{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002343","ANALYSIS_ID":"AN003827","VERSION":"1","CREATED_ON":"November 14, 2022, 8:57 am"},

"PROJECT":{"PROJECT_TITLE":"Serine and lipid metabolism","PROJECT_SUMMARY":"We analyzed paw skin sphingolipids 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":"The impact of myriocin and dietary serine restriction on paw skin sphingolipid diversity","STUDY_SUMMARY":"We analyzed paw skin 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":"47","NUM_MALES":"47"},

"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":"301.d"}
},
{
"Subject ID":"-",
"Sample ID":"302",
"Factors":{"Group":"Low fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"302.d"}
},
{
"Subject ID":"-",
"Sample ID":"303",
"Factors":{"Group":"Low fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"303.d"}
},
{
"Subject ID":"-",
"Sample ID":"304",
"Factors":{"Group":"Low fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"304.d"}
},
{
"Subject ID":"-",
"Sample ID":"305",
"Factors":{"Group":"Low fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"305.d"}
},
{
"Subject ID":"-",
"Sample ID":"306",
"Factors":{"Group":"Low fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"306.d"}
},
{
"Subject ID":"-",
"Sample ID":"307",
"Factors":{"Group":"Low fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"307.d"}
},
{
"Subject ID":"-",
"Sample ID":"308",
"Factors":{"Group":"Low fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"308.d"}
},
{
"Subject ID":"-",
"Sample ID":"309",
"Factors":{"Group":"Low fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"309.d"}
},
{
"Subject ID":"-",
"Sample ID":"310",
"Factors":{"Group":"Low fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"310.d"}
},
{
"Subject ID":"-",
"Sample ID":"311",
"Factors":{"Group":"Low fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"311.d"}
},
{
"Subject ID":"-",
"Sample ID":"312",
"Factors":{"Group":"Low fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"312.d"}
},
{
"Subject ID":"-",
"Sample ID":"313",
"Factors":{"Group":"High fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"313.d"}
},
{
"Subject ID":"-",
"Sample ID":"314",
"Factors":{"Group":"High fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"314.d"}
},
{
"Subject ID":"-",
"Sample ID":"315",
"Factors":{"Group":"High fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"315.d"}
},
{
"Subject ID":"-",
"Sample ID":"316",
"Factors":{"Group":"High fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"316.d"}
},
{
"Subject ID":"-",
"Sample ID":"317",
"Factors":{"Group":"High fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"317.d"}
},
{
"Subject ID":"-",
"Sample ID":"318",
"Factors":{"Group":"High fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"318.d"}
},
{
"Subject ID":"-",
"Sample ID":"319",
"Factors":{"Group":"High fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"319.d"}
},
{
"Subject ID":"-",
"Sample ID":"320",
"Factors":{"Group":"High fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"320.d"}
},
{
"Subject ID":"-",
"Sample ID":"321",
"Factors":{"Group":"High fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"321.d"}
},
{
"Subject ID":"-",
"Sample ID":"322",
"Factors":{"Group":"High fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"322.d"}
},
{
"Subject ID":"-",
"Sample ID":"323",
"Factors":{"Group":"High fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"323.d"}
},
{
"Subject ID":"-",
"Sample ID":"324",
"Factors":{"Group":"High fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"324.d"}
},
{
"Subject ID":"-",
"Sample ID":"325",
"Factors":{"Group":"Serine/glycine-free high fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"325.d"}
},
{
"Subject ID":"-",
"Sample ID":"326",
"Factors":{"Group":"Serine/glycine-free high fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"326.d"}
},
{
"Subject ID":"-",
"Sample ID":"327",
"Factors":{"Group":"Serine/glycine-free high fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"327.d"}
},
{
"Subject ID":"-",
"Sample ID":"328",
"Factors":{"Group":"Serine/glycine-free high fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"328.d"}
},
{
"Subject ID":"-",
"Sample ID":"329",
"Factors":{"Group":"Serine/glycine-free high fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"329.d"}
},
{
"Subject ID":"-",
"Sample ID":"330",
"Factors":{"Group":"Serine/glycine-free high fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"330.d"}
},
{
"Subject ID":"-",
"Sample ID":"331",
"Factors":{"Group":"Serine/glycine-free high fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"331.d"}
},
{
"Subject ID":"-",
"Sample ID":"332",
"Factors":{"Group":"Serine/glycine-free high fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"332.d"}
},
{
"Subject ID":"-",
"Sample ID":"333",
"Factors":{"Group":"Serine/glycine-free high fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"333.d"}
},
{
"Subject ID":"-",
"Sample ID":"334",
"Factors":{"Group":"Serine/glycine-free high fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"334.d"}
},
{
"Subject ID":"-",
"Sample ID":"335",
"Factors":{"Group":"Serine/glycine-free high fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"335.d"}
},
{
"Subject ID":"-",
"Sample ID":"336",
"Factors":{"Group":"Serine/glycine-free high fat diet + vehicle"},
"Additional sample data":{"RAW_FILE_NAME":"336.d"}
},
{
"Subject ID":"-",
"Sample ID":"337",
"Factors":{"Group":"Serine/glycine-free high fat diet + myriocin"},
"Additional sample data":{"RAW_FILE_NAME":"337.d"}
},
{
"Subject ID":"-",
"Sample ID":"338",
"Factors":{"Group":"Serine/glycine-free high fat diet + myriocin"},
"Additional sample data":{"RAW_FILE_NAME":"338.d"}
},
{
"Subject ID":"-",
"Sample ID":"340",
"Factors":{"Group":"Serine/glycine-free high fat diet + myriocin"},
"Additional sample data":{"RAW_FILE_NAME":"340.d"}
},
{
"Subject ID":"-",
"Sample ID":"341",
"Factors":{"Group":"Serine/glycine-free high fat diet + myriocin"},
"Additional sample data":{"RAW_FILE_NAME":"341.d"}
},
{
"Subject ID":"-",
"Sample ID":"342",
"Factors":{"Group":"Serine/glycine-free high fat diet + myriocin"},
"Additional sample data":{"RAW_FILE_NAME":"342.d"}
},
{
"Subject ID":"-",
"Sample ID":"343",
"Factors":{"Group":"Serine/glycine-free high fat diet + myriocin"},
"Additional sample data":{"RAW_FILE_NAME":"343.d"}
},
{
"Subject ID":"-",
"Sample ID":"344",
"Factors":{"Group":"Serine/glycine-free high fat diet + myriocin"},
"Additional sample data":{"RAW_FILE_NAME":"344.d"}
},
{
"Subject ID":"-",
"Sample ID":"345",
"Factors":{"Group":"Serine/glycine-free high fat diet + myriocin"},
"Additional sample data":{"RAW_FILE_NAME":"345.d"}
},
{
"Subject ID":"-",
"Sample ID":"346",
"Factors":{"Group":"Serine/glycine-free high fat diet + myriocin"},
"Additional sample data":{"RAW_FILE_NAME":"346.d"}
},
{
"Subject ID":"-",
"Sample ID":"347",
"Factors":{"Group":"Serine/glycine-free high fat diet + myriocin"},
"Additional sample data":{"RAW_FILE_NAME":"347.d"}
},
{
"Subject ID":"-",
"Sample ID":"348",
"Factors":{"Group":"Serine/glycine-free high fat diet + myriocin"},
"Additional sample data":{"RAW_FILE_NAME":"348.d"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Paw skin samples were collected using Wollenberger clamps pre-cooled to the temperature of liquid nitrogen and stored at -80 C until analysis.","SAMPLE_TYPE":"Paw skin","STORAGE_CONDITIONS":"-80℃"},

