#METABOLOMICS WORKBENCH dsl15_20170822_094043 DATATRACK_ID:1222 STUDY_ID:ST000870 ANALYSIS_ID:AN001417 PROJECT_ID:PR000603 VERSION 1 CREATED_ON October 2, 2017, 4:26 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 Saccharomyces cerevisiae (F2) hybrids (part ST:STUDY_TITLE II) ST:STUDY_SUMMARY Metabolomic profiles were compiled from oak and wine yeast parents, and their F2 ST:STUDY_SUMMARY hybrids. 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, BC240,147 individual BC240/BC233 F2 hybrid segregants #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 F2_2A1 28 Parent:F2_2A1 batch=1 SUBJECT_SAMPLE_FACTORS F2_2A6 29 Parent:F2_2A6 batch=1 SUBJECT_SAMPLE_FACTORS F2_2A7 30 Parent:F2_2A7 batch=1 SUBJECT_SAMPLE_FACTORS F2_2A8 31 Parent:F2_2A8 batch=1 SUBJECT_SAMPLE_FACTORS F2_2A9 32 Parent:F2_2A9 batch=1 SUBJECT_SAMPLE_FACTORS F2_2A11 33 Parent:F2_2A11 batch=1 SUBJECT_SAMPLE_FACTORS F2_2B1 34 Parent:F2_2B1 batch=1 SUBJECT_SAMPLE_FACTORS F2_2B4 35 Parent:F2_2B4 batch=1 SUBJECT_SAMPLE_FACTORS F2_2B6 36 Parent:F2_2B6 batch=1 SUBJECT_SAMPLE_FACTORS F2_2B9 37 Parent:F2_2B9 batch=1 SUBJECT_SAMPLE_FACTORS F2_2B11 38 Parent:F2_2B11 batch=1 SUBJECT_SAMPLE_FACTORS F2_2C1 39 Parent:F2_2C1 batch=1 SUBJECT_SAMPLE_FACTORS F2_2C4 40 Parent:F2_2C4 batch=1 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SUBJECT_SAMPLE_FACTORS F2_2E10 59 Parent:F2_2E10 batch=1 SUBJECT_SAMPLE_FACTORS F2_2G5 60 Parent:F2_2G5 batch=1 SUBJECT_SAMPLE_FACTORS F2_2G6 61 Parent:F2_2G6 batch=1 SUBJECT_SAMPLE_FACTORS F2_2G8 62 Parent:F2_2G8 batch=1 SUBJECT_SAMPLE_FACTORS F2_2G9 63 Parent:F2_2G9 batch=1 SUBJECT_SAMPLE_FACTORS F2_2G10 64 Parent:F2_2G10 batch=1 SUBJECT_SAMPLE_FACTORS F2_2A1 65 Parent:F2_2A1 batch=1 SUBJECT_SAMPLE_FACTORS F2_2A3 66 Parent:F2_2A3 batch=1 SUBJECT_SAMPLE_FACTORS F2_2A4 67 Parent:F2_2A4 batch=1 SUBJECT_SAMPLE_FACTORS F2_2A6 68 Parent:F2_2A6 batch=1 SUBJECT_SAMPLE_FACTORS F2_2A8 69 Parent:F2_2A8 batch=1 SUBJECT_SAMPLE_FACTORS F2_2A9 70 Parent:F2_2A9 batch=1 SUBJECT_SAMPLE_FACTORS F2_2E12 71 Parent:F2_2E12 batch=1 SUBJECT_SAMPLE_FACTORS F2_2F2 72 Parent:F2_2F2 batch=1 SUBJECT_SAMPLE_FACTORS F2_2F5 73 Parent:F2_2F5 batch=1 SUBJECT_SAMPLE_FACTORS F2_2F6 74 Parent:F2_2F6 batch=1 SUBJECT_SAMPLE_FACTORS F2_2F8 75 Parent:F2_2F8 batch=1 