{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001283","ANALYSIS_ID":"AN002127","VERSION":"1","CREATED_ON":"November 25, 2019, 1:12 pm"},

"PROJECT":{"PROJECT_TITLE":"Nitric Oxide (NO) effect on mitochondrial metabolic rewiring in M1 Macrophages","PROJECT_TYPE":"metabolomics","PROJECT_SUMMARY":"Study of Metabolome of WT and Nos2 KO Bone Marrow Derived Macrophages in resting state or activated for 24h with LPS","INSTITUTE":"National Cancer Institute","LAST_NAME":"Palmieri","FIRST_NAME":"Erika M","ADDRESS":"1050 Boyles street, Frederick MD 21702","EMAIL":"erikamariana.palmieri@nih.gov","PHONE":"3018461946"},

"STUDY":{"STUDY_TITLE":"Nitric Oxide (NO) effect on mitochondrial metabolic rewiring in M1 Macrophages","STUDY_SUMMARY":"Study of Metabolome of WT and Nos2 KO Bone Marrow Derived Macrophages in resting state or activated for 24h with LPS","INSTITUTE":"National Cancer Institute","LAST_NAME":"Palmieri","FIRST_NAME":"Erika M","ADDRESS":"1050 Boyles street, Frederick MD 21702","EMAIL":"erikamariana.palmieri@nih.gov","PHONE":"3018461946"},

"SUBJECT":{"SUBJECT_TYPE":"Cultured cells","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"5 - NOS2/ BMM_001",
"Factors":{"Hours":"24","LPS (ng/mL)":"-"}
},
{
"Subject ID":"-",
"Sample ID":"5 - NOS2/ BMM_002",
"Factors":{"Hours":"24","LPS (ng/mL)":"-"}
},
{
"Subject ID":"-",
"Sample ID":"5 - NOS2/ BMM_003",
"Factors":{"Hours":"24","LPS (ng/mL)":"-"}
},
{
"Subject ID":"-",
"Sample ID":"5 - NOS2/ BMM_004",
"Factors":{"Hours":"24","LPS (ng/mL)":"-"}
},
{
"Subject ID":"-",
"Sample ID":"5 - NOS2/ BMM_005",
"Factors":{"Hours":"24","LPS (ng/mL)":"-"}
},
{
"Subject ID":"-",
"Sample ID":"6 - NOS2/ BMM + LPS_006",
"Factors":{"Hours":"24","LPS (ng/mL)":"100"}
},
{
"Subject ID":"-",
"Sample ID":"6 - NOS2/ BMM + LPS_007",
"Factors":{"Hours":"24","LPS (ng/mL)":"100"}
},
{
"Subject ID":"-",
"Sample ID":"6 - NOS2/ BMM + LPS_008",
"Factors":{"Hours":"24","LPS (ng/mL)":"100"}
},
{
"Subject ID":"-",
"Sample ID":"6 - NOS2/ BMM + LPS_009",
"Factors":{"Hours":"24","LPS (ng/mL)":"100"}
},
{
"Subject ID":"-",
"Sample ID":"6 - NOS2/ BMM + LPS_010",
"Factors":{"Hours":"24","LPS (ng/mL)":"100"}
},
{
"Subject ID":"-",
"Sample ID":"1 - Wild Type BMM_011",
"Factors":{"Hours":"24","LPS (ng/mL)":"-"}
},
{
"Subject ID":"-",
"Sample ID":"1 - Wild Type BMM_012",
"Factors":{"Hours":"24","LPS (ng/mL)":"-"}
},
{
"Subject ID":"-",
"Sample ID":"1 - Wild Type BMM_013",
"Factors":{"Hours":"24","LPS (ng/mL)":"-"}
},
{
"Subject ID":"-",
"Sample ID":"1 - Wild Type BMM_014",
"Factors":{"Hours":"24","LPS (ng/mL)":"-"}
},
{
"Subject ID":"-",
"Sample ID":"1 - Wild Type BMM_015",
"Factors":{"Hours":"24","LPS (ng/mL)":"-"}
},
{
"Subject ID":"-",
"Sample ID":"2 - Wild Type BMM + LPS_016",
"Factors":{"Hours":"24","LPS (ng/mL)":"100"}
},
{
