{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002339","ANALYSIS_ID":"AN003822","VERSION":"1","CREATED_ON":"November 11, 2022, 4:46 pm"},

"PROJECT":{"PROJECT_TITLE":"Serine and lipid metabolism","PROJECT_SUMMARY":"We analyzed hepatic polar and lipid metabolites in mice (C57BL/6J) in response to two dietary interventions. The first was: 1) low fat (LFD), 2) serine/glycine-free LFD (-SG LFD), high fat (HFD), and serine/glycine-free HFD (-SG HFD). And the second was: 1) low fat (LFD), high fat (HFD), serine/glycine-free HFD (-SG HFD), and serine/glycine-free HFD (-SG HFD) with myriocin (0.3 mg/kg every other day) treatment. The goal of the study was to determine the impact of dietary serine/glycine restriction and myriocin treatment on the hepatic lipidome.","INSTITUTE":"Salk Institute for Biological Studies","DEPARTMENT":"Molecular and Cell Biology Laboratory","LABORATORY":"Metallo Lab","LAST_NAME":"Handzlik","FIRST_NAME":"Michal","ADDRESS":"10010 N Torrey Pines Rd, La Jolla, California, 92037, USA","EMAIL":"mhandzlik@salk.edu","PHONE":"2069601945","FUNDING_SOURCE":"R01CA234245"},

"STUDY":{"STUDY_TITLE":"Myriocin rescue of serine-associated hepatic lipid diversity","STUDY_SUMMARY":"We analyzed hepatic polar and lipid metabolites in mice (C57BL/6J) in response to two dietary interventions. The first was: 1) low fat (LFD), 2) serine/glycine-free LFD (-SG LFD), high fat (HFD), and serine/glycine-free HFD (-SG HFD). And the second was: 1) low fat (LFD), high fat (HFD), serine/glycine-free HFD (-SG HFD), and serine/glycine-free HFD (-SG HFD) with myriocin (0.3 mg/kg every other day) treatment. The goal of the study was to determine the impact of dietary serine/glycine restriction and myriocin treatment on the hepatic lipidome.","INSTITUTE":"Salk Institute for Biological Studies","DEPARTMENT":"Molecular and Cell Biology Laboratory","LABORATORY":"Metallo Lab","LAST_NAME":"Handzlik","FIRST_NAME":"Michal","ADDRESS":"10010 N Torrey Pines Rd, La Jolla, California, 92037, USA","EMAIL":"mhandzlik@salk.edu","PHONE":"2069601945","NUM_GROUPS":"LFD, -SG LFD, HFD, -SG HFD, LFD+Veh, HFD+Veh, -SG HFD+Veh, -SG HFD+Myr","TOTAL_SUBJECTS":"88","NUM_MALES":"88"},