SUBJECT_SAMPLE_FACTORS F2_2F11 76 Parent:F2_2F11 batch=1 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SUBJECT_SAMPLE_FACTORS F2_8A10 394 Parent:F2_8A10 batch=1 SUBJECT_SAMPLE_FACTORS F2_8A11 395 Parent:F2_8A11 batch=1 SUBJECT_SAMPLE_FACTORS F2_8A12 396 Parent:F2_8A12 batch=1 SUBJECT_SAMPLE_FACTORS F2_8B5 397 Parent:F2_8B5 batch=1 SUBJECT_SAMPLE_FACTORS F2_8B6 398 Parent:F2_8B6 batch=1 SUBJECT_SAMPLE_FACTORS F2_8B9 399 Parent:F2_8B9 batch=1 SUBJECT_SAMPLE_FACTORS F2_8B11 400 Parent:F2_8B11 batch=1 SUBJECT_SAMPLE_FACTORS F2_8C1 401 Parent:F2_8C1 batch=1 SUBJECT_SAMPLE_FACTORS F2_8C4 402 Parent:F2_8C4 batch=1 SUBJECT_SAMPLE_FACTORS F2_8C6 403 Parent:F2_8C6 batch=1 SUBJECT_SAMPLE_FACTORS F2_8C7 404 Parent:F2_8C7 batch=1 SUBJECT_SAMPLE_FACTORS F2_8C9 405 Parent:F2_8C9 batch=1 SUBJECT_SAMPLE_FACTORS F2_8C12 406 Parent:F2_8C12 batch=1 SUBJECT_SAMPLE_FACTORS F2_8D2 407 Parent:F2_8D2 batch=1 SUBJECT_SAMPLE_FACTORS F2_8D5 408 Parent:F2_8D5 batch=1 SUBJECT_SAMPLE_FACTORS F2_8D7 409 Parent:F2_8D7 batch=1 SUBJECT_SAMPLE_FACTORS F2_8D8 410 Parent:F2_8D8 batch=1 SUBJECT_SAMPLE_FACTORS F2_8D11 411 Parent:F2_8D11 batch=1 SUBJECT_SAMPLE_FACTORS F2_8F10 412 Parent:F2_8F10 batch=1 SUBJECT_SAMPLE_FACTORS F2_8F11 413 Parent:F2_8F11 batch=1 SUBJECT_SAMPLE_FACTORS F2_8G1 414 Parent:F2_8G1 batch=1 SUBJECT_SAMPLE_FACTORS F2_8G5 415 Parent:F2_8G5 batch=1 SUBJECT_SAMPLE_FACTORS F2_8A1 416 Parent:F2_8A1 batch=1 SUBJECT_SAMPLE_FACTORS F2_8A2 417 Parent:F2_8A2 batch=1 SUBJECT_SAMPLE_FACTORS F2_8A3 418 Parent:F2_8A3 batch=1 SUBJECT_SAMPLE_FACTORS F2_8A5 419 Parent:F2_8A5 batch=1 SUBJECT_SAMPLE_FACTORS F2_8A6 420 Parent:F2_8A6 batch=1 SUBJECT_SAMPLE_FACTORS F2_8A9 421 Parent:F2_8A9 batch=1 SUBJECT_SAMPLE_FACTORS F2_8A10 422 Parent:F2_8A10 batch=1 SUBJECT_SAMPLE_FACTORS F2_8A11 423 Parent:F2_8A11 batch=1 SUBJECT_SAMPLE_FACTORS F2_8A12 424 Parent:F2_8A12 batch=1 SUBJECT_SAMPLE_FACTORS F2_8B5 425 Parent:F2_8B5 batch=1 SUBJECT_SAMPLE_FACTORS F2_8B6 426 Parent:F2_8B6 batch=1 SUBJECT_SAMPLE_FACTORS F2_8B9 427 Parent:F2_8B9 batch=1 SUBJECT_SAMPLE_FACTORS F2_8B11 428 Parent:F2_8B11 batch=1 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Parent:F2_8A3 batch=1 SUBJECT_SAMPLE_FACTORS F2_8A6 447 Parent:F2_8A6 batch=1 SUBJECT_SAMPLE_FACTORS F2_8A9 448 Parent:F2_8A9 