{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002734","ANALYSIS_ID":"AN004432","VERSION":"1","CREATED_ON":"June 8, 2023, 8:29 pm"},

"PROJECT":{"PROJECT_TITLE":"Integrative multi-omics analysis of oncogenic EZH2 mutants: from epigenetic reprogramming to molecular signatures","PROJECT_SUMMARY":"Metabolic study of Enhancer of zeste homolog 2 (EZH2) isogenic mutants with gain-of-function (GOF) and loss-of-function (LOF) enzymatic activity in HEK-293T cell lines.","INSTITUTE":"The Ohio State University","DEPARTMENT":"Chemistry and Biochemistry","LAST_NAME":"Aldana","FIRST_NAME":"Julian","ADDRESS":"460 W 12th Ave, Columbus, OH 43210","EMAIL":"aldanaaroca.1@osu.edu","PHONE":"+1 614-292-6136"},

"STUDY":{"STUDY_TITLE":"Integrative multi-omics analysis of oncogenic EZH2 mutants: from epigenetic reprogramming to molecular signatures","STUDY_SUMMARY":"Metabolic study of Enhancer of zeste homolog 2 (EZH2) isogenic mutants with gain-of-function (GOF) and loss-of-function (LOF) enzymatic activity in HEK-293T cell lines.","INSTITUTE":"The Ohio State University","DEPARTMENT":"Chemistry and Biochemistry","LAST_NAME":"Aldana","FIRST_NAME":"Julian","ADDRESS":"460 W 12th Ave, Columbus, OH 43210","EMAIL":"aldanaaroca.1@osu.edu","PHONE":"+1 614-292-6136","NUM_GROUPS":"4","TOTAL_SUBJECTS":"12"},

"SUBJECT":{"SUBJECT_TYPE":"Cultured cells","SUBJECT_SPECIES":"Homo sapiens","TAXONOMY_ID":"9606","GENDER":"Female","CELL_BIOSOURCE_OR_SUPPLIER":"American Tissue Culture Collection (ATCC)","CELL_STRAIN_DETAILS":"HEK-293T","CELL_PASSAGE_NUMBER":"2"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"A677G_1",
"Factors":{"Factor":"A677G-mutant"},
"Additional sample data":{"Ionization mode":"ESI (+)","RAW_FILE_NAME":"A677G_1.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"A677G_2",
"Factors":{"Factor":"A677G-mutant"},
"Additional sample data":{"Ionization mode":"ESI (+)","RAW_FILE_NAME":"A677G_2.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"A677G_3",
"Factors":{"Factor":"A677G-mutant"},
"Additional sample data":{"Ionization mode":"ESI (+)","RAW_FILE_NAME":"A677G_3.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"DM_1",
"Factors":{"Factor":"F667I/H689A-mutant"},
"Additional sample data":{"Ionization mode":"ESI (+)","RAW_FILE_NAME":"DM_1.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"DM_2",
"Factors":{"Factor":"F667I/H689A-mutant"},
"Additional sample data":{"Ionization mode":"ESI (+)","RAW_FILE_NAME":"DM_2.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"DM_3",
"Factors":{"Factor":"F667I/H689A-mutant"},
"Additional sample data":{"Ionization mode":"ESI (+)","RAW_FILE_NAME":"DM_3.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"Y641F_1",
"Factors":{"Factor":"Y641F-mutant"},
"Additional sample data":{"Ionization mode":"ESI (+)","RAW_FILE_NAME":"Y641F_1.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"Y641F_2",
"Factors":{"Factor":"Y641F-mutant"},
"Additional sample data":{"Ionization mode":"ESI (+)","RAW_FILE_NAME":"Y641F_2.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"Y641F_3",
"Factors":{"Factor":"Y641F-mutant"},
"Additional sample data":{"Ionization mode":"ESI (+)","RAW_FILE_NAME":"Y641F_3.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"WT_1",
"Factors":{"Factor":"Wild-type"},
"Additional sample data":{"Ionization mode":"ESI (+)","RAW_FILE_NAME":"WT_1.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"WT_2",
"Factors":{"Factor":"Wild-type"},
"Additional sample data":{"Ionization mode":"ESI (+)","RAW_FILE_NAME":"WT_2.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"WT_3",
"Factors":{"Factor":"Wild-type"},
"Additional sample data":{"Ionization mode":"ESI (+)","RAW_FILE_NAME":"WT_3.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"QC_0",
"Factors":{"Factor":"Quality control"},
"Additional sample data":{"Ionization mode":"ESI (+)","RAW_FILE_NAME":"QC_0.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"QC_1",
"Factors":{"Factor":"Quality control"},
"Additional sample data":{"Ionization mode":"ESI (+)","RAW_FILE_NAME":"QC_1.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"QC_2",
"Factors":{"Factor":"Quality control"},
"Additional sample data":{"Ionization mode":"ESI (+)","RAW_FILE_NAME":"QC_2.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"QC_3",
"Factors":{"Factor":"Quality control"},
"Additional sample data":{"Ionization mode":"ESI (+)","RAW_FILE_NAME":"QC_3.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"QC_4",
"Factors":{"Factor":"Quality control"},
"Additional sample data":{"Ionization mode":"ESI (+)","RAW_FILE_NAME":"QC_4.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"A677G_1_neg",
"Factors":{"Factor":"A677G-mutant"},
"Additional sample data":{"Ionization mode":"ESI (-)","RAW_FILE_NAME":"A677G_1_neg.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"A677G_2_neg",
"Factors":{"Factor":"A677G-mutant"},
"Additional sample data":{"Ionization mode":"ESI (-)","RAW_FILE_NAME":"A677G_2_neg.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"A677G_3_neg",
"Factors":{"Factor":"A677G-mutant"},
"Additional sample data":{"Ionization mode":"ESI (-)","RAW_FILE_NAME":"A677G_3_neg.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"DM_1_neg",
"Factors":{"Factor":"F667I/H689A-mutant"},
"Additional sample data":{"Ionization mode":"ESI (-)","RAW_FILE_NAME":"DM_1_neg.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"DM_2_neg",
"Factors":{"Factor":"F667I/H689A-mutant"},
"Additional sample data":{"Ionization mode":"ESI (-)","RAW_FILE_NAME":"DM_2_neg.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"DM_3_neg",
"Factors":{"Factor":"F667I/H689A-mutant"},
"Additional sample data":{"Ionization mode":"ESI (-)","RAW_FILE_NAME":"DM_3_neg.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"Y641F_1_neg",
"Factors":{"Factor":"Y641F-mutant"},
"Additional sample data":{"Ionization mode":"ESI (-)","RAW_FILE_NAME":"Y641F_1_neg.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"Y641F_2_neg",
"Factors":{"Factor":"Y641F-mutant"},
"Additional sample data":{"Ionization mode":"ESI (-)","RAW_FILE_NAME":"Y641F_2_neg.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"Y641F_3_neg",
"Factors":{"Factor":"Y641F-mutant"},
"Additional sample data":{"Ionization mode":"ESI (-)","RAW_FILE_NAME":"Y641F_3_neg.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"WT_1_neg",
"Factors":{"Factor":"Wild-type"},
"Additional sample data":{"Ionization mode":"ESI (-)","RAW_FILE_NAME":"WT_1_neg.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"WT_2_neg",
"Factors":{"Factor":"Wild-type"},
"Additional sample data":{"Ionization mode":"ESI (-)","RAW_FILE_NAME":"WT_2_neg.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"WT_3_neg",
"Factors":{"Factor":"Wild-type"},
"Additional sample data":{"Ionization mode":"ESI (-)","RAW_FILE_NAME":"WT_3_neg.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"QC_0_neg",
"Factors":{"Factor":"Quality control"},
"Additional sample data":{"Ionization mode":"ESI (-)","RAW_FILE_NAME":"QC_0_neg.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"QC_1_neg",
"Factors":{"Factor":"Quality control"},
"Additional sample data":{"Ionization mode":"ESI (-)","RAW_FILE_NAME":"QC_1_neg.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"QC_2_neg",
"Factors":{"Factor":"Quality control"},
"Additional sample data":{"Ionization mode":"ESI (-)","RAW_FILE_NAME":"QC_2_neg.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"QC_3_neg",
"Factors":{"Factor":"Quality control"},
"Additional sample data":{"Ionization mode":"ESI (-)","RAW_FILE_NAME":"QC_3_neg.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"QC_4_neg",
"Factors":{"Factor":"Quality control"},
"Additional sample data":{"Ionization mode":"ESI (-)","RAW_FILE_NAME":"QC_4_neg.mzML"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"HEK-293T cells were acquired from ATCC CRL-1573","SAMPLE_TYPE":"HEK cells","STORAGE_CONDITIONS":"-80℃"},

