#METABOLOMICS WORKBENCH dsl15_20170822_102033_mwtab.txt DATATRACK_ID:1223 STUDY_ID:ST000868 ANALYSIS_ID:AN001416 PROJECT_ID:PR000603 VERSION 1 CREATED_ON October 2, 2017, 4:12 pm #PROJECT PR:PROJECT_TITLE Causal genetic variation underlying metabolome differences PR:PROJECT_SUMMARY A goal of biology is to predict the phenotypes of individuals, such as side PR:PROJECT_SUMMARY effects to drugs, from their genotypes. Genetic variants that cause disease can PR:PROJECT_SUMMARY change an individual’s total metabolite profile, or metabolome. Understanding PR:PROJECT_SUMMARY the function of these genetic variants may help predict novel phenotypes. We PR:PROJECT_SUMMARY used an unbiased method in yeast to show that genetic differences in two genes PR:PROJECT_SUMMARY change the levels of several urea cycle metabolites. Leveraging knowledge of the PR:PROJECT_SUMMARY urea cycle, we then predicted and validated the sensitivity of yeast strains to PR:PROJECT_SUMMARY a particular drug. The interpretability of our results demonstrates the promise PR:PROJECT_SUMMARY of using genetic variants underlying differences in the metabolome to predict PR:PROJECT_SUMMARY novel phenotypes from genotype. PR:INSTITUTE Washington University in St. Louis PR:LAST_NAME Swain Lenz PR:FIRST_NAME Devjanee PR:ADDRESS 4515 McKinley Avenue, Saint Louis, Missouri, 63110, USA PR:EMAIL devjanee.swain.lenz@duke.edu PR:PHONE 314-362-3679 #STUDY ST:STUDY_TITLE Untargeted metabolomic profile of oak and wine yeast strains ST:STUDY_SUMMARY Metabolomic profiles were compiled from oak and wine yeast parents over three ST:STUDY_SUMMARY extraction times (batch). Included in this study are extraction controls. ST:INSTITUTE Washington University in St. Louis ST:LAST_NAME Swain Lenz ST:FIRST_NAME Devjanee ST:ADDRESS 4515 McKinley Avenue, Saint Louis, Missouri, 63110, USA ST:EMAIL devjanee.swain.lenz@duke.edu ST:PHONE 314-362-3679 #SUBJECT SU:SUBJECT_TYPE Fungal SU:SUBJECT_SPECIES Saccharomyces cerevisiae SU:TAXONOMY_ID 4932 SU:GENOTYPE_STRAIN BC233, BC240 #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Additional sample data SUBJECT_SAMPLE_FACTORS BC240(UCD2120) 1 Parent:BC240(UCD2120) Batch=1 SUBJECT_SAMPLE_FACTORS BC233(YPS606) 2 Parent:BC233(YPS606) Batch=1 SUBJECT_SAMPLE_FACTORS BC233(YPS606) 3 Parent:BC233(YPS606) Batch=1 SUBJECT_SAMPLE_FACTORS BC240(UCD2120) 4 Parent:BC240(UCD2120) Batch=1 SUBJECT_SAMPLE_FACTORS BC240(UCD2120) 5 Parent:BC240(UCD2120) Batch=1 SUBJECT_SAMPLE_FACTORS BC233(YPS606) 6 Parent:BC233(YPS606) Batch=1 SUBJECT_SAMPLE_FACTORS BC233(YPS606) 7 Parent:BC233(YPS606) Batch=1 SUBJECT_SAMPLE_FACTORS BC240(UCD2120) 8 Parent:BC240(UCD2120) Batch=1 SUBJECT_SAMPLE_FACTORS BC240(UCD2120) 9 Parent:BC240(UCD2120) Batch=1 SUBJECT_SAMPLE_FACTORS BC233(YPS606) 10 Parent:BC233(YPS606) Batch=1 SUBJECT_SAMPLE_FACTORS BC233(YPS606) 11 Parent:BC233(YPS606) Batch=1 SUBJECT_SAMPLE_FACTORS BC240(UCD2120) 12 Parent:BC240(UCD2120) Batch=1 SUBJECT_SAMPLE_FACTORS no cells/no media 14 Parent:no cells/no media Batch=1 SUBJECT_SAMPLE_FACTORS media only 15 Parent:media only Batch=1 SUBJECT_SAMPLE_FACTORS no cells/no media 16 Parent:no cells/no media Batch=1 SUBJECT_SAMPLE_FACTORS media only 17 Parent:media only Batch=1 SUBJECT_SAMPLE_FACTORS no cells/no media 18 Parent:no cells/no media Batch=1 SUBJECT_SAMPLE_FACTORS media only 19 Parent:media only Batch=1 SUBJECT_SAMPLE_FACTORS no cells/no media 20 Parent:no cells/no media Batch=1 SUBJECT_SAMPLE_FACTORS media only 21 Parent:media only Batch=1 SUBJECT_SAMPLE_FACTORS no cells/no media 22 Parent:no cells/no media Batch=1 SUBJECT_SAMPLE_FACTORS media only 23 Parent:media only Batch=1 SUBJECT_SAMPLE_FACTORS no cells/no media 24 Parent:no cells/no media Batch=1 