"SUBJECT":{"SUBJECT_TYPE":"Mammal","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090","GENOTYPE_STRAIN":"C57BL/6J","AGE_OR_AGE_RANGE":"8-32-week-old","WEIGHT_OR_WEIGHT_RANGE":"25-50","GENDER":"Male","ANIMAL_ANIMAL_SUPPLIER":"JAX","ANIMAL_HOUSING":"5/cage","ANIMAL_LIGHT_CYCLE":"12h dark/12 h light","ANIMAL_FEED":"Special diets; see group labeling","ANIMAL_WATER":"Ad libitum"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"301",
"Factors":{"Group":"Low fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"L_301.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"302",
"Factors":{"Group":"Low fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"L_302.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"303",
"Factors":{"Group":"Low fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"L_303.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"304",
"Factors":{"Group":"Low fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"L_304.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"305",
"Factors":{"Group":"Low fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"L_305.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"306",
"Factors":{"Group":"Low fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"L_306.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"307",
"Factors":{"Group":"Low fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"L_307.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"308",
"Factors":{"Group":"Low fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"L_308.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"309",
"Factors":{"Group":"Low fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"L_309.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"310",
"Factors":{"Group":"Low fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"L_310.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"311",
"Factors":{"Group":"Low fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"L_311.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"312",
"Factors":{"Group":"Low fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"L_312.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"313",
"Factors":{"Group":"High fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"L_313.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"314",
"Factors":{"Group":"High fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"L_314.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"315",
"Factors":{"Group":"High fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"L_315.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"316",
"Factors":{"Group":"High fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"L_316.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"317",
"Factors":{"Group":"High fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"L_317.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"318",
"Factors":{"Group":"High fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"L_318.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"319",
"Factors":{"Group":"High fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"L_319.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"320",
"Factors":{"Group":"High fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"L_320.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"321",
"Factors":{"Group":"High fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"L_321.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"322",
"Factors":{"Group":"High fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"L_322.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"323",
"Factors":{"Group":"High fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"L_323.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"324",
"Factors":{"Group":"High fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"L_324.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"325",
"Factors":{"Group":"Serine/glycine-free high fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"L_325.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"326",
"Factors":{"Group":"Serine/glycine-free high fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"L_326.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"327",
"Factors":{"Group":"Serine/glycine-free high fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"L_327.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"328",
"Factors":{"Group":"Serine/glycine-free high fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"L_328.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"329",
"Factors":{"Group":"Serine/glycine-free high fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"L_329.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"330",
"Factors":{"Group":"Serine/glycine-free high fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"L_330.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"331",
"Factors":{"Group":"Serine/glycine-free high fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"L_331.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"332",
"Factors":{"Group":"Serine/glycine-free high fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"L_332.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"333",
"Factors":{"Group":"Serine/glycine-free high fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"L_333.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"334",
"Factors":{"Group":"Serine/glycine-free high fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"L_334.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"335",
"Factors":{"Group":"Serine/glycine-free high fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"L_335.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"336",
"Factors":{"Group":"Serine/glycine-free high fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"L_336.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"337",
"Factors":{"Group":"Serine/glycine-free high fat diet + myriocin"},
"Additional sample data":{"RAW_FILE_NAME":"L_337.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"338",
"Factors":{"Group":"Serine/glycine-free high fat diet + myriocin"},
"Additional sample data":{"RAW_FILE_NAME":"L_338.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"340",
"Factors":{"Group":"Serine/glycine-free high fat diet + myriocin"},
"Additional sample data":{"RAW_FILE_NAME":"L_340.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"341",
"Factors":{"Group":"Serine/glycine-free high fat diet + myriocin"},
"Additional sample data":{"RAW_FILE_NAME":"L_341.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"342",
"Factors":{"Group":"Serine/glycine-free high fat diet + myriocin"},
"Additional sample data":{"RAW_FILE_NAME":"L_342.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"343",
"Factors":{"Group":"Serine/glycine-free high fat diet + myriocin"},
"Additional sample data":{"RAW_FILE_NAME":"L_343.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"344",
"Factors":{"Group":"Serine/glycine-free high fat diet + myriocin"},
"Additional sample data":{"RAW_FILE_NAME":"L_344.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"345",
"Factors":{"Group":"Serine/glycine-free high fat diet + myriocin"},
"Additional sample data":{"RAW_FILE_NAME":"L_345.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"346",
"Factors":{"Group":"Serine/glycine-free high fat diet + myriocin"},
"Additional sample data":{"RAW_FILE_NAME":"L_346.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"347",
"Factors":{"Group":"Serine/glycine-free high fat diet + myriocin"},
"Additional sample data":{"RAW_FILE_NAME":"L_347.mzXML"}
},
{
"Subject ID":"-",
"Sample ID":"348",
"Factors":{"Group":"Serine/glycine-free high fat diet + myriocin"},
"Additional sample data":{"RAW_FILE_NAME":"L_348.mzXML"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Liver samples were collected using Wollenberger clamps pre-cooled to the temperature of liquid nitrogen and stored at -80 C until analysis.","SAMPLE_TYPE":"Liver","STORAGE_CONDITIONS":"-80℃"},

"TREATMENT":{"TREATMENT_SUMMARY":"Animals were subjected to 4 different conditions for a period of 24 weeks: 1) low fat diet + vehicle, 2) high fat diet + vehicle, 3) serine/glycine-free high fat diet + vehicle, and 4) serine/glycine-free high fat diet + myriocin."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Samples were extracted with 400 ul of methanol (-20 C), 100 ul of water (ice-cold), 400 saline (ice-cold), and 1000 ul of chloroform (-20 C).","PROCESSING_STORAGE_CONDITIONS":"Room temperature","EXTRACT_STORAGE":"4℃"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"30% to 43% B from 3-8 min, then from 43% to 50% B from 8-9 min, then 50-90% B from 9-18 min, then 90-99% B from 18-26 min, then held at 99% B from 26-30 min, before returning to 30% B in 6 min and held for a further 4 min","CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Thermo Vanquish","COLUMN_NAME":"Thermo Accucore C30, 150 x 2.1mm, 2.6µm particle","FLOW_RATE":"0.2 ml/min","COLUMN_TEMPERATURE":"40","SOLVENT_A":"40:60 v/v water: acetonitrile with 10 mM ammonium formate and 0.1% formic acid","SOLVENT_B":"10:90 v/v acetonitrile: 2-propanol with 10 mM ammonium formate and 0.1% formic acid"},

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

"MS":{"INSTRUMENT_NAME":"Thermo Q Exactive Orbitrap","INSTRUMENT_TYPE":"Ion trap","MS_TYPE":"ESI","ION_MODE":"POSITIVE","MS_COMMENTS":"El-MAVEN"},

