{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001809","ANALYSIS_ID":"AN002932","VERSION":"1","CREATED_ON":"May 28, 2021, 1:03 pm"},

"PROJECT":{"PROJECT_SUMMARY":"Diet composition, calories, and fasting times contribute to maintenance of health. Here, middle-aged mice were maintained for 5 months on 4:10 feeding cycles, consisting of 4 days of very low-calorie intake (VLCI) achieved with either standard laboratory chow (SD) or a fasting mimicking diet (FMD), followed by 10 days of ad libitum access to SD. Fat and lean mass loss was accompanied with improved performance, glucoregulation, and metabolic flexibility independent of diet composition. However, only the 4:10/SD cycles elicited a long-lasting metabolomic reprograming in serum and liver that was preserved six days after refeeding. Challenged with an obesogenic diet, cycles of VLCI achieved with either high-fat diet (HFD) or FMD during the low-calorie period did not prevent diet-induced obesity nor did they elicited a long-lasting metabolic memory, despite achieving modest metabolic flexibility. Our results highlight the importance of diet composition in mediating the metabolic benefits of short cycles of VLCI.","INSTITUTE":"National Institutes of Health","DEPARTMENT":"Experimental Gerontology Section and Translational Gerontology Branch, NIA","FIRST_NAME":"Rafael","ADDRESS":"251 Bayview Blvd. Suite 100/Room 5C214. Baltimore, MD 21224","EMAIL":"deCaboRa@grc.nia.nih.gov","PHONE":"+1-410-558-8510","PROJECT_TITLE":"The Metabolic Benefits of Short Cycles of Very Low Caloric Intake are Dependent on Diet Composition in Middle-Aged Mice","LAST_NAME":"de Cabo"},

"STUDY":{"STUDY_TITLE":"The Metabolic Benefits of Short Cycles of Very Low Caloric Intake are Dependent on Diet Composition in Middle-Aged Mice","STUDY_SUMMARY":"Diet composition, calories, and fasting times contribute to maintenance of health. Here, middle-aged mice were maintained for 5 months on 4:10 feeding cycles, consisting of 4 days of very low-calorie intake (VLCI) achieved with either standard laboratory chow (SD) or a fasting mimicking diet (FMD), followed by 10 days of ad libitum access to SD. Fat and lean mass loss was accompanied with improved performance, glucoregulation, and metabolic flexibility independent of diet composition. However, only the 4:10/SD cycles elicited a long-lasting metabolomic reprograming in serum and liver that was preserved six days after refeeding. Challenged with an obesogenic diet, cycles of VLCI achieved with either high-fat diet (HFD) or FMD during the low-calorie period did not prevent diet-induced obesity nor did they elicited a long-lasting metabolic memory, despite achieving modest metabolic flexibility. Our results highlight the importance of diet composition in mediating the metabolic benefits of short cycles of VLCI.","INSTITUTE":"National Institutes of Health","DEPARTMENT":"Experimental Gerontology Section and Translational Gerontology Branch, NIA","LAST_NAME":"de Cabo","FIRST_NAME":"Rafael","ADDRESS":"251 Bayview Blvd. Suite 100/Room 5C214. Baltimore, MD 21224","EMAIL":"deCaboRa@grc.nia.nih.gov","PHONE":"+1-410-558-8510"},