"Subject ID":"-",
"Sample ID":"2 - Wild Type BMM + LPS_017",
"Factors":{"Hours":"24","LPS (ng/mL)":"100"}
},
{
"Subject ID":"-",
"Sample ID":"2 - Wild Type BMM + LPS_018",
"Factors":{"Hours":"24","LPS (ng/mL)":"100"}
},
{
"Subject ID":"-",
"Sample ID":"2 - Wild Type BMM + LPS_019",
"Factors":{"Hours":"24","LPS (ng/mL)":"100"}
},
{
"Subject ID":"-",
"Sample ID":"2 - Wild Type BMM + LPS_020",
"Factors":{"Hours":"24","LPS (ng/mL)":"100"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"WT and Nos2KO BMDM (~107 cells per sample) were treated with vehicle (PBS) or 100ng/mL of LPS 24 hours. Cells were then washed, gently scraped, pelleted, snap frozen in liquid nitrogen and sent to West Coast Metabolomic Center at the University of California, Davis (Davis, CA) for metabolomic analyses.","SAMPLE_TYPE":"Macrophages"},

"TREATMENT":{"TREATMENT_SUMMARY":"WT and Nos2KO BMDM (~107 cells per sample) were treated with vehicle (PBS) or 100ng/mL of LPS 24 hours. Cells were then washed, gently scraped, pelleted, snap frozen in liquid nitrogen and sent to West Coast Metabolomic Center at the University of California, Davis (Davis, CA) for metabolomic analyses."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"WT and Hif1a-/- BMDM (~107 cells per sample) were treated with vehicle (PBS) or 100ng/mL of LPS + 50ng/mL for 18 hours. Cells were then washed, gently scraped, pelleted, snap frozen in liquid nitrogen and sent to West Coast Metabolomic Center at the University of California, Davis (Davis, CA) for metabolomic analyses."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"GC","INSTRUMENT_NAME":"Agilent 6890N","COLUMN_NAME":"Restek Rtx-5Sil MS (30 x 0.25mm, 0.25um)"},

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

"MS":{"INSTRUMENT_NAME":"Leco Pegasus III GC TOF","INSTRUMENT_TYPE":"GC-TOF","MS_TYPE":"EI","ION_MODE":"POSITIVE","MS_COMMENTS":"Raw GC-TOF MS data files were preprocessed directly after data acquisition and stored as ChromaTOF-specific peg files, as generic txt result files and additionally as generic ANDI MS cdf files. ChromaTOF version 4.0 was used for data preprocessing without smoothing, 3 s peak width, baseline subtraction just above the noise level, and automatic mass spectral deconvolution and peak detection at signal/noise (s/n) levels of 5:1 throughout the chromatogram. Results in .txt format were exported to a data server with absolute spectra intensities and further processed by a filtering algorithm implemented in the metabolomics BinBase database. The BinBase algorithm (rtx5) used the following settings: validity of chromatogram (107 counts/s), unbiased retention index marker detection (MS similarity > 800, validity of intensity range for high m/z"},

"MS_METABOLITE_DATA":{
"Units":"normalized peak height",

