#METABOLOMICS WORKBENCH jliu381_20181024_223224 DATATRACK_ID:1554 STUDY_ID:ST001086 ANALYSIS_ID:AN001771 PROJECT_ID:PR000725 VERSION 1 CREATED_ON October 31, 2018, 11:48 am #PROJECT PR:PROJECT_TITLE Targeted metabolomics of SETD2 isogenic cell lines PR:PROJECT_SUMMARY SETD2, the histone methyltransferase responsible for the trimethylation of PR:PROJECT_SUMMARY H3K36, is inactivated in approximately 10-32% of clear renal cell carcinoma PR:PROJECT_SUMMARY (ccRCC) cases. To reveal the impact of SETD2 loss on metabolic alterations in PR:PROJECT_SUMMARY ccRCC. In this study, SETD2 null isogenic 38E/38F clones derived from 786-O PR:PROJECT_SUMMARY cells were generated by zinc finger nucleases, and the cellular metabolic PR:PROJECT_SUMMARY changes were analyzed by GC-MS-based targeted metabolomics. PR:INSTITUTE Arizona State University PR:DEPARTMENT College of Health Solutions PR:LAST_NAME Liu PR:FIRST_NAME Jingping PR:ADDRESS 13208 E. Shea Blvd, Scottsdale, AZ PR:EMAIL jliu381@asu.edu PR:PHONE 4802078529 #STUDY ST:STUDY_TITLE Targeted GC-MS of SETD2 isogenic cell lines ST:STUDY_SUMMARY In this study, SETD2 null isogenic 38E/38F clones derived from 786-O cells were ST:STUDY_SUMMARY generated by zinc finger nucleases, and the cellular metabolic changes of 786-O ST:STUDY_SUMMARY (WT) and 38E/38F isogenic cell lines (n=3 per group) were analyzed by ST:STUDY_SUMMARY GC-MS-based targeted metabolomics. ST:INSTITUTE Arizona State University ST:DEPARTMENT College of Health Solutions ST:LAST_NAME Liu ST:FIRST_NAME Jingping ST:ADDRESS 13208 E. Shea Blvd, Scottsdale, AZ ST:EMAIL jliu381@asu.edu ST:PHONE 4802078529 #SUBJECT SU:SUBJECT_TYPE Cultured cells SU:SUBJECT_SPECIES Homo sapiens SU:TAXONOMY_ID 9606 #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Additional sample data SUBJECT_SAMPLE_FACTORS - 786-O rep1 Genotype:Wild-type SUBJECT_SAMPLE_FACTORS - 786-O rep2 Genotype:Wild-type SUBJECT_SAMPLE_FACTORS - 786-O rep3 Genotype:Wild-type SUBJECT_SAMPLE_FACTORS - 38-E rep1 Genotype:SETD2-mutation SUBJECT_SAMPLE_FACTORS - 38-E rep2 Genotype:SETD2-mutation SUBJECT_SAMPLE_FACTORS - 38-E rep3 Genotype:SETD2-mutation SUBJECT_SAMPLE_FACTORS - 38-F rep1 Genotype:SETD2-mutation SUBJECT_SAMPLE_FACTORS - 38-F rep2 Genotype:SETD2-mutation SUBJECT_SAMPLE_FACTORS - 38-F rep3 Genotype:SETD2-mutation #COLLECTION CO:COLLECTION_SUMMARY Quickly aspirate cell culture medium from 3.5 cm plates, gently dispense 2 mL of CO:COLLECTION_SUMMARY PBS to rinse cells, shake the plate back and forth for 2 s and then quickly CO:COLLECTION_SUMMARY remove the PBS. Immediately add 1 mL 8:2 methanol:H2O (on dry ice) into the CO:COLLECTION_SUMMARY plates placed on dry ice to quench cell metabolism, store samples at -80℃. CO:SAMPLE_TYPE Cultured cells #TREATMENT TR:TREATMENT_SUMMARY The cell lines including 786-O and 38E/38F were cultured in RPMI 1640 medium TR:TREATMENT_SUMMARY supplemented with 10% FBS, 1% penicillin/streptomycin, and 2 mM L-glutamine. TR:TREATMENT_SUMMARY After culture at 37 °C, 5% CO2 condition for 24 h, the cells were collected for TR:TREATMENT_SUMMARY GC-MS analysis. #SAMPLEPREP SP:SAMPLEPREP_SUMMARY Sampleprep Summary: Scrape all the cells from culture dishes