batch=1 SUBJECT_SAMPLE_FACTORS F2_8B5 449 Parent:F2_8B5 batch=1 SUBJECT_SAMPLE_FACTORS F2_8B6 450 Parent:F2_8B6 batch=1 SUBJECT_SAMPLE_FACTORS F2_8B9 451 Parent:F2_8B9 batch=1 SUBJECT_SAMPLE_FACTORS F2_8B11 452 Parent:F2_8B11 batch=1 SUBJECT_SAMPLE_FACTORS F2_8C1 453 Parent:F2_8C1 batch=1 SUBJECT_SAMPLE_FACTORS F2_8C4 454 Parent:F2_8C4 batch=1 SUBJECT_SAMPLE_FACTORS F2_8C6 455 Parent:F2_8C6 batch=1 SUBJECT_SAMPLE_FACTORS F2_8C7 456 Parent:F2_8C7 batch=1 SUBJECT_SAMPLE_FACTORS F2_8C9 457 Parent:F2_8C9 batch=1 SUBJECT_SAMPLE_FACTORS F2_8C112 458 Parent:F2_8C112 batch=1 SUBJECT_SAMPLE_FACTORS F2_8D2 459 Parent:F2_8D2 batch=1 SUBJECT_SAMPLE_FACTORS F2_8D5 460 Parent:F2_8D5 batch=1 SUBJECT_SAMPLE_FACTORS F2_8D7 461 Parent:F2_8D7 batch=1 SUBJECT_SAMPLE_FACTORS F2_8D8 462 Parent:F2_8D8 batch=1 SUBJECT_SAMPLE_FACTORS F2_8E2 463 Parent:F2_8E2 batch=1 SUBJECT_SAMPLE_FACTORS F2_8F10 464 Parent:F2_8F10 batch=1 SUBJECT_SAMPLE_FACTORS F2_8F11 465 Parent:F2_8F11 batch=1 SUBJECT_SAMPLE_FACTORS F2_8G1 466 Parent:F2_8G1 batch=1 SUBJECT_SAMPLE_FACTORS F2_8G5 467 Parent:F2_8G5 batch=1 SUBJECT_SAMPLE_FACTORS F2_8A1 468 Parent:F2_8A1 batch=1 SUBJECT_SAMPLE_FACTORS F2_8A3 469 Parent:F2_8A3 batch=1 SUBJECT_SAMPLE_FACTORS F2_8A7 470 Parent:F2_8A7 batch=1 SUBJECT_SAMPLE_FACTORS F2_8A7 471 Parent:F2_8A7 batch=1 SUBJECT_SAMPLE_FACTORS BC233_BC240_mix STD_5 Parent:BC233_BC240_mix batch=1 SUBJECT_SAMPLE_FACTORS BC233_BC240_mix STD_6 Parent:BC233_BC240_mix batch=1 SUBJECT_SAMPLE_FACTORS BC233_BC240_mix STD_6b Parent:BC233_BC240_mix batch=1 SUBJECT_SAMPLE_FACTORS BC233_BC240_mix STD_6c Parent:BC233_BC240_mix batch=1 SUBJECT_SAMPLE_FACTORS BC233_BC240_mix STD_6d Parent:BC233_BC240_mix batch=1 SUBJECT_SAMPLE_FACTORS BC233_BC240_mix STD_7 Parent:BC233_BC240_mix batch=1 SUBJECT_SAMPLE_FACTORS BC233_BC240_mix STD_7b Parent:BC233_BC240_mix batch=1 SUBJECT_SAMPLE_FACTORS BC233_BC240_mix STD_7c Parent:BC233_BC240_mix batch=1 SUBJECT_SAMPLE_FACTORS BC233_BC240_mix STD_8 Parent:BC233_BC240_mix batch=1 SUBJECT_SAMPLE_FACTORS BC233_BC240_mix STD_8b Parent:BC233_BC240_mix batch=1 SUBJECT_SAMPLE_FACTORS BC233_BC240_mix STD_8c Parent:BC233_BC240_mix batch=1 #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 ST000870_AN001417_Results.txt UNITS:normalized peak intensity #END