"Data":[{"Metabolite":"xylulose NIST","5 - NOS2/ BMM_001":"113","5 - NOS2/ BMM_002":"132","5 - NOS2/ BMM_003":"87","5 - NOS2/ BMM_004":"66","5 - NOS2/ BMM_005":"101","6 - NOS2/ BMM + LPS_006":"145","6 - NOS2/ BMM + LPS_007":"171","6 - NOS2/ BMM + LPS_008":"157","6 - NOS2/ BMM + LPS_009":"74","6 - NOS2/ BMM + LPS_010":"177","1 - Wild Type BMM_011":"118","1 - Wild Type BMM_012":"","1 - Wild Type BMM_013":"104","1 - Wild Type BMM_014":"90","1 - Wild Type BMM_015":"76","2 - Wild Type BMM + LPS_016":"165","2 - Wild Type BMM + LPS_017":"153","2 - Wild Type BMM + LPS_018":"130","2 - Wild Type BMM + LPS_019":"110","2 - Wild Type BMM + LPS_020":"106"},{"Metabolite":"xylose","5 - NOS2/ BMM_001":"251","5 - NOS2/ BMM_002":"323","5 - NOS2/ BMM_003":"216","5 - NOS2/ BMM_004":"359","5 - NOS2/ BMM_005":"341","6 - NOS2/ BMM + LPS_006":"422","6 - NOS2/ BMM + LPS_007":"365","6 - NOS2/ BMM + LPS_008":"311","6 - NOS2/ BMM + LPS_009":"315","6 - NOS2/ BMM + LPS_010":"406","1 - Wild Type BMM_011":"294","1 - Wild Type BMM_012":"413","1 - Wild Type BMM_013":"462","1 - Wild Type BMM_014":"458","1 - Wild Type BMM_015":"323","2 - Wild Type BMM + LPS_016":"476","2 - Wild Type BMM + LPS_017":"231","2 - Wild Type BMM + LPS_018":"269","2 - Wild Type BMM + LPS_019":"247","2 - Wild Type BMM + LPS_020":"185"},{"Metabolite":"xylitol","5 - NOS2/ BMM_001":"122","5 - NOS2/ BMM_002":"107","5 - NOS2/ BMM_003":"204","5 - NOS2/ BMM_004":"120","5 - NOS2/ BMM_005":"122","6 - NOS2/ BMM + LPS_006":"161","6 - NOS2/ BMM + LPS_007":"270","6 - NOS2/ BMM + LPS_008":"202","6 - NOS2/ BMM + LPS_009":"224","6 - NOS2/ BMM + LPS_010":"267","1 - Wild Type BMM_011":"94","1 - Wild Type BMM_012":"103","1 - Wild Type BMM_013":"178","1 - Wild Type BMM_014":"92","1 - Wild Type BMM_015":"131","2 - Wild Type BMM + LPS_016":"159","2 - Wild Type BMM + LPS_017":"184","2 - Wild Type BMM + LPS_018":"134","2 - Wild Type BMM + LPS_019":"183","2 - Wild Type BMM + LPS_020":"220"},{"Metabolite":"xanthine","5 - NOS2/ BMM_001":"528","5 - NOS2/ BMM_002":"638","5 - NOS2/ BMM_003":"192","5 - NOS2/ BMM_004":"1155","5 - NOS2/ BMM_005":"672","6 - NOS2/ BMM + LPS_006":"376","6 - NOS2/ BMM + LPS_007":"397","6 - NOS2/ BMM + LPS_008":"713","6 - NOS2/ BMM + LPS_009":"465","6 - NOS2/ BMM + LPS_010":"596","1 - Wild Type BMM_011":"841","1 - Wild Type BMM_012":"566","1 - Wild Type BMM_013":"1198","1 - Wild Type BMM_014":"202","1 - Wild Type BMM_015":"511","2 - Wild Type BMM + LPS_016":"988","2 - Wild Type BMM + LPS_017":"225","2 - Wild Type BMM + LPS_018":"196","2 - Wild Type BMM + LPS_019":"257","2 - Wild Type BMM + LPS_020":"299"},{"Metabolite":"valine","5 - NOS2/ BMM_001":"22534","5 - NOS2/ BMM_002":"26594","5 - NOS2/ BMM_003":"28823","5 - NOS2/ BMM_004":"25969","5 - NOS2/ BMM_005":"28622","6 - NOS2/ BMM + LPS_006":"36668","6 - NOS2/ BMM + LPS_007":"80194","6 - NOS2/ BMM + LPS_008":"47243","6 - NOS2/ BMM + LPS_009":"30194","6 - NOS2/ BMM + LPS_010":"29768","1 - Wild Type BMM_011":"18078","1 - Wild Type BMM_012":"18097","1 - Wild Type BMM_013":"24900","1 - Wild Type BMM_014":"32338","1 - Wild Type BMM_015":"43817","2 - Wild Type BMM + LPS_016":"41194","2 - Wild Type BMM + LPS_017":"33329","2 - Wild Type BMM + LPS_018":"39505","2 - Wild Type BMM + LPS_019":"44980","2 - Wild Type BMM + LPS_020":"29734"},{"Metabolite":"uridine-5'-monophosphate","5 - NOS2/ BMM_001":"6738","5 - NOS2/ BMM_002":"9040","5 - NOS2/ BMM_003":"6036","5 - NOS2/ BMM_004":"7339","5 - NOS2/ BMM_005":"6830","6 - NOS2/ BMM + LPS_006":"9476","6 - NOS2/ BMM + LPS_007":"10326","6 - NOS2/ BMM + LPS_008":"7913","6 - NOS2/ BMM + LPS_009":"5108","6 - NOS2/ BMM + LPS_010":"7403","1 - Wild Type BMM_011":"5661","1 - Wild Type BMM_012":"5475","1 - Wild Type BMM_013":"8688","1 - Wild Type BMM_014":"5173","1 - Wild Type BMM_015":"5192","2 - Wild Type BMM + LPS_016":"8925","2 - Wild Type BMM + LPS_017":"8288","2 - Wild Type BMM + LPS_018":"4171","2 - Wild Type BMM + LPS_019":"7970","2 - Wild Type BMM + LPS_020":"6040"},{"Metabolite":"uric acid","5 - NOS2/ BMM_001":"1192","5 - NOS2/ BMM_002":"1346","5 - NOS2/ BMM_003":"2014","5 - NOS2/ BMM_004":"969","5 - NOS2/ BMM_005":"1156","6 - NOS2/ BMM + LPS_006":"2206","6 - NOS2/ BMM + LPS_007":"2180","6 - NOS2/ BMM + LPS_008":"2446","6 - NOS2/ BMM + LPS_009":"3493","6 - NOS2/ BMM + LPS_010":"3065","1 - Wild Type BMM_011":"735","1 - Wild Type BMM_012":"854","1 - Wild Type BMM_013":"1175","1 - Wild Type BMM_014":"985","1 - Wild Type BMM_015":"1245","2 - Wild Type BMM + LPS_016":"1538","2 - Wild Type BMM + LPS_017":"1440","2 - Wild Type BMM + LPS_018":"1613","2 - Wild Type BMM + LPS_019":"1626","2 - Wild Type BMM + LPS_020":"1598"},{"Metabolite":"urea","5 - NOS2/ BMM_001":"3275","5 - NOS2/ BMM_002":"2999","5 - NOS2/ BMM_003":"4210","5 - NOS2/ BMM_004":"3557","5 - NOS2/ BMM_005":"2808","6 - NOS2/ BMM + LPS_006":"6395","6 - NOS2/ BMM + LPS_007":"7293","6 - NOS2/ BMM + LPS_008":"9334","6 - NOS2/ BMM + LPS_009":"9355","6 - NOS2/ BMM + LPS_010":"8443","1 - Wild Type BMM_011":"1861","1 - Wild Type BMM_012":"3315","1 - Wild Type BMM_013":"2065","1 - Wild Type BMM_014":"1832","1 - Wild Type BMM_015":"2030","2 - Wild Type BMM + LPS_016":"2989","2 - Wild Type BMM + LPS_017":"5229","2 - Wild Type BMM + LPS_018":"4861","2 - Wild Type BMM + LPS_019":"6019","2 - Wild Type BMM + LPS_020":"5339"},{"Metabolite":"uracil","5 - NOS2/ BMM_001":"128","5 - NOS2/ BMM_002":"143","5 - NOS2/ BMM_003":"477","5 - NOS2/ BMM_004":"157","5 - NOS2/ BMM_005":"183","6 - NOS2/ BMM + LPS_006":"529","6 - NOS2/ BMM + LPS_007":"597","6 - NOS2/ BMM + LPS_008":"700","6 - NOS2/ BMM + LPS_009":"673","6 - NOS2/ BMM + LPS_010":"543","1 - Wild Type