_name": "LD 12:12",
          "ignored": "false"
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          "origin": "group of seedlings",
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            "background": "Columbia (Col)",
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          "ignored": "false"
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          "origin": "group of seedlings",
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          "marker": "TOC1",
          "growth_cond_name": "WC 27oC:12oC in LL",
          "experiment_cond_name": "WC 27oC:12oC in LL",
          "ignored": "false"
        }
      ]
    }
  },
  "pedro": {
    "@xmlns:xsi": "http://www.w3.org/2001/XMLSchema-instance",
    "@xsi:schemaLocation": "/W:/communal/DataDescription/models/literature/model/full_literature.xsd",
    "name": "McWatters A.t. Col-0 WT clock RNA timeseries",
    "purpose": "Harriet McWatters study to compare clock gene expression with light and temperature entrainment, published in Flis et al. 2015",
    "description": "data are col0 8 d seedlings grown on sucrose in either LD 12:12 at 20 oC or WC 27:12 in LL.\nGene expression normalised on btub4 control RNA in same sample at same time. Each datapoint is mean of two biological replicates (each with three technical replicates).",
    "comments": "Experiment by Harriet McWatters lab in Oxford, perhaps ca. 2007. Published in Flis et al. RS Open Biology 2015.\nPrep details From Knight, Thomson and McWatters PP 2008: \"seedlings were grown on plates containing 1× MS salts with 0.8% to 1% agar and, where indicated, supplemented with 3% (w/v) Suc. In all cases, media pH was corrected to pH 5.8. Unless otherwise stated, seeds were surface-sterilized before being stratified in the dark at 4°C for 48 h prior to transfer to the growth chamber. Plants were grown in Sanyo MLR-350 growth chambers at a constant temperature (20°C). The light level during photoperiods or constant light was 50 μmol m−2 s−1.\"",
    "pubmed_id": "0000",
    "provenance": {
      "pub_title": "Defining the robust behaviour of the plant clock gene circuit with absolute RNA timeseries and open infrastructure.",
      "first_author": "Harriet G. McWatters",
      "group": "McWatters",
      "pub_date": "2015-09-01"
    },
    "growth_condition": [
      {
        "name": "LD12:12",
        "medium": "Agar 1.5% MS 1 3% Sucrose",
        "stratification": "2 days at 4C",
        "growth_space": "Sanyo MLR-350 growth chamber",
        "duration": "7",
        "comment": "Actually less agar (0.8-1%) according to the paper",
        "temperature_conditions": {
          "constant_temp": {
            "cycle_length": "24",
            "base_temp": "20"
          }
        },
        "light_conditions": {
          "light_channel": {
            "spectrum": "white",
            "intensity": "50",
            "source": "tube",
            "diurnal_light": {
              "cycle_length": "24",
              "start_time": "0",
              "duration": "12"
            }
          }
        },
        "pH": {
          "settings": {
            "const": {
              "base_value": "5.8"
            }
          }
        }
      },
      {
        "name": "WC 27oC:12oC in LL",
        "medium": "Agar 1.5% MS 1 3% Sucrose",
        "stratification": "2 days at 4C",
        "growth_space": "Sanyo MLR-350 chamber",
        "duration": "7",
        "comment": "Actually less agar (0.8-1%) according to the paper",
        "temperature_conditions": {
          "diurnal_temp": {
            "cycle_length": "24",
            "base_temp": "12",
            "second_temp": "27",
            "start_time": "0",
            "duration": "12"
          }
        },
        "light_conditions": {
          "light_channel": {
            "spectrum": "white",
            "intensity": "50",
            "source": "tube",
            "constant_light": {
              "cycle_length": "24"
            }
          }
        },
        "pH": {
          "settings": {
            "const": {
              "base_value": "5.8"
            }
          }
        }
      }
    ],
    "experimental_condition": [
      {
        "name": "LD 12:12",
        "medium": "Agar 1.5% MS 1 3% Sucrose",
        "growth_space": "Sanyo MLR-350",
        "duration": "1",
        "comment": "same as entraining condition",
        "temperature_conditions": {
          "constant_temp": {
            "cycle_length": "24",
            "base_temp": "20"
          }
        },
        "light_conditions": {
          "light_channel": {
            "spectrum": "white",
            "intensity": "50",
            "source": "tube",
            "diurnal_light": {
              "cycle_length": "24",
              "start_time": "0",
              "duration": "12"
            }
          }
        },
        "pH": {
          "settings": {
            "const": {
              "base_value": "5.8"
            }
          }
        }
      },
      {
        "name": "WC 27oC:12oC in LL",
        "medium": "Agar 1.5% MS 1 3% Sucrose",
        "duration": "1",
        "comment": "same as entraining condition",
        "temperature_conditions": {
          "diurnal_temp": {
            "cycle_length": "24",
            "base_temp": "12",
            "second_temp": "27",
            "start_time": "0",
            "duration": "12"
          }
        },
        "light_conditions": {
          "light_channel": {
            "spectrum": "white",
            "intensity": "50",
            "source": "tube",
            "constant_light": {
              "cycle_length": "24"
            }
          }
        },
        "pH": {
          "settings": {
            "const": {
              "base_value": "5.8"
            }
          }
        }
      }
    ],
    "measurement": {
      "technique": "RT-PCR",
      "equipment": "SYBR Green PCR Master mix (Applied Biosystems [4309155]) using an Applied Biosystems Prism-7300.",
      "description": "From Knight et al. 2008: Samples of 20 to 30 seedlings were collected every 3 h and snap-frozen in liquid nitrogen; the first sample was collected at subjective dawn on day 14, after 24 h in LL. Similarly, for analysis of flowering time gene expression, seedlings were grown on plates as described above in LD 16:8 photoperiods for 13 d and sampled every 2 h on day 14 in a free-running cycle. RNA was extracted (RNeasy kit, Qiagen [74904] with additional DNAse digestion) from each sample and cDNA synthesized (Taq-Man, Applied Biosystems [N808-0234] reverse transcriptase kit) for each time point. Real-time reverse transcription (RT)-PCR was carried out in triplicate with SYBR Green PCR Master mix (Applied Biosystems [4309155]) using an Applied Biosystems Prism-7300. Levels of specific mRNA and βTUBULIN4 (βTUB4) controls were calculated by the standard curve method (Applied Biosystems user bulletin 2); the relative expression (arbitrary units) of each gene of interest was obtained by dividing by contemporaneous βTUB4 expression. No-RT and no-template controls were included as negative controls for each set of reactions. Two or three independent biological repeats gave similar results."
