{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000868","ANALYSIS_ID":"AN001416","VERSION":"1","CREATED_ON":"October 2, 2017, 4:12 pm"},

"PROJECT":{"PROJECT_TITLE":"Causal genetic variation underlying metabolome differences","PROJECT_SUMMARY":"A goal of biology is to predict the phenotypes of individuals, such as side effects to drugs, from their genotypes. Genetic variants that cause disease can change an individual’s total metabolite profile, or metabolome. Understanding the function of these genetic variants may help predict novel phenotypes. We used an unbiased method in yeast to show that genetic differences in two genes change the levels of several urea cycle metabolites. Leveraging knowledge of the urea cycle, we then predicted and validated the sensitivity of yeast strains to a particular drug. The interpretability of our results demonstrates the promise of using genetic variants underlying differences in the metabolome to predict novel phenotypes from genotype.","INSTITUTE":"Washington University in St. Louis","LAST_NAME":"Swain Lenz","FIRST_NAME":"Devjanee","ADDRESS":"4515 McKinley Avenue, Saint Louis, Missouri, 63110, USA","EMAIL":"devjanee.swain.lenz@duke.edu","PHONE":"314-362-3679"},

"STUDY":{"STUDY_TITLE":"Untargeted metabolomic profile of oak and wine yeast strains","STUDY_SUMMARY":"Metabolomic profiles were compiled from oak and wine yeast parents over three extraction times (batch). Included in this study are extraction controls.","INSTITUTE":"Washington University in St. Louis","LAST_NAME":"Swain Lenz","FIRST_NAME":"Devjanee","ADDRESS":"4515 McKinley Avenue, Saint Louis, Missouri, 63110, USA","EMAIL":"devjanee.swain.lenz@duke.edu","PHONE":"314-362-3679"},