SUBJECT_SAMPLE_FACTORS media only 25 Parent:media only Batch=1 SUBJECT_SAMPLE_FACTORS no cells/no media 26 Parent:no cells/no media Batch=1 SUBJECT_SAMPLE_FACTORS BC233(YPS606) 2015_03_21_B Parent:BC233(YPS606) Batch=2 SUBJECT_SAMPLE_FACTORS BC233(YPS606) 2015_03_21_J Parent:BC233(YPS606) Batch=2 SUBJECT_SAMPLE_FACTORS BC240(UCD2120) 2015_04_07_B Parent:BC240(UCD2120) Batch=2 SUBJECT_SAMPLE_FACTORS BC233(YPS606) 2015_04_08_D Parent:BC233(YPS606) Batch=2 SUBJECT_SAMPLE_FACTORS BC240(UCD2120) 2015_04_08_J Parent:BC240(UCD2120) Batch=2 SUBJECT_SAMPLE_FACTORS no cells/no media 2015_04_13_P Parent:no cells/no media Batch=2 SUBJECT_SAMPLE_FACTORS no cells/no media 2015_04_14_P Parent:no cells/no media Batch=2 SUBJECT_SAMPLE_FACTORS BC240(UCD2120) 2015_04_15_H Parent:BC240(UCD2120) Batch=2 SUBJECT_SAMPLE_FACTORS no cells/no media 2015_04_15_P Parent:no cells/no media Batch=2 SUBJECT_SAMPLE_FACTORS no cells/no media 2015_04_21_P Parent:no cells/no media Batch=2 SUBJECT_SAMPLE_FACTORS no cells/no media 2015_04_22_F Parent:no cells/no media Batch=2 SUBJECT_SAMPLE_FACTORS BC233(YPS606) 2015_10_27_K Parent:BC233(YPS606) Batch=3 SUBJECT_SAMPLE_FACTORS no cells/no media 2015_10_27_N Parent:no cells/no media Batch=3 SUBJECT_SAMPLE_FACTORS BC240(UCD2120) 2015_10_28_G Parent:BC240(UCD2120) Batch=3 SUBJECT_SAMPLE_FACTORS no cells/no media 2015_10_28_N Parent:no cells/no media Batch=3 SUBJECT_SAMPLE_FACTORS BC233(YPS606) 2015_10_30_B Parent:BC233(YPS606) Batch=3 SUBJECT_SAMPLE_FACTORS BC240(UCD2120) 2015_10_30_D Parent:BC240(UCD2120) Batch=3 SUBJECT_SAMPLE_FACTORS no cells/no media 2015_10_30_N Parent:no cells/no media Batch=3 SUBJECT_SAMPLE_FACTORS BC233(YPS606) 2015_11_02_A Parent:BC233(YPS606) Batch=3 SUBJECT_SAMPLE_FACTORS BC240(UCD2120) 2015_11_02_D Parent:BC240(UCD2120) Batch=3 SUBJECT_SAMPLE_FACTORS BC240(UCD2120) 2015_11_11_E Parent:BC240(UCD2120) Batch=3 SUBJECT_SAMPLE_FACTORS BC233(YPS606) 2015_11_11_F Parent:BC233(YPS606) Batch=3 SUBJECT_SAMPLE_FACTORS BC240(UCD2120) 2015_11_13_S Parent:BC240(UCD2120) Batch=3 SUBJECT_SAMPLE_FACTORS BC233(YPS606) 2015_11_14_E Parent:BC233(YPS606) Batch=3 SUBJECT_SAMPLE_FACTORS BC233(YPS606) 2015_11_16_B Parent:BC233(YPS606) Batch=3 SUBJECT_SAMPLE_FACTORS BC240(UCD2120) 2015_11_16_N Parent:BC240(UCD2120) Batch=3 #COLLECTION CO:COLLECTION_SUMMARY Cells were grown at 30°C in synthetic dextrose media (0.145% yeast nitrogen CO:COLLECTION_SUMMARY base minus amino acids/ammonium sulfate, 0.5% ammonium sulfate, 2% dextrose) to CO:COLLECTION_SUMMARY an OD of 0.55 - 0.65. We harvested cells by vacuum filter. #TREATMENT TR:TREATMENT_SUMMARY Cells were grown at 30°C in synthetic dextrose media (0.145% yeast nitrogen TR:TREATMENT_SUMMARY base minus amino acids/ammonium sulfate, 0.5% ammonium sulfate, 2% dextrose) to TR:TREATMENT_SUMMARY an OD of 0.55 - 0.65. Different genotypes were used, and media was made at three TR:TREATMENT_SUMMARY separate times (batch). #SAMPLEPREP SP:SAMPLEPREP_SUMMARY We harvested cells by vacuum filter, and extracted hydrophilic metabolites from SP:SAMPLEPREP_SUMMARY 0.2 um filters using 40:40:20% (v/v/v) methanol/acetonitrile/water8. We froze SP:SAMPLEPREP_SUMMARY and thawed extracts at -80 °C and -20 °C, respectively, three times. We SP:SAMPLEPREP_SUMMARY pelleted cells, and stored the supernatant at -80 °C until we performed mass SP:SAMPLEPREP_SUMMARY spectrometry #CHROMATOGRAPHY CH:CHROMATOGRAPHY_TYPE None (Direct infusion) CH:INSTRUMENT_NAME None CH:COLUMN_NAME none #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:MS_COMMENTS - MS:INSTRUMENT_NAME Thermo LTQ Discovery Orbitrap MS:INSTRUMENT_TYPE Orbitrap MS:MS_TYPE API MS:ION_MODE NEGATIVE MS:MS_RESULTS_FILE ST000868_AN001416_Results.txt UNITS:normalized peak intensity #END