#METABOLOMICS WORKBENCH dsl15_20170822_102809 DATATRACK_ID:1224 STUDY_ID:ST000871 ANALYSIS_ID:AN001415 PROJECT_ID:PR000603 VERSION 1 CREATED_ON August 28, 2017, 11:27 am #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 reciprocal hemizygotes (oak/win hybrid, genes ST:STUDY_TITLE AUA1, ARG82) (part III) ST:STUDY_SUMMARY Metabolomic profiles were compiled from reciprocal hemizygotes (oak/win hybrid, ST:STUDY_SUMMARY genes AUA1, ARG82) (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 #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Additional sample data SUBJECT_SAMPLE_FACTORS ARG81W::KAN 1 2015_10_26_C Batch:3 SUBJECT_SAMPLE_FACTORS ARG81O::KAN 3 2015_10_26_E Batch:3 SUBJECT_SAMPLE_FACTORS ARG81O::KAN 4 2015_10_26_I Batch:3 SUBJECT_SAMPLE_FACTORS media only 2015_10_26_M Batch:3 SUBJECT_SAMPLE_FACTORS ARG81W::KAN 3 2015_10_27_A Batch:3 SUBJECT_SAMPLE_FACTORS ARG81O::KAN 3 2015_10_27_D Batch:3 SUBJECT_SAMPLE_FACTORS ARG81O::KAN 2 2015_10_27_E Batch:3 SUBJECT_SAMPLE_FACTORS ARG81W::KAN 2 2015_10_27_H Batch:3 SUBJECT_SAMPLE_FACTORS ARG81O::KAN 1 2015_10_27_J Batch:3 SUBJECT_SAMPLE_FACTORS media only 2015_10_27_M Batch:3 SUBJECT_SAMPLE_FACTORS no cells/no media 2015_10_27_N Batch:3 SUBJECT_SAMPLE_FACTORS ARG81W::KAN 2 2015_10_28_C Batch:3 SUBJECT_SAMPLE_FACTORS ARG81O::KAN 4 2015_10_28_E Batch:3 SUBJECT_SAMPLE_FACTORS ARG81O::KAN 3 2015_10_28_H Batch:3 SUBJECT_SAMPLE_FACTORS ARG81O::KAN 1 2015_10_28_I Batch:3 SUBJECT_SAMPLE_FACTORS ARG81W::KAN 1 2015_10_28_J Batch:3 SUBJECT_SAMPLE_FACTORS media only 2015_10_28_M Batch:3 SUBJECT_SAMPLE_FACTORS no cells/no media 2015_10_28_N Batch:3 SUBJECT_SAMPLE_FACTORS ARG81W::KAN 3 2015_10_30_A Batch:3 SUBJECT_SAMPLE_FACTORS ARG81O::KAN 2 2015_10_30_E Batch:3 SUBJECT_SAMPLE_FACTORS ARG81W::KAN 1 2015_10_30_F Batch:3 SUBJECT_SAMPLE_FACTORS ARG81W::KAN 3 2015_10_30_G Batch:3 SUBJECT_SAMPLE_FACTORS ARG81W::KAN 2 2015_10_30_H Batch:3 SUBJECT_SAMPLE_FACTORS ARG81O::KAN 2 2015_10_30_I Batch:3 SUBJECT_SAMPLE_FACTORS ARG81O::KAN 4 2015_10_30_J Batch:3 SUBJECT_SAMPLE_FACTORS no cells/no media 2015_10_30_N Batch:3 SUBJECT_SAMPLE_FACTORS ARG81O::KAN 1 2015_11_02_G Batch:3 SUBJECT_SAMPLE_FACTORS AUA1W::KAN 5 2015_11_11_C Batch:3 SUBJECT_SAMPLE_FACTORS AUA1W::KAN 4 2015_11_11_D Batch:3 SUBJECT_SAMPLE_FACTORS AUA1W::KAN 1 2015_11_11_H Batch:3 SUBJECT_SAMPLE_FACTORS AUA1O::KAN 1 2015_11_11_J Batch:3 SUBJECT_SAMPLE_FACTORS AUA1W::KAN 2 2015_11_11_K Batch:3 SUBJECT_SAMPLE_FACTORS AUA1O::KAN 5 2015_11_11_N Batch:3 SUBJECT_SAMPLE_FACTORS AUA1O::KAN 4 2015_11_11_O Batch:3 SUBJECT_SAMPLE_FACTORS AUA1O::KAN 3 2015_11_11_P Batch:3 SUBJECT_SAMPLE_FACTORS AUA1O::KAN 2 2015_11_11_S Batch:3 SUBJECT_SAMPLE_FACTORS AUA1O::KAN 5 2015_11_13_B Batch:3 SUBJECT_SAMPLE_FACTORS AUA1O::KAN 4 2015_11_13_D Batch:3 SUBJECT_SAMPLE_FACTORS AUA1W::KAN 5 2015_11_13_E Batch:3 SUBJECT_SAMPLE_FACTORS AUA1W::KAN 1 2015_11_13_F Batch:3 SUBJECT_SAMPLE_FACTORS AUA1O::KAN 3 2015_11_13_K Batch:3 SUBJECT_SAMPLE_FACTORS AUA1W::KAN 2 2015_11_13_M Batch:3 SUBJECT_SAMPLE_FACTORS AUA1W::KAN 4 2015_11_13_O Batch:3 SUBJECT_SAMPLE_FACTORS AUA1W::KAN 3 2015_11_13_R Batch:3 SUBJECT_SAMPLE_FACTORS AUA1O::KAN 3 2015_11_14_A Batch:3 SUBJECT_SAMPLE_FACTORS AUA1O::KAN 2 2015_11_14_B Batch:3 SUBJECT_SAMPLE_FACTORS AUA1W::KAN 5 2015_11_14_C Batch:3 SUBJECT_SAMPLE_FACTORS AUA1W::KAN 1 2015_11_14_D Batch:3 SUBJECT_SAMPLE_FACTORS AUA1O::KAN 4 2015_11_14_J Batch:3 SUBJECT_SAMPLE_FACTORS AUA1O::KAN 1 2015_11_14_L Batch:3 SUBJECT_SAMPLE_FACTORS AUA1O::KAN 5 2015_11_14_P Batch:3 SUBJECT_SAMPLE_FACTORS AUA1W::KAN 2 2015_11_14_Q Batch:3 SUBJECT_SAMPLE_FACTORS AUA1W::KAN 4 2015_11_14_R Batch:3 SUBJECT_SAMPLE_FACTORS AUA1W::KAN 3 2015_11_14_S Batch:3 SUBJECT_SAMPLE_FACTORS AUA1W::KAN 3 2015_11_16_C Batch:3 SUBJECT_SAMPLE_FACTORS AUA1O::KAN 2 2015_11_16_D Batch:3 SUBJECT_SAMPLE_FACTORS AUA1O::KAN 1 2015_11_16_M Batch:3 SUBJECT_SAMPLE_FACTORS BC233_BC240_mix STD_14 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 ST000871_AN001415_Results.txt UNITS:normalized peak intensity #END