{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001086","ANALYSIS_ID":"AN001771","VERSION":"1","CREATED_ON":"October 31, 2018, 11:48 am"},

"PROJECT":{"PROJECT_TITLE":"Targeted metabolomics of SETD2 isogenic cell lines","PROJECT_SUMMARY":"SETD2, the histone methyltransferase responsible for the trimethylation of H3K36, is inactivated in approximately 10-32% of clear renal cell carcinoma (ccRCC) cases. To reveal the impact of SETD2 loss on metabolic alterations in ccRCC. In this study, SETD2 null isogenic 38E/38F clones derived from 786-O cells were generated by zinc finger nucleases, and the cellular metabolic changes were analyzed by GC-MS-based targeted metabolomics.","INSTITUTE":"Arizona State University","DEPARTMENT":"College of Health Solutions","LAST_NAME":"Liu","FIRST_NAME":"Jingping","ADDRESS":"13208 E. Shea Blvd, Scottsdale, AZ","EMAIL":"jliu381@asu.edu","PHONE":"4802078529"},

"STUDY":{"STUDY_TITLE":"Targeted GC-MS of SETD2 isogenic cell lines","STUDY_SUMMARY":"In this study, SETD2 null isogenic 38E/38F clones derived from 786-O cells were generated by zinc finger nucleases, and the cellular metabolic changes of 786-O (WT) and 38E/38F isogenic cell lines (n=3 per group) were analyzed by GC-MS-based targeted metabolomics.","INSTITUTE":"Arizona State University","DEPARTMENT":"College of Health Solutions","LAST_NAME":"Liu","FIRST_NAME":"Jingping","ADDRESS":"13208 E. Shea Blvd, Scottsdale, AZ","EMAIL":"jliu381@asu.edu","PHONE":"4802078529"},

"SUBJECT":{"SUBJECT_TYPE":"Cultured cells","SUBJECT_SPECIES":"Homo sapiens","TAXONOMY_ID":"9606"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"786-O rep1",
"Factors":{"Genotype":"Wild-type"}
},
{
"Subject ID":"-",
"Sample ID":"786-O rep2",
"Factors":{"Genotype":"Wild-type"}
},
{
"Subject ID":"-",
"Sample ID":"786-O rep3",
"Factors":{"Genotype":"Wild-type"}
},
{
"Subject ID":"-",
"Sample ID":"38-E rep1",
"Factors":{"Genotype":"SETD2-mutation"}
},
{
"Subject ID":"-",
"Sample ID":"38-E rep2",
"Factors":{"Genotype":"SETD2-mutation"}
},
{
"Subject ID":"-",
"Sample ID":"38-E rep3",
"Factors":{"Genotype":"SETD2-mutation"}
},
{
"Subject ID":"-",
"Sample ID":"38-F rep1",
"Factors":{"Genotype":"SETD2-mutation"}
},
{
"Subject ID":"-",
"Sample ID":"38-F rep2",
"Factors":{"Genotype":"SETD2-mutation"}
},
{
"Subject ID":"-",
"Sample ID":"38-F rep3",
"Factors":{"Genotype":"SETD2-mutation"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Quickly aspirate cell culture medium from 3.5 cm plates, gently dispense 2 mL of PBS to rinse cells, shake the plate back and forth for 2 s and then quickly remove the PBS. Immediately add 1 mL 8:2 methanol:H2O (on dry ice) into the plates placed on dry ice to quench cell metabolism, store samples at -80℃.","SAMPLE_TYPE":"Cultured cells"},

"TREATMENT":{"TREATMENT_SUMMARY":"The cell lines including 786-O and 38E/38F were cultured in RPMI 1640 medium supplemented with 10% FBS, 1% penicillin/streptomycin, and 2 mM L-glutamine. After culture at 37 °C, 5% CO2 condition for 24 h, the cells were collected for GC-MS analysis."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Sampleprep Summary: Scrape all the cells from culture dishes on dry ice, and transfer them into a 2 mL Eppendorf, spin the mixture at 14000 rpm for 10 min at 4°C. Remove all the soluble extract into a vial and completely dry samples. The extracted samples were incubated with 30 μL O-methylhydroxylamine hydrochloride solution in pyridine (Sigma-Aldrich, St. Louis, MO, USA) at 60°C for 90 min. Next, 70 μL of N-tert-Butyldimethylsilyl-N-methyltrifluoroacetamide (MTBSTFA) were added and placed at 60 °C for 30 min. After centrifuge at 14000 rpm for 10 min, 70 μL of supernatant was transferred to a clean glass GC insert tube."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"GC","INSTRUMENT_NAME":"Agilent 7890A","COLUMN_NAME":"Agilent DB5-MS (30m × 0.25mm, 0.25um)","FLOW_RATE":"0.5 mL/min","INJECTION_TEMPERATURE":"250°C","TRANSFERLINE_TEMPERATURE":"290°C"},

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

"MS":{"MS_COMMENTS":"-","INSTRUMENT_NAME":"Agilent 5975C","INSTRUMENT_TYPE":"Single quadrupole","MS_TYPE":"EI","ION_MODE":"POSITIVE","ION_SOURCE_TEMPERATURE":"230°C","IONIZATION":"70 eV","SCANNING_RANGE":"50-600 m/z"},

