{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002930","ANALYSIS_ID":"AN004807","VERSION":"1","CREATED_ON":"October 11, 2023, 2:16 pm"},

"PROJECT":{"PROJECT_TITLE":"Role of hypoxia inducible factor-1a (HIF1a) in Skeletal Muscle Physiology","PROJECT_SUMMARY":"Hypoxia-inducible factor (HIF)-1a is continuously synthesized and degraded in normoxia, whereas during hypoxia, HIF1a stabilization restricts cellular oxygen utilization. Less is known about HIF1a function(s) and sex-specific effects during normoxia in the basal state. Since skeletal muscle is the largest protein store in mammals and protein homeostasis has high energy demands, we determined HIF1a function at baseline during normoxia in skeletal muscle with the use of untargeted metabolomics.","INSTITUTE":"Cleveland Clinic","DEPARTMENT":"Inflammation and Immunity","LABORATORY":"Dasarathy Lab","LAST_NAME":"Dasarathy","FIRST_NAME":"Srinivasan","ADDRESS":"9500 Euclid Avenue","EMAIL":"dasaras@ccf.org","PHONE":"2163799846","FUNDING_SOURCE":"NIH"},

"STUDY":{"STUDY_TITLE":"Role of Hypoxia-inducible factor-1a (HIF1a)in Skeletal Muscle Physiology (C2C12 myotube model)","STUDY_SUMMARY":"Hypoxia-inducible factor (HIF)-1a is continuously synthesized and degraded in normoxia, whereas during hypoxia, HIF1a stabilization restricts cellular oxygen utilization. Less is known about HIF1a function(s) and sex-specific effects during normoxia in the basal state. Since skeletal muscle is the largest protein store in mammals and protein homeostasis has high energy demands, we determined HIF1a function at baseline during normoxia in C2C12 murine myotubes with the use of untargeted metabolomics. 114 samples of extracted metabolites from cells were analyzed using LCMS. We identified that metabolites, especially those in the glycolytic pathway and TCA cycle, were differentially expressed in cells with HIF1a KO compared to WT.","INSTITUTE":"Cleveland Clinic","DEPARTMENT":"Inflamation and Immunity","LABORATORY":"Dasarathy Lab","LAST_NAME":"Dasarathy","FIRST_NAME":"Srinivasan","ADDRESS":"9500 Euclid Avenue","EMAIL":"dasaras@ccf.org","PHONE":"2163799846"},

"SUBJECT":{"SUBJECT_TYPE":"Cultured cells","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090","AGE_OR_AGE_RANGE":"Passage 4-8","GENDER":"Female"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"WT C2C12 unit1 M_Dasarathy_Nicole_114Cells_02042022_HILIC_NEG189",
"Factors":{"Genotype":"Wild-type","Treatment":"Untreated"},
"Additional sample data":{"Column":"HILIC","Mode":"Negative","RAW_FILE_NAME":"WT C2C12 unit1 M_Dasarathy_Nicole_114Cells_02042022_HILIC_NEG189"}
},
{
"Subject ID":"-",
"Sample ID":"WT C2C12 unit2 M_Dasarathy_Nicole_114Cells_02042022_HILIC_NEG190",
"Factors":{"Genotype":"Wild-type","Treatment":"Untreated"},