    },
    "sample_preparation": {
      "method": "From Knight et al. 2008: Samples of 20 to 30 seedlings were collected every 3 h and snap-frozen in liquid nitrogen; the first sample was collected at subjective dawn on day 14, after 24 h in LL. Similarly, for analysis of flowering time gene expression, seedlings were grown on plates as described above in LD 16:8 photoperiods for 13 d and sampled every 2 h on day 14 in a free-running cycle. RNA was extracted (RNeasy kit, Qiagen [74904] with additional DNAse digestion) from each sample and cDNA synthesized (Taq-Man, Applied Biosystems [N808-0234] reverse transcriptase kit) for each time point."
    },
    "samples": {
      "sample": [
        {
          "sample_id": "1",
          "sample_type": "group of seedlings",
          "origin": "group of seedlings",
          "growth_stage": "seedling",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Columbia (Col)",
            "genotype": "Wild Type"
          },
          "marker": "CCA1",
          "growth_cond_name": "LD12:12",
          "experiment_cond_name": "LD 12:12"
        },
        {
          "sample_id": "2",
          "sample_type": "group of seedlings",
          "origin": "group of seedlings",
          "growth_stage": "seedling",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Columbia (Col)",
            "genotype": "Wild Type"
          },
          "marker": "CCA1",
          "growth_cond_name": "LD12:12",
          "experiment_cond_name": "LD 12:12"
        },
        {
          "sample_id": "3",
          "sample_type": "group of seedlings",
          "origin": "group of seedlings",
          "growth_stage": "seedling",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Columbia (Col)",
            "genotype": "Wild Type"
          },
          "marker": "TOC1",
          "growth_cond_name": "LD12:12",
          "experiment_cond_name": "LD 12:12"
        },
        {
          "sample_id": "4",
          "sample_type": "group of seedlings",
          "origin": "group of seedlings",
          "growth_stage": "seedling",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Columbia (Col)",
            "genotype": "Wild Type"
          },
          "marker": "TOC1",
          "growth_cond_name": "LD12:12",
          "experiment_cond_name": "LD 12:12"
        },
        {
          "sample_id": "5",
          "sample_type": "group of seedlings",
          "origin": "group of seedlings",
          "growth_stage": "seedling",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Columbia (Col)",
            "genotype": "Wild Type"
          },
          "marker": "CCA1",
          "growth_cond_name": "WC 27oC:12oC in LL",
          "experiment_cond_name": "WC 27oC:12oC in LL"
        },
        {
          "sample_id": "6",
          "sample_type": "group of seedlings",
          "origin": "group of seedlings",
          "growth_stage": "seedling",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Columbia (Col)",
            "genotype": "Wild Type"
          },
          "marker": "CCA1",
          "growth_cond_name": "WC 27oC:12oC in LL",
          "experiment_cond_name": "WC 27oC:12oC in LL"
        },
        {
          "sample_id": "7",
          "sample_type": "group of seedlings",
          "origin": "group of seedlings",
          "growth_stage": "seedling",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Columbia (Col)",
            "genotype": "Wild Type"
          },
          "marker": "TOC1",
          "growth_cond_name": "WC 27oC:12oC in LL",
          "experiment_cond_name": "WC 27oC:12oC in LL"
        },
        {
          "sample_id": "8",
          "sample_type": "group of seedlings",
          "origin": "group of seedlings",
          "growth_stage": "seedling",
          "genetic_info": {
            "species": "Arabidopsis thaliana",
            "background": "Columbia (Col)",
            "genotype": "Wild Type"
          },
          "marker": "TOC1",
          "growth_cond_name": "WC 27oC:12oC in LL",
          "experiment_cond_name": "WC 27oC:12oC in LL"
        }
      ]
    }
  },
  "biblio": {
    "principal": "Harriet G. McWatters",
    "institution": "University of Oxford",
    "curator": "Andrew J. Millar"
  }
}