BMM_011":"162","1 - Wild Type BMM_012":"157","1 - Wild Type BMM_013":"111","1 - Wild Type BMM_014":"103","1 - Wild Type BMM_015":"198","2 - Wild Type BMM + LPS_016":"201","2 - Wild Type BMM + LPS_017":"713","2 - Wild Type BMM + LPS_018":"406","2 - Wild Type BMM + LPS_019":"724","2 - Wild Type BMM + LPS_020":"575"},{"Metabolite":"UDP GlcNAc","5 - NOS2/ BMM_001":"424","5 - NOS2/ BMM_002":"470","5 - NOS2/ BMM_003":"461","5 - NOS2/ BMM_004":"456","5 - NOS2/ BMM_005":"500","6 - NOS2/ BMM + LPS_006":"682","6 - NOS2/ BMM + LPS_007":"181","6 - NOS2/ BMM + LPS_008":"527","6 - NOS2/ BMM + LPS_009":"585","6 - NOS2/ BMM + LPS_010":"379","1 - Wild Type BMM_011":"381","1 - Wild Type BMM_012":"384","1 - Wild Type BMM_013":"533","1 - Wild Type BMM_014":"393","1 - Wild Type BMM_015":"427","2 - Wild Type BMM + LPS_016":"405","2 - Wild Type BMM + LPS_017":"512","2 - Wild Type BMM + LPS_018":"416","2 - Wild Type BMM + LPS_019":"596","2 - Wild Type BMM + LPS_020":"610"},{"Metabolite":"UDP-glucuronic acid","5 - NOS2/ BMM_001":"794","5 - NOS2/ BMM_002":"939","5 - NOS2/ BMM_003":"1141","5 - NOS2/ BMM_004":"746","5 - NOS2/ BMM_005":"917","6 - NOS2/ BMM + LPS_006":"2306","6 - NOS2/ BMM + LPS_007":"1535","6 - NOS2/ BMM + LPS_008":"1452","6 - NOS2/ BMM + LPS_009":"1908","6 - NOS2/ BMM + LPS_010":"1951","1 - Wild Type BMM_011":"847","1 - Wild Type BMM_012":"1039","1 - Wild Type BMM_013":"1208","1 - Wild Type BMM_014":"861","1 - Wild Type BMM_015":"892","2 - Wild Type BMM + LPS_016":"930","2 - Wild Type BMM + LPS_017":"1303","2 - Wild Type BMM + LPS_018":"1210","2 - Wild Type BMM + LPS_019":"1352","2 - Wild Type BMM + LPS_020":"1259"},{"Metabolite":"tyrosine","5 - NOS2/ BMM_001":"35082","5 - NOS2/ BMM_002":"40782","5 - NOS2/ BMM_003":"34604","5 - NOS2/ BMM_004":"48228","5 - NOS2/ BMM_005":"46260","6 - NOS2/ BMM + LPS_006":"51480","6 - NOS2/ BMM + LPS_007":"50248","6 - NOS2/ BMM + LPS_008":"52683","6 - NOS2/ BMM + LPS_009":"54094","6 - NOS2/ BMM + LPS_010":"53132","1 - Wild Type BMM_011":"33286","1 - Wild Type BMM_012":"30148","1 - Wild Type BMM_013":"44585","1 - Wild Type BMM_014":"28400","1 - Wild Type BMM_015":"36930","2 - Wild Type BMM + LPS_016":"49480","2 - Wild Type BMM + LPS_017":"42177","2 - Wild Type BMM + LPS_018":"47756","2 - Wild Type BMM + LPS_019":"45513","2 - Wild Type BMM + LPS_020":"49064"},{"Metabolite":"tryptophan","5 - NOS2/ BMM_001":"10048","5 - NOS2/ BMM_002":"11255","5 - NOS2/ BMM_003":"10788","5 - NOS2/ BMM_004":"12892","5 - NOS2/ BMM_005":"12651","6 - NOS2/ BMM + LPS_006":"13055","6 - NOS2/ BMM + LPS_007":"15770","6 - NOS2/ BMM + LPS_008":"15468","6 - NOS2/ BMM + LPS_009":"15600","6 - NOS2/ BMM + LPS_010":"12801","1 - Wild Type BMM_011":"8502","1 - Wild Type BMM_012":"7710","1 - Wild Type BMM_013":"11777","1 - Wild Type BMM_014":"7891","1 - Wild Type