"Additional sample data":{"Column":"HILIC","Mode":"Negative","RAW_FILE_NAME":"WT C2C12 unit2 M_Dasarathy_Nicole_114Cells_02042022_HILIC_NEG190"}
},
{
"Subject ID":"-",
"Sample ID":"WT C2C12 unit3 M_Dasarathy_Nicole_114Cells_02042022_HILIC_NEG191",
"Factors":{"Genotype":"Wild-type","Treatment":"Untreated"},
"Additional sample data":{"Column":"HILIC","Mode":"Negative","RAW_FILE_NAME":"WT C2C12 unit3 M_Dasarathy_Nicole_114Cells_02042022_HILIC_NEG191"}
},
{
"Subject ID":"-",
"Sample ID":"WT C2C12 UnT4 M_Dasarathy_Nicole_114Cells_02042022_HILIC_NEG201",
"Factors":{"Genotype":"Wild-type","Treatment":"Untreated"},
"Additional sample data":{"Column":"HILIC","Mode":"Negative","RAW_FILE_NAME":"WT C2C12 UnT4 M_Dasarathy_Nicole_114Cells_02042022_HILIC_NEG201"}
},
{
"Subject ID":"-",
"Sample ID":"WT C2C12 UnT5 M_Dasarathy_Nicole_114Cells_02042022_HILIC_NEG202",
"Factors":{"Genotype":"Wild-type","Treatment":"Untreated"},
"Additional sample data":{"Column":"HILIC","Mode":"Negative","RAW_FILE_NAME":"WT C2C12 UnT5 M_Dasarathy_Nicole_114Cells_02042022_HILIC_NEG202"}
},
{
"Subject ID":"-",
"Sample ID":"WT C2C12 UnT6 M_Dasarathy_Nicole_114Cells_02042022_HILIC_NEG203",
"Factors":{"Genotype":"Wild-type","Treatment":"Untreated"},
"Additional sample data":{"Column":"HILIC","Mode":"Negative","RAW_FILE_NAME":"WT C2C12 UnT6 M_Dasarathy_Nicole_114Cells_02042022_HILIC_NEG203"}
},
{
"Subject ID":"-",
"Sample ID":"WT C2C12 UnT7 M_Dasarathy_Nicole_114Cells_02042022_HILIC_NEG204",
"Factors":{"Genotype":"Wild-type","Treatment":"Untreated"},
"Additional sample data":{"Column":"HILIC","Mode":"Negative","RAW_FILE_NAME":"WT C2C12 UnT7 M_Dasarathy_Nicole_114Cells_02042022_HILIC_NEG204"}
},
{
"Subject ID":"-",
"Sample ID":"WT C2C12 UnT8 M_Dasarathy_Nicole_114Cells_02042022_HILIC_NEG205",
"Factors":{"Genotype":"Wild-type","Treatment":"Untreated"},
"Additional sample data":{"Column":"HILIC","Mode":"Negative","RAW_FILE_NAME":"WT C2C12 UnT8 M_Dasarathy_Nicole_114Cells_02042022_HILIC_NEG205"}
},
{
"Subject ID":"-",
"Sample ID":"WT C2C12 UnT9 M_Dasarathy_Nicole_114Cells_02042022_HILIC_NEG206",
"Factors":{"Genotype":"Wild-type","Treatment":"Untreated"},
"Additional sample data":{"Column":"HILIC","Mode":"Negative","RAW_FILE_NAME":"WT C2C12 UnT9 M_Dasarathy_Nicole_114Cells_02042022_HILIC_NEG206"}
},
{
"Subject ID":"-",
"Sample ID":"HIF KO C2C12 UnT1 M_Dasarathy_Nicole_114Cells_02042022_HILIC_NEG249",
"Factors":{"Genotype":"HIF1a KO","Treatment":"Untreated"},
"Additional sample data":{"Column":"HILIC","Mode":"Negative","RAW_FILE_NAME":"HIF KO C2C12 UnT1 M_Dasarathy_Nicole_114Cells_02042022_HILIC_NEG249"}
},
{
"Subject ID":"-",
"Sample ID":"HIF KO C2C12 UnT2 M_Dasarathy_Nicole_114Cells_02042022_HILIC_NEG250",
"Factors":{"Genotype":"HIF1a KO","Treatment":"Untreated"},