"SUBJECT":{"SUBJECT_TYPE":"Fungal","SUBJECT_SPECIES":"Saccharomyces cerevisiae","TAXONOMY_ID":"4932","GENOTYPE_STRAIN":"BC233, BC240"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"BC240(UCD2120)",
"Sample ID":"1",
"Factors":{"Parent":"BC240(UCD2120)"},
"Additional sample data":{"Batch":"1"}
},
{
"Subject ID":"BC233(YPS606)",
"Sample ID":"2",
"Factors":{"Parent":"BC233(YPS606)"},
"Additional sample data":{"Batch":"1"}
},
{
"Subject ID":"BC233(YPS606)",
"Sample ID":"3",
"Factors":{"Parent":"BC233(YPS606)"},
"Additional sample data":{"Batch":"1"}
},
{
"Subject ID":"BC240(UCD2120)",
"Sample ID":"4",
"Factors":{"Parent":"BC240(UCD2120)"},
"Additional sample data":{"Batch":"1"}
},
{
"Subject ID":"BC240(UCD2120)",
"Sample ID":"5",
"Factors":{"Parent":"BC240(UCD2120)"},
"Additional sample data":{"Batch":"1"}
},
{
"Subject ID":"BC233(YPS606)",
"Sample ID":"6",
"Factors":{"Parent":"BC233(YPS606)"},
"Additional sample data":{"Batch":"1"}
},
{
"Subject ID":"BC233(YPS606)",
"Sample ID":"7",
"Factors":{"Parent":"BC233(YPS606)"},
"Additional sample data":{"Batch":"1"}
},
{
"Subject ID":"BC240(UCD2120)",
"Sample ID":"8",
"Factors":{"Parent":"BC240(UCD2120)"},
"Additional sample data":{"Batch":"1"}
},
{
"Subject ID":"BC240(UCD2120)",
"Sample ID":"9",
"Factors":{"Parent":"BC240(UCD2120)"},
"Additional sample data":{"Batch":"1"}
},
{
"Subject ID":"BC233(YPS606)",
"Sample ID":"10",
"Factors":{"Parent":"BC233(YPS606)"},
"Additional sample data":{"Batch":"1"}
},
{
"Subject ID":"BC233(YPS606)",
"Sample ID":"11",
"Factors":{"Parent":"BC233(YPS606)"},
"Additional sample data":{"Batch":"1"}
},
{
"Subject ID":"BC240(UCD2120)",
"Sample ID":"12",
"Factors":{"Parent":"BC240(UCD2120)"},
"Additional sample data":{"Batch":"1"}
},
{
"Subject ID":"no cells/no media",
"Sample ID":"14",
"Factors":{"Parent":"no cells/no media"},
"Additional sample data":{"Batch":"1"}
},
{
"Subject ID":"media only",
"Sample ID":"15",
"Factors":{"Parent":"media only"},
"Additional sample data":{"Batch":"1"}
},
{
"Subject ID":"no cells/no media",
"Sample ID":"16",
"Factors":{"Parent":"no cells/no media"},
"Additional sample data":{"Batch":"1"}
},
{
"Subject ID":"media only",
"Sample ID":"17",
"Factors":{"Parent":"media only"},
"Additional sample data":{"Batch":"1"}
},
{
"Subject ID":"no cells/no media",
"Sample ID":"18",
"Factors":{"Parent":"no cells/no media"},
"Additional sample data":{"Batch":"1"}
},
{
"Subject ID":"media only",
"Sample ID":"19",
"Factors":{"Parent":"media only"},
"Additional sample data":{"Batch":"1"}
},
{
"Subject ID":"no cells/no media",
"Sample ID":"20",
"Factors":{"Parent":"no cells/no media"},
"Additional sample data":{"Batch":"1"}
},
{
"Subject ID":"media only",
"Sample ID":"21",
"Factors":{"Parent":"media only"},
"Additional sample data":{"Batch":"1"}
},
{
"Subject ID":"no cells/no media",
"Sample ID":"22",
"Factors":{"Parent":"no cells/no media"},
"Additional sample data":{"Batch":"1"}
},
{
"Subject ID":"media only",
"Sample ID":"23",
"Factors":{"Parent":"media only"},
"Additional sample data":{"Batch":"1"}
},
{
"Subject ID":"no cells/no media",
"Sample ID":"24",
"Factors":{"Parent":"no cells/no media"},
"Additional sample data":{"Batch":"1"}
},
{
"Subject ID":"media only",
"Sample ID":"25",
"Factors":{"Parent":"media only"},
"Additional sample data":{"Batch":"1"}
},
{
"Subject ID":"no cells/no media",
"Sample ID":"26",
"Factors":{"Parent":"no cells/no media"},
"Additional sample data":{"Batch":"1"}
},
{
"Subject ID":"BC233(YPS606)",
"Sample ID":"2015_03_21_B",
"Factors":{"Parent":"BC233(YPS606)"},
"Additional sample data":{"Batch":"2"}
},
{
"Subject ID":"BC233(YPS606)",
"Sample ID":"2015_03_21_J",
"Factors":{"Parent":"BC233(YPS606)"},
"Additional sample data":{"Batch":"2"}
},
{
"Subject ID":"BC240(UCD2120)",
"Sample ID":"2015_04_07_B",
"Factors":{"Parent":"BC240(UCD2120)"},
"Additional sample data":{"Batch":"2"}
},
{
"Subject ID":"BC233(YPS606)",
"Sample ID":"2015_04_08_D",
"Factors":{"Parent":"BC233(YPS606)"},
"Additional sample data":{"Batch":"2"}
},
{
"Subject ID":"BC240(UCD2120)",
"Sample ID":"2015_04_08_J",
"Factors":{"Parent":"BC240(UCD2120)"},
"Additional sample data":{"Batch":"2"}
},
{
"Subject ID":"no cells/no media",
"Sample ID":"2015_04_13_P",
"Factors":{"Parent":"no cells/no media"},