"TREATMENT":{"TREATMENT_SUMMARY":"Animals were subjected to 4 different conditions for a period of 24 weeks: 1) low fat diet, 2) high fat diet, 3) serine/glycine-free high fat diet, and 4) serine/glycine-free high fat diet with 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":"The gradient elution program consisted of the following profile: 0 min, 82% B; 3 min, 82% B; 4 min, 90% B, 18 min, 99% B; 25 min, 99%, 27 min, 82% B, 30 min, 82% B.","CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Agilent 6460C","COLUMN_NAME":"Spectra 3 μm C8SR 150 × 3 mm inner diameter, Peeke Scientific","FLOW_RATE":"0.5 ml/min","COLUMN_TEMPERATURE":"40","SOLVENT_A":"100% HPLC-grade water containing 2 mM ammonium formate and 0.2% formic acid","SOLVENT_B":"100% methanol containing 0.2% formic acid and 1 mM ammonium formate"},

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

"MS":{"INSTRUMENT_NAME":"Agilent 6460 QQQ","INSTRUMENT_TYPE":"Triple quadrupole","MS_TYPE":"ESI","ION_MODE":"POSITIVE","MS_COMMENTS":"Mass Hunter"},

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

"Data":[{"Metabolite":"Cer 18:1/16:0","301":"122.8549707","302":"88.33579097","303":"112.4814909","304":"125.8680773","305":"16.61904977","306":"70.56769062","307":"67.89730485","308":"117.3052925","309":"124.8330539","310":"90.72538114","311":"83.28451667","312":"71.01015103","313":"131.5844757","314":"124.7331712","315":"227.2147684","316":"107.8224206","317":"97.33688717","318":"106.1117246","319":"100.6719193","320":"72.81809119","321":"46.99339379","322":"57.55803334","323":"71.52773767","324":"54.40182715","325":"80.19039993","326":"73.56075409","327":"63.75748724","328":"98.10150359","329":"77.21868764","330":"49.67664294","331":"78.65036855","332":"84.58148799","333":"164.9450388","334":"83.8915892","335":"89.70858409","336":"73.82067792","337":"154.0514139","338":"52.45938044","340":"147.3897782","341":"70.86690998","342":"99.40270195","343":"33.28447956","344":"106.7975026","345":"523.9056618","346":"112.0053996","347":"43.61773749","348":"93.41285856"},{"Metabolite":"Cer 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