"Additional sample data":{"Column":"HILIC","Mode":"Negative","RAW_FILE_NAME":"HIF KO C2C12 UnT2 M_Dasarathy_Nicole_114Cells_02042022_HILIC_NEG250"}
},
{
"Subject ID":"-",
"Sample ID":"HIF KO C2C12 UnT3 M_Dasarathy_Nicole_114Cells_02042022_HILIC_NEG251",
"Factors":{"Genotype":"HIF1a KO","Treatment":"Untreated"},
"Additional sample data":{"Column":"HILIC","Mode":"Negative","RAW_FILE_NAME":"HIF KO C2C12 UnT3 M_Dasarathy_Nicole_114Cells_02042022_HILIC_NEG251"}
},
{
"Subject ID":"-",
"Sample ID":"HIF KO C2C12 UnT4 M_Dasarathy_Nicole_114Cells_02042022_HILIC_NEG252",
"Factors":{"Genotype":"HIF1a KO","Treatment":"Untreated"},
"Additional sample data":{"Column":"HILIC","Mode":"Negative","RAW_FILE_NAME":"HIF KO C2C12 UnT4 M_Dasarathy_Nicole_114Cells_02042022_HILIC_NEG252"}
},
{
"Subject ID":"-",
"Sample ID":"HIF KO C2C12 UnT5 M_Dasarathy_Nicole_114Cells_02042022_HILIC_NEG253",
"Factors":{"Genotype":"HIF1a KO","Treatment":"Untreated"},
"Additional sample data":{"Column":"HILIC","Mode":"Negative","RAW_FILE_NAME":"HIF KO C2C12 UnT5 M_Dasarathy_Nicole_114Cells_02042022_HILIC_NEG253"}
},
{
"Subject ID":"-",
"Sample ID":"HIF KO C2C12 UnT6 M_Dasarathy_Nicole_114Cells_02042022_HILIC_NEG254",
"Factors":{"Genotype":"HIF1a KO","Treatment":"Untreated"},
"Additional sample data":{"Column":"HILIC","Mode":"Negative","RAW_FILE_NAME":"HIF KO C2C12 UnT6 M_Dasarathy_Nicole_114Cells_02042022_HILIC_NEG254"}
},
{
"Subject ID":"-",
"Sample ID":"WT C2C12 unit1 M_Dasarathy_Nicole_114Cells_02042022_HILIC_POS189",
"Factors":{"Genotype":"Wild-type","Treatment":"Untreated"},
"Additional sample data":{"Column":"HILIC","Mode":"Positive","RAW_FILE_NAME":"WT C2C12 unit1 M_Dasarathy_Nicole_114Cells_02042022_HILIC_POS189"}
},
{
"Subject ID":"-",
"Sample ID":"WT C2C12 unit2 M_Dasarathy_Nicole_114Cells_02042022_HILIC_POS190",
"Factors":{"Genotype":"Wild-type","Treatment":"Untreated"},
"Additional sample data":{"Column":"HILIC","Mode":"Positive","RAW_FILE_NAME":"WT C2C12 unit2 M_Dasarathy_Nicole_114Cells_02042022_HILIC_POS190"}
},
{
"Subject ID":"-",
"Sample ID":"WT C2C12 unit3 M_Dasarathy_Nicole_114Cells_02042022_HILIC_POS191",
"Factors":{"Genotype":"Wild-type","Treatment":"Untreated"},
"Additional sample data":{"Column":"HILIC","Mode":"Positive","RAW_FILE_NAME":"WT C2C12 unit3 M_Dasarathy_Nicole_114Cells_02042022_HILIC_POS191"}
},
{
"Subject ID":"-",
"Sample ID":"WT C2C12 UnT4 M_Dasarathy_Nicole_114Cells_02042022_HILIC_POS201",
"Factors":{"Genotype":"Wild-type","Treatment":"Untreated"},
"Additional sample data":{"Column":"HILIC","Mode":"Positive","RAW_FILE_NAME":"WT C2C12 UnT4 M_Dasarathy_Nicole_114Cells_02042022_HILIC_POS201"}
},
{
"Subject ID":"-",
"Sample ID":"WT C2C12 UnT5 M_Dasarathy_Nicole_114Cells_02042022_HILIC_POS202",
"Factors":{"Genotype":"Wild-type","Treatment":"Untreated"},