"MS_METABOLITE_DATA":{
"Units":"pmole/ug",

"Data":[{"Metabolite":"Lactate","786-O rep1":"58.10607","786-O rep2":"61.61175","786-O rep3":"43.46","38-E rep1":"31.06999","38-E rep2":"41.29203","38-E rep3":"46.43195","38-F rep1":"29.888","38-F rep2":"38.20992","38-F rep3":"25.59586"},{"Metabolite":"Succinate","786-O rep1":"0.564642","786-O rep2":"1.185374","786-O rep3":"0.813217","38-E rep1":"1.283617","38-E rep2":"1.730575","38-E rep3":"1.291269","38-F rep1":"0.866918","38-F rep2":"0.978369","38-F rep3":"0.740564"},{"Metabolite":"Fumarate","786-O rep1":"0.254165","786-O rep2":"0.325853","786-O rep3":"0.2337","38-E rep1":"0.291722","38-E rep2":"0.334525","38-E rep3":"0.460743","38-F rep1":"0.436472","38-F rep2":"0.476206","38-F rep3":"0.336574"},{"Metabolite":"Oxaloacetate","786-O rep1":"0","786-O rep2":"0","786-O rep3":"0","38-E rep1":"0","38-E rep2":"0","38-E rep3":"0","38-F rep1":"0","38-F rep2":"0","38-F rep3":"0"},{"Metabolite":"α-Ketoglutarate","786-O rep1":"0.100781","786-O rep2":"0.095843","786-O rep3":"0.042723","38-E rep1":"0.178187","38-E rep2":"0.135907","38-E rep3":"0.183634","38-F rep1":"0.372147","38-F rep2":"0.224725","38-F rep3":"0.158176"},{"Metabolite":"Malate","786-O rep1":"1.051511","786-O rep2":"1.77141","786-O rep3":"1.170534","38-E rep1":"1.564412","38-E rep2":"1.945175","38-E rep3":"2.998501","38-F rep1":"2.537524","38-F rep2":"2.765253","38-F rep3":"1.9131"},{"Metabolite":"Aspartate","786-O rep1":"1.125651","786-O rep2":"1.336688","786-O rep3":"1.072446","38-E rep1":"2.034551","38-E rep2":"3.183649","38-E rep3":"2.989099","38-F rep1":"2.296467","38-F rep2":"2.84556","38-F rep3":"1.735897"},{"Metabolite":"2-Hydroxyglutarate","786-O rep1":"0.139388","786-O rep2":"0.149611","786-O rep3":"0.082812","38-E rep1":"0.123103","38-E rep2":"0.133739","38-E rep3":"0.132376","38-F rep1":"0.11567","38-F rep2":"0.117894","38-F rep3":"0.067892"},{"Metabolite":"Glutamate","786-O rep1":"23.12394","786-O rep2":"40.85939","786-O rep3":"28.81189","38-E rep1":"35.63481","38-E rep2":"44.51025","38-E rep3":"44.30002","38-F rep1":"38.73059","38-F rep2":"38.98803","38-F rep3":"36.35525"},{"Metabolite":"cis-Aconitic Acid","786-O rep1":"0.01216","786-O rep2":"0.016236","786-O rep3":"0.009817","38-E rep1":"0.01672","38-E rep2":"0.014724","38-E rep3":"0.021761","38-F rep1":"0.015894","38-F rep2":"0.020102","38-F rep3":"0.012276"},{"Metabolite":"Citrate","786-O rep1":"0.960231","786-O rep2":"1.159267","786-O rep3":"0.565582","38-E rep1":"1.318814","38-E rep2":"1.241837","38-E rep3":"2.168567","38-F rep1":"1.476703","38-F rep2":"1.159748","38-F rep3":"0.916632"},{"Metabolite":"Isocitrate","786-O rep1":"0.021495","786-O rep2":"0.030921","786-O rep3":"0.014977","38-E rep1":"0.028633","38-E rep2":"0.024717","38-E rep3":"0.04327","38-F rep1":"0.032398","38-F rep2":"0.025001","38-F rep3":"0.020415"}],

"Metabolites":[{"Metabolite":"Lactate","rtimes (min)":"12.79","quantified m/z":"261.1","PubChem ID":"107689","KEGG ID":"C00186"},{"Metabolite":"Succinate","rtimes (min)":"15.91","quantified m/z":"289.1","PubChem ID":"1110","KEGG ID":"C00042"},{"Metabolite":"Fumarate","rtimes (min)":"16.29","quantified m/z":"287.1","PubChem ID":"444972","KEGG ID":"C00122"},{"Metabolite":"Oxaloacetate","rtimes (min)":"17.14","quantified m/z":"332.1","PubChem ID":"970","KEGG ID":"C00036"},{"Metabolite":"α-Ketoglutarate","rtimes (min)":"18.39","quantified m/z":"346.2","PubChem ID":"51","KEGG ID":"C00026"},{"Metabolite":"Malate","rtimes (min)":"19.39","quantified m/z":"419.3","PubChem ID":"222656","KEGG ID":"C00149"},{"Metabolite":"Aspartate","rtimes (min)":"19.77","quantified m/z":"418.3","PubChem ID":"5960","KEGG ID":"C00049"},{"Metabolite":"2-Hydroxyglutarate","rtimes (min)":"20.36","quantified m/z":"433.2","PubChem ID":"439391","KEGG ID":"C01087"},{"Metabolite":"Glutamate","rtimes (min)":"20.87","quantified m/z":"432.2","PubChem ID":"33032","KEGG ID":"C00025"},{"Metabolite":"cis-Aconitic Acid","rtimes (min)":"21.78","quantified m/z":"459.3","PubChem ID":"643757","KEGG ID":"C00417"},{"Metabolite":"Citrate","rtimes (min)":"23.56","quantified m/z":"591.4","PubChem ID":"311","KEGG ID":"C00158"},{"Metabolite":"Isocitrate","rtimes (min)":"23.65","quantified m/z":"591.4","PubChem ID":"1198","KEGG ID":"C00311"}]
}

}