"Additional sample data":{"Batch":"2"}
},
{
"Subject ID":"no cells/no media",
"Sample ID":"2015_04_14_P",
"Factors":{"Parent":"no cells/no media"},
"Additional sample data":{"Batch":"2"}
},
{
"Subject ID":"BC240(UCD2120)",
"Sample ID":"2015_04_15_H",
"Factors":{"Parent":"BC240(UCD2120)"},
"Additional sample data":{"Batch":"2"}
},
{
"Subject ID":"no cells/no media",
"Sample ID":"2015_04_15_P",
"Factors":{"Parent":"no cells/no media"},
"Additional sample data":{"Batch":"2"}
},
{
"Subject ID":"no cells/no media",
"Sample ID":"2015_04_21_P",
"Factors":{"Parent":"no cells/no media"},
"Additional sample data":{"Batch":"2"}
},
{
"Subject ID":"no cells/no media",
"Sample ID":"2015_04_22_F",
"Factors":{"Parent":"no cells/no media"},
"Additional sample data":{"Batch":"2"}
},
{
"Subject ID":"BC233(YPS606)",
"Sample ID":"2015_10_27_K",
"Factors":{"Parent":"BC233(YPS606)"},
"Additional sample data":{"Batch":"3"}
},
{
"Subject ID":"no cells/no media",
"Sample ID":"2015_10_27_N",
"Factors":{"Parent":"no cells/no media"},
"Additional sample data":{"Batch":"3"}
},
{
"Subject ID":"BC240(UCD2120)",
"Sample ID":"2015_10_28_G",
"Factors":{"Parent":"BC240(UCD2120)"},
"Additional sample data":{"Batch":"3"}
},
{
"Subject ID":"no cells/no media",
"Sample ID":"2015_10_28_N",
"Factors":{"Parent":"no cells/no media"},
"Additional sample data":{"Batch":"3"}
},
{
"Subject ID":"BC233(YPS606)",
"Sample ID":"2015_10_30_B",
"Factors":{"Parent":"BC233(YPS606)"},
"Additional sample data":{"Batch":"3"}
},
{
"Subject ID":"BC240(UCD2120)",
"Sample ID":"2015_10_30_D",
"Factors":{"Parent":"BC240(UCD2120)"},
"Additional sample data":{"Batch":"3"}
},
{
"Subject ID":"no cells/no media",
"Sample ID":"2015_10_30_N",
"Factors":{"Parent":"no cells/no media"},
"Additional sample data":{"Batch":"3"}
},
{
"Subject ID":"BC233(YPS606)",
"Sample ID":"2015_11_02_A",
"Factors":{"Parent":"BC233(YPS606)"},
"Additional sample data":{"Batch":"3"}
},
{
"Subject ID":"BC240(UCD2120)",
"Sample ID":"2015_11_02_D",
"Factors":{"Parent":"BC240(UCD2120)"},
"Additional sample data":{"Batch":"3"}
},
{
"Subject ID":"BC240(UCD2120)",
"Sample ID":"2015_11_11_E",
"Factors":{"Parent":"BC240(UCD2120)"},
"Additional sample data":{"Batch":"3"}
},
{
"Subject ID":"BC233(YPS606)",
"Sample ID":"2015_11_11_F",
"Factors":{"Parent":"BC233(YPS606)"},
"Additional sample data":{"Batch":"3"}
},
{
"Subject ID":"BC240(UCD2120)",
"Sample ID":"2015_11_13_S",
"Factors":{"Parent":"BC240(UCD2120)"},
"Additional sample data":{"Batch":"3"}
},
{
"Subject ID":"BC233(YPS606)",
"Sample ID":"2015_11_14_E",
"Factors":{"Parent":"BC233(YPS606)"},
"Additional sample data":{"Batch":"3"}
},
{
"Subject ID":"BC233(YPS606)",
"Sample ID":"2015_11_16_B",
"Factors":{"Parent":"BC233(YPS606)"},
"Additional sample data":{"Batch":"3"}
},
{
"Subject ID":"BC240(UCD2120)",
"Sample ID":"2015_11_16_N",
"Factors":{"Parent":"BC240(UCD2120)"},
"Additional sample data":{"Batch":"3"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Cells were grown at 30°C in synthetic dextrose media (0.145% yeast nitrogen base minus amino acids/ammonium sulfate, 0.5% ammonium sulfate, 2% dextrose) to an OD of 0.55 - 0.65. We harvested cells by vacuum filter."},

"TREATMENT":{"TREATMENT_SUMMARY":"Cells were grown at 30°C in synthetic dextrose media (0.145% yeast nitrogen base minus amino acids/ammonium sulfate, 0.5% ammonium sulfate, 2% dextrose) to an OD of 0.55 - 0.65. Different genotypes were used, and media was made at three separate times (batch)."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"We harvested cells by vacuum filter, and extracted hydrophilic metabolites from 0.2 um filters using 40:40:20% (v/v/v) methanol/acetonitrile/water8. We froze and thawed extracts at -80 °C and -20 °C, respectively, three times. We pelleted cells, and stored the supernatant at -80 °C until we performed mass spectrometry"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"None (Direct infusion)","INSTRUMENT_NAME":"None","COLUMN_NAME":"none"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS"},

"MS":{"MS_COMMENTS":"-","INSTRUMENT_NAME":"Thermo LTQ Discovery Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"API","ION_MODE":"NEGATIVE","MS_RESULTS_FILE":"ST000868_AN001416_Results.txt UNITS:normalized peak intensity"}

}