BMM_015":"10319","2 - Wild Type BMM + LPS_016":"14532","2 - Wild Type BMM + LPS_017":"13387","2 - Wild Type BMM + LPS_018":"13521","2 - Wild Type BMM + LPS_019":"12676","2 - Wild Type BMM + LPS_020":"10609"},{"Metabolite":"threonine","5 - NOS2/ BMM_001":"24079","5 - NOS2/ BMM_002":"25252","5 - NOS2/ BMM_003":"23769","5 - NOS2/ BMM_004":"36203","5 - NOS2/ BMM_005":"30409","6 - NOS2/ BMM + LPS_006":"33074","6 - NOS2/ BMM + LPS_007":"29775","6 - NOS2/ BMM + LPS_008":"42046","6 - NOS2/ BMM + LPS_009":"36592","6 - NOS2/ BMM + LPS_010":"36972","1 - Wild Type BMM_011":"22287","1 - Wild Type BMM_012":"23001","1 - Wild Type BMM_013":"26286","1 - Wild Type BMM_014":"19164","1 - Wild Type BMM_015":"21089","2 - Wild Type BMM + LPS_016":"28938","2 - Wild Type BMM + LPS_017":"31388","2 - Wild Type BMM + LPS_018":"32671","2 - Wild Type BMM + LPS_019":"33019","2 - Wild Type BMM + LPS_020":"34370"},{"Metabolite":"taurine","5 - NOS2/ BMM_001":"241043","5 - NOS2/ BMM_002":"161529","5 - NOS2/ BMM_003":"149725","5 - NOS2/ BMM_004":"170476","5 - NOS2/ BMM_005":"182491","6 - NOS2/ BMM + LPS_006":"226427","6 - NOS2/ BMM + LPS_007":"266553","6 - NOS2/ BMM + LPS_008":"260140","6 - NOS2/ BMM + LPS_009":"235984","6 - NOS2/ BMM + LPS_010":"283271","1 - Wild Type BMM_011":"207083","1 - Wild Type BMM_012":"188445","1 - Wild Type BMM_013":"204732","1 - Wild Type BMM_014":"237411","1 - Wild Type BMM_015":"203309","2 - Wild Type BMM + LPS_016":"205881","2 - Wild Type BMM + LPS_017":"238285","2 - Wild Type BMM + LPS_018":"211070","2 - Wild Type BMM + LPS_019":"185812","2 - Wild Type BMM + LPS_020":"164534"},{"Metabolite":"tagatose","5 - NOS2/ BMM_001":"1936","5 - NOS2/ BMM_002":"2037","5 - NOS2/ BMM_003":"1812","5 - NOS2/ BMM_004":"1927","5 - NOS2/ BMM_005":"1927","6 - NOS2/ BMM + LPS_006":"2925","6 - NOS2/ BMM + LPS_007":"2260","6 - NOS2/ BMM + LPS_008":"2149","6 - NOS2/ BMM + LPS_009":"2732","6 - NOS2/ BMM + LPS_010":"2320","1 - Wild Type BMM_011":"1906","1 - Wild Type BMM_012":"1949","1 - Wild Type BMM_013":"2645","1 - Wild Type BMM_014":"1905","1 - Wild Type BMM_015":"1832","2 - Wild Type BMM + LPS_016":"2084","2 - Wild Type BMM + LPS_017":"2195","2 - Wild Type BMM + LPS_018":"2250","2 - Wild Type BMM + LPS_019":"2297","2 - Wild Type BMM + LPS_020":"2284"},{"Metabolite":"sulfuric acid","5 - NOS2/ BMM_001":"215","5 - NOS2/ BMM_002":"171","5 - NOS2/ BMM_003":"157","5 - NOS2/ BMM_004":"121","5 - NOS2/ BMM_005":"63","6 - NOS2/ BMM + LPS_006":"277","6 - NOS2/ BMM + LPS_007":"445","6 - NOS2/ BMM + LPS_008":"73","6 - NOS2/ BMM + LPS_009":"419","6 - NOS2/ BMM + LPS_010":"243","1 - Wild Type BMM_011":"244","1 - Wild Type BMM_012":"65","1 - Wild Type BMM_013":"209","1 - Wild Type BMM_014":"465","1 - Wild Type BMM_015":"123","2 - 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}