"TREATMENT":{"TREATMENT_SUMMARY":"HEK-293T cells at 80% confluency were infected in the presence of polybrene for 16 h in DMEM with lentivirus constructs containing either wild-type (WT) EZH2, A677G-mutant (A677G) EZH2, Y641F-mutant (Y641F) EZH2, or H689A/F667I-mutant (DM) EZH2. Infected cells were selected for resistance to blasticidin (10 μg/mL) for 10 days to ensure monoclonal populations.","CELL_MEDIA":"DMEM supplemented with 10%FBS and 1% Pen/Strep","CELL_PCT_CONFLUENCE":"80"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Approximately 10 million cells per sample were washed with PBS at room tem-perature and harvested with a mixture of ice-cold methanol:water (80:20). Cell lysis was carried out by four freeze-and-thaw cycles with liquid nitrogen and dry-ice with vortexing between cycles. Supernatant was then dried on SpeedVac concentrator and samples stored at -80ºC. Dried extracts were resuspended in a mixture of Acetonitrile:Water (25:75)."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"HILIC","INSTRUMENT_NAME":"Agilent 6545","COLUMN_NAME":"Phenomenex Kinetex HILIC (100 X 2.1mm, 2.6um)","SOLVENT_A":"100% water; 0.1 % formic acid; 10 mM ammonium formate","SOLVENT_B":"100% acetonitrile; 0.1 % formic acid;10 mM ammonium formate","FLOW_GRADIENT":"98–55% B in 45 min; 55% B during 4 min; 55–98% in 2 min; and column re-equilibration for 15 min","FLOW_RATE":"0.3 mL/min","COLUMN_TEMPERATURE":"30"},

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

"MS":{"INSTRUMENT_NAME":"Agilent 6545 QTOF","INSTRUMENT_TYPE":"QTOF","MS_TYPE":"ESI","ION_MODE":"POSITIVE","MS_COMMENTS":"OpenMS (v2.6.0) was employed for feature detection, alignment, assembly, and de-convolution.","MS_RESULTS_FILE":"ST002734_AN004432_Results.txt UNITS:Peak area Has m/z:Yes Has RT:Yes RT units:Seconds"}

}