"MS_METABOLITE_DATA":{
"Units":"normalized ion count/mg protein",

"Data":[{"Metabolite":"TG 44:0","301":"3.251341785","302":"3.24783292","303":"2.747673708","304":"1.908401748","305":"3.743936412","306":"3.945500796","307":"1.490620229","308":"2.215176993","309":"2.482010322","310":"3.195280198","311":"4.137627798","312":"2.404682175","313":"0.621402381","314":"0.568343626","315":"0.652734874","316":"1.107262857","317":"0.878431087","318":"1.354332795","319":"1.041449237","320":"1.400316276","321":"0.48650573","322":"0.306738244","323":"1.130087492","324":"0.827892518","325":"0.331465658","326":"0.450650722","327":"0.55005266","328":"1.04885787","329":"0.78988699","330":"0.530506818","331":"0.935663609","332":"0.870923817","333":"0.467920982","334":"0.660829844","335":"0.371145346","336":"0.896358979","337":"0.406705498","338":"0.409536235","340":"0.463861247","341":"0.300387844","342":"0.582879393","343":"0.435712395","344":"0.786660559","345":"0.354399707","346":"0.565191367","347":"0.992535261","348":"0.344306054"},{"Metabolite":"TG 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45:1","301":"4.08340646","302":"2.686415895","303":"3.273823661","304":"1.585335177","305":"4.128976792","306":"4.005042953","307":"1.403400879","308":"2.305588593","309":"1.850833838","310":"3.127344614","311":"3.827665011","312":"2.29113229","313":"0.487270273","314":"0.616525521","315":"0.53220394","316":"0.934974062","317":"0.755933346","318":"0.818350934","319":"0.932143535","320":"1.370745717","321":"0.361278988","322":"0.216969592","323":"0.693757064","324":"0.544039975","325":"0.11900477","326":"0.142345526","327":"0.293452991","328":"1.018481706","329":"0.547901344","330":"0.2920546","331":"0.700667559","332":"0.597870869","333":"0.254069854","334":"0.27372905","335":"0.136153424","336":"0.422905442","337":"0.318831726","338":"0.244842625","340":"0.339243527","341":"0.139236848","342":"0.192476682","343":"0.1425846","344":"0.363795577","345":"0.11271921","346":"0.24847058","347":"0.799044811","348":"0.172522212"},{"Metabolite":"TG 46:0","301":"18.47825194","302":"14.28337011","303":"9.812556075","304":"6.535769314","305":"12.34119851","306":"15.43535822","307":"5.348320256","308":"9.192066724","309":"12.63801492","310":"13.43830101","311":"18.61124375","312":"9.645077696","313":"2.275494177","314":"3.184503967","315":"0.882109661","316":"4.74390433","317":"2.539603864","318":"4.863377139","319":"3.867802798","320":"4.77105066","321":"1.667229838","322":"1.238974191","323":"3.364622381","324":"2.403866613","325":"0.79510253","326":"1.592038325","327":"2.154092599","328":"4.294908251","329":"2.744226709","330":"1.73796112","331":"3.313280907","332":"3.596053457","333":"0.876808225","334":"2.818750684","335":"0.928644203","336":"3.277467905","337":"1.011376597","338":"1.024366644","340":"2.09460947","341":"0.767695955","342":"1.923168293","343":"1.034020409","344":"2.435592825","345":"0.630608759","346":"2.243242739","347":"3.805735222","348":"1.061094345"},{"Metabolite":"TG 47:0","301":"4.948427136","302":"3.347252135","303":"3.636661849","304":"2.135006657","305":"4.939976473","306":"5.755866342","307":"1.738358414","308":"2.80960242","309":"3.698037965","310":"4.290060154","311":"6.383797818","312":"4.217510065","313":"1.825969269","314":"1.834138066","315":"1.966311449","316":"2.282705669","317":"1.556837961","318":"2.420406898","319":"2.322192425","320":"2.782364689","321":"1.235364967","322":"1.102902815","323":"1.876288583","324":"1.600219263","325":"0.945899786","326":"1.865141843","327":"1.956817766","328":"2.476782446","329":"2.778069084","330":"1.35559124","331":"2.081240911","332":"2.234840115","333":"0.93958129","334":"2.310117324","335":"1.45143058","336":"2.111147941","337":"0.903553337","338":"0.76015941","340":"1.173712768","341":"0.647937662","342":"1.539866603","343":"0.587061655","344":"1.414132834","345":"0.476163885","346":"1.0444701","347":"1.918384234","348":"0.621337779"},{"Metabolite":"TG 47:1","301":"24.19767155","302":"14.96780527","303":"15.02355149","304":"9.086468353","305":"19.50689978","306":"20.61222836","307":"8.323059711","308":"12.4575509","309":"10.77754625","310":"17.89343469","311":"21.24833181","312":"13.62610462","313":"4.352117732","314":"4.797475931","315":"3.992098943","316":"5.079639126","317":"4.220687157","318":"6.178942694","319":"6.413216045","320":"7.034874203","321":"2.884989594","322":"2.398502417","323":"4.93329564","324":"4.24230651","325":"1.249040372","326":"2.487903757","327":"2.809162126","328":"6.451933369","329":"5.06429858","330":"2.53838604","331":"4.958959528","332":"4.077301568","333":"2.244710265","334":"3.923969192","335":"1.956437614","336":"4.502248116","337":"1.308250065","338":"1.316711571","340":"2.362425477","341":"0.7870331","342":"2.130803274","343":"0.928191061","344":"2.426077756","345":"0.671923523","346":"1.773661709","347":"4.300633415","348":"1.272599733"},{"Metabolite":"TG 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