"Additional sample data":{"Column":"HILIC","Mode":"Positive","RAW_FILE_NAME":"WT C2C12 UnT5 M_Dasarathy_Nicole_114Cells_02042022_HILIC_POS202"}
},
{
"Subject ID":"-",
"Sample ID":"WT C2C12 UnT6 M_Dasarathy_Nicole_114Cells_02042022_HILIC_POS203",
"Factors":{"Genotype":"Wild-type","Treatment":"Untreated"},
"Additional sample data":{"Column":"HILIC","Mode":"Positive","RAW_FILE_NAME":"WT C2C12 UnT6 M_Dasarathy_Nicole_114Cells_02042022_HILIC_POS203"}
},
{
"Subject ID":"-",
"Sample ID":"WT C2C12 UnT7 M_Dasarathy_Nicole_114Cells_02042022_HILIC_POS204",
"Factors":{"Genotype":"Wild-type","Treatment":"Untreated"},
"Additional sample data":{"Column":"HILIC","Mode":"Positive","RAW_FILE_NAME":"WT C2C12 UnT7 M_Dasarathy_Nicole_114Cells_02042022_HILIC_POS204"}
},
{
"Subject ID":"-",
"Sample ID":"WT C2C12 UnT8 M_Dasarathy_Nicole_114Cells_02042022_HILIC_POS205",
"Factors":{"Genotype":"Wild-type","Treatment":"Untreated"},
"Additional sample data":{"Column":"HILIC","Mode":"Positive","RAW_FILE_NAME":"WT C2C12 UnT8 M_Dasarathy_Nicole_114Cells_02042022_HILIC_POS205"}
},
{
"Subject ID":"-",
"Sample ID":"WT C2C12 UnT9 M_Dasarathy_Nicole_114Cells_02042022_HILIC_POS206",
"Factors":{"Genotype":"Wild-type","Treatment":"Untreated"},
"Additional sample data":{"Column":"HILIC","Mode":"Positive","RAW_FILE_NAME":"WT C2C12 UnT9 M_Dasarathy_Nicole_114Cells_02042022_HILIC_POS206"}
},
{
"Subject ID":"-",
"Sample ID":"HIF KO C2C12 UnT1 M_Dasarathy_Nicole_114Cells_02042022_HILIC_POS249",
"Factors":{"Genotype":"HIF1a KO","Treatment":"Untreated"},
"Additional sample data":{"Column":"HILIC","Mode":"Positive","RAW_FILE_NAME":"HIF KO C2C12 UnT1 M_Dasarathy_Nicole_114Cells_02042022_HILIC_POS249"}
},
{
"Subject ID":"-",
"Sample ID":"HIF KO C2C12 UnT2 M_Dasarathy_Nicole_114Cells_02042022_HILIC_POS250",
"Factors":{"Genotype":"HIF1a KO","Treatment":"Untreated"},
"Additional sample data":{"Column":"HILIC","Mode":"Positive","RAW_FILE_NAME":"HIF KO C2C12 UnT2 M_Dasarathy_Nicole_114Cells_02042022_HILIC_POS250"}
},
{
"Subject ID":"-",
"Sample ID":"HIF KO C2C12 UnT3 M_Dasarathy_Nicole_114Cells_02042022_HILIC_POS251",
"Factors":{"Genotype":"HIF1a KO","Treatment":"Untreated"},
"Additional sample data":{"Column":"HILIC","Mode":"Positive","RAW_FILE_NAME":"HIF KO C2C12 UnT3 M_Dasarathy_Nicole_114Cells_02042022_HILIC_POS251"}
},
{
"Subject ID":"-",
"Sample ID":"HIF KO C2C12 UnT4 M_Dasarathy_Nicole_114Cells_02042022_HILIC_POS252",
"Factors":{"Genotype":"HIF1a KO","Treatment":"Untreated"},
"Additional sample data":{"Column":"HILIC","Mode":"Positive","RAW_FILE_NAME":"HIF KO C2C12 UnT4 M_Dasarathy_Nicole_114Cells_02042022_HILIC_POS252"}
},
{
"Subject ID":"-",
"Sample ID":"HIF KO C2C12 UnT5 M_Dasarathy_Nicole_114Cells_02042022_HILIC_POS253",
"Factors":{"Genotype":"HIF1a KO","Treatment":"Untreated"},