on dry ice, and SP:SAMPLEPREP_SUMMARY transfer them into a 2 mL Eppendorf, spin the mixture at 14000 rpm for 10 min at SP:SAMPLEPREP_SUMMARY 4°C. Remove all the soluble extract into a vial and completely dry samples. The SP:SAMPLEPREP_SUMMARY extracted samples were incubated with 30 μL O-methylhydroxylamine hydrochloride SP:SAMPLEPREP_SUMMARY solution in pyridine (Sigma-Aldrich, St. Louis, MO, USA) at 60°C for 90 min. SP:SAMPLEPREP_SUMMARY Next, 70 μL of N-tert-Butyldimethylsilyl-N-methyltrifluoroacetamide (MTBSTFA) SP:SAMPLEPREP_SUMMARY were added and placed at 60 °C for 30 min. After centrifuge at 14000 rpm for 10 SP:SAMPLEPREP_SUMMARY min, 70 μL of supernatant was transferred to a clean glass GC insert tube. #CHROMATOGRAPHY CH:CHROMATOGRAPHY_TYPE GC CH:INSTRUMENT_NAME Agilent 7890A CH:COLUMN_NAME Agilent DB5-MS (30m × 0.25mm, 0.25um) CH:FLOW_RATE 0.5 mL/min CH:INJECTION_TEMPERATURE 250°C CH:TRANSFERLINE_TEMPERATURE 290°C #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:MS_COMMENTS - MS:INSTRUMENT_NAME Agilent 5975C MS:INSTRUMENT_TYPE Single quadrupole MS:MS_TYPE EI MS:ION_MODE POSITIVE MS:ION_SOURCE_TEMPERATURE 230°C MS:IONIZATION 70 eV MS:SCANNING_RANGE 50-600 m/z #MS_METABOLITE_DATA MS_METABOLITE_DATA:UNITS pmole/ug MS_METABOLITE_DATA_START Samples 786-O rep1 786-O rep2 786-O rep3 38-E rep1 38-E rep2 38-E rep3 38-F rep1 38-F rep2 38-F rep3 Factors Genotype:Wild-type Genotype:Wild-type Genotype:Wild-type Genotype:SETD2-mutation Genotype:SETD2-mutation Genotype:SETD2-mutation Genotype:SETD2-mutation Genotype:SETD2-mutation Genotype:SETD2-mutation Lactate 58.10607 61.61175 43.46 31.06999 41.29203 46.43195 29.888 38.20992 25.59586 Succinate 0.564642 1.185374 0.813217 1.283617 1.730575 1.291269 0.866918 0.978369 0.740564 Fumarate 0.254165 0.325853 0.2337 0.291722 0.334525 0.460743 0.436472 0.476206 0.336574 Oxaloacetate 0 0 0 0 0 0 0 0 0 α-Ketoglutarate 0.100781 0.095843 0.042723 0.178187 0.135907 0.183634 0.372147 0.224725 0.158176 Malate 1.051511 1.77141 1.170534 1.564412 1.945175 2.998501 2.537524 2.765253 1.9131 Aspartate 1.125651 1.336688 1.072446 2.034551 3.183649 2.989099 2.296467 2.84556 1.735897 2-Hydroxyglutarate 0.139388 0.149611 0.082812 0.123103 0.133739 0.132376 0.11567 0.117894 0.067892 Glutamate 23.12394 40.85939 28.81189 35.63481 44.51025 44.30002 38.73059 38.98803 36.35525 cis-Aconitic Acid 0.01216 0.016236 0.009817 0.01672 0.014724 0.021761 0.015894 0.020102 0.012276 Citrate 0.960231 1.159267 0.565582 1.318814 1.241837 2.168567 1.476703 1.159748 0.916632 Isocitrate 0.021495 0.030921 0.014977 0.028633 0.024717 0.04327 0.032398 0.025001 0.020415 MS_METABOLITE_DATA_END #METABOLITES METABOLITES_START metabolite_name rtimes (min) quantified m/z PubChem ID KEGG ID Lactate 12.79 261.1 107689 C00186 Succinate 15.91 289.1 1110 C00042 Fumarate 16.29 287.1 444972 C00122 Oxaloacetate 17.14 332.1 970 C00036 α-Ketoglutarate 18.39 346.2 51 C00026 Malate 19.39 419.3 222656 C00149 Aspartate 19.77 418.3 5960 C00049 2-Hydroxyglutarate 20.36 433.2 439391 C01087 Glutamate 20.87 432.2 33032 C00025 cis-Aconitic Acid 21.78 459.3 643757 C00417 Citrate 23.56 591.4 311 C00158 Isocitrate 23.65 591.4 1198 C00311 METABOLITES_END #END