"Additional sample data":{"Column":"HILIC","Mode":"Positive","RAW_FILE_NAME":"HIF KO C2C12 UnT5 M_Dasarathy_Nicole_114Cells_02042022_HILIC_POS253"}
},
{
"Subject ID":"-",
"Sample ID":"HIF KO C2C12 UnT6 M_Dasarathy_Nicole_114Cells_02042022_HILIC_POS254",
"Factors":{"Genotype":"HIF1a KO","Treatment":"Untreated"},
"Additional sample data":{"Column":"HILIC","Mode":"Positive","RAW_FILE_NAME":"HIF KO C2C12 UnT6 M_Dasarathy_Nicole_114Cells_02042022_HILIC_POS254"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Metabolites were extracted from myotubes and skeletal muscle using chilled methanol containing 6 labeled internal standards (Betaine-d9, Carnitine-d9, Estrone-13C3, Cholesterol-13C3, Valeric acid-d9, Choline-d13). After centrifugation at 14,000g for 20 minutes to precipitate the protein pellet, the supernatant was removed, dried, and reconstituted in 5% acetonitrile. LC/MS (liquid chromatography/mass spectrometry) analysis was then performed, including on pooled quality control samples.","SAMPLE_TYPE":"Skeletal myotubes"},

"TREATMENT":{"TREATMENT_SUMMARY":"Cells were not treated (Untreated, UnT)"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Metabolites were extracted from myotubes and skeletal muscle using chilled methanol containing 6 labeled internal standards (Betaine-d9, Carnitine-d9, Estrone-13C3, Cholesterol-13C3, Valeric acid-d9, Choline-d13). After centrifugation at 14,000g for 20 minutes to precipitate the protein pellet, the supernatant was removed, dried, and reconstituted in 5% acetonitrile. LC/MS (liquid chromatography/mass spectrometry) analysis was then performed, including on pooled quality control samples."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"HILIC","INSTRUMENT_NAME":"Thermo Vanquish","COLUMN_NAME":"Waters ACQUITY UPLC BEH Amide (150 x 2.1mm,1.7um)","SOLVENT_A":"100% water;10 mM ammonium acetate; 0.125% acetic acid","SOLVENT_B":"5% water/95% acetonitrile;10 mM ammonium acetate; 0.125% acetic acid","FLOW_GRADIENT":"Time (min.) Flow Rate (mL/min) %B 0.0 0.2 100 2.0 0.2 70 4.0 0.2 60 5.5 0.2 60 10.5 0.2 50 11.5 0.2 50 12.0 0.2 100 16.0 0.2 100","FLOW_RATE":"0.2 mL/min","COLUMN_TEMPERATURE":"40"},

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

"MS":{"INSTRUMENT_NAME":"Thermo Q Exactive Focus","INSTRUMENT_TYPE":"QTRAP","MS_TYPE":"ESI","ION_MODE":"POSITIVE","MS_COMMENTS":"Data dependent acquisitions (DDA) on the pooled representative QC samples include MS full scans at a resolution of 120,000 and HCD MS/MS scans taken on the top 5 most abundant ions at a resolution of 30,000 with dynamic exclusion. The resolution of the MS2 scans were taken at a stepped NCE energy of 10.0, 20.0 and 30.0.","MS_RESULTS_FILE":"ST002930_AN004807_Results.txt UNITS:relative abundance Has m/z:Yes Has RT:Yes RT units:Seconds"}

}