"SUBJECT":{"SUBJECT_TYPE":"Mammal","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090"},
"SUBJECT_SAMPLE_FACTORS":[
{
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{
"Subject ID":"liver",
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"Factors":{"treatment":"AL-Liver"},
"Additional sample data":{"RAW_FILE_NAME":"180530aJKsa03_1.cdf"}
},
{
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{
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},
{
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{
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{
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{
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{
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"Additional sample data":{"RAW_FILE_NAME":"180530aJKsa10_1.cdf"}
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{
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{
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{
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{
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{
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{
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},
{
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{
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"Additional sample data":{"RAW_FILE_NAME":"180530aJKsa18_1.cdf"}
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{
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{
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{
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{
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{
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{
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{
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"Additional sample data":{"RAW_FILE_NAME":"180530aJKsa25_1.cdf"}
},
{
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"Factors":{"treatment":"ALHF-Liver"},
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},
{
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},
{
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"Additional sample data":{"RAW_FILE_NAME":"180530aJKsa28_1.cdf"}
},
{
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"Additional sample data":{"RAW_FILE_NAME":"180530aJKsa29_1.cdf"}
},
{
"Subject ID":"liver",
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{
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{
"Subject ID":"liver",
"Sample ID":"L-FMD075_164",
"Factors":{"treatment":"ALHF-Liver"},
"Additional sample data":{"RAW_FILE_NAME":"180530aJKsa32_1.cdf"}
},
{
"Subject ID":"liver",
"Sample ID":"L-FMD019_068",
"Factors":{"treatment":"FMD-Liver"},
"Additional sample data":{"RAW_FILE_NAME":"180530aJKsa33_1.cdf"}
},
{
"Subject ID":"liver",
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"Factors":{"treatment":"FMD-Liver"},
"Additional sample data":{"RAW_FILE_NAME":"180530aJKsa34_1.cdf"}
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{
"Subject ID":"liver",
"Sample ID":"L-FMD021_070",
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"Additional sample data":{"RAW_FILE_NAME":"180530aJKsa35_1.cdf"}
},
{
"Subject ID":"liver",
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"Additional sample data":{"RAW_FILE_NAME":"180530aJKsa36_1.cdf"}
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{
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{
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{
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{
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{
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},
{
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},
{
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{
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},
{
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},
{
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},
{
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{
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{
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},
{
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},
{
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"Additional sample data":{"RAW_FILE_NAME":"180531aJKsa31_1.cdf"}
},
{
"Subject ID":"liver",
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"Factors":{"treatment":"iFMD-Liver"},
"Additional sample data":{"RAW_FILE_NAME":"180531aJKsa32_1.cdf"}
},
{
"Subject ID":"liver",
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"Factors":{"treatment":"iFMD-Liver"},
"Additional sample data":{"RAW_FILE_NAME":"180531aJKsa33_1.cdf"}
},
{
"Subject ID":"liver",
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"Additional sample data":{"RAW_FILE_NAME":"180531aJKsa34_1.cdf"}
},
{
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},
{
"Subject ID":"liver",
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},
{
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},
{
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},
{
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},
{
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"Factors":{"treatment":"HFMD-Liver"},
"Additional sample data":{"RAW_FILE_NAME":"180531aJKsa40_1.cdf"}
},
{
"Subject ID":"liver",
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"Factors":{"treatment":"HFMD-Liver"},
"Additional sample data":{"RAW_FILE_NAME":"180531aJKsa41_1.cdf"}
},
{
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"Factors":{"treatment":"HFMD-Liver"},
"Additional sample data":{"RAW_FILE_NAME":"180531aJKsa42_1.cdf"}
},
{
"Subject ID":"liver",
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"Factors":{"treatment":"HFMD-Liver"},
"Additional sample data":{"RAW_FILE_NAME":"180531aJKsa43_1.cdf"}
},
{
"Subject ID":"liver",
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"Factors":{"treatment":"HFMD-Liver"},
"Additional sample data":{"RAW_FILE_NAME":"180531aJKsa44_1.cdf"}
},
{
"Subject ID":"liver",
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"Factors":{"treatment":"HFMD-Liver"},
"Additional sample data":{"RAW_FILE_NAME":"180531aJKsa45_1.cdf"}
},
{
"Subject ID":"liver",
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"Factors":{"treatment":"HFMD-Liver"},
"Additional sample data":{"RAW_FILE_NAME":"180531aJKsa46_1.cdf"}
},
{
"Subject ID":"liver",
"Sample ID":"L-FMD089_176",
"Factors":{"treatment":"HFMD-Liver"},
"Additional sample data":{"RAW_FILE_NAME":"180531aJKsa47_1.cdf"}
},
{
"Subject ID":"liver",
"Sample ID":"L-FMD090_177",
"Factors":{"treatment":"HFMD-Liver"},
"Additional sample data":{"RAW_FILE_NAME":"180531aJKsa48_1.cdf"}
},
{
"Subject ID":"liver",
"Sample ID":"L-FMD091_178",
"Factors":{"treatment":"HFMD-Liver"},
"Additional sample data":{"RAW_FILE_NAME":"180531aJKsa49_1.cdf"}
},
{
"Subject ID":"liver",
"Sample ID":"L-FMD092_179",
"Factors":{"treatment":"HFMD-Liver"},
"Additional sample data":{"RAW_FILE_NAME":"180531aJKsa50_1.cdf"}
},
{
"Subject ID":"liver",
"Sample ID":"L-FMD093_180",
"Factors":{"treatment":"HFMD-Liver"},
"Additional sample data":{"RAW_FILE_NAME":"180601aJKsa01_1.cdf"}
},
{
"Subject ID":"Serum",
"Sample ID":"S-FMD002_001",
"Factors":{"treatment":"AL-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180601aJKsa02_1.cdf"}
},
{
"Subject ID":"Serum",
"Sample ID":"S-FMD004_002",
"Factors":{"treatment":"AL-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180601aJKsa03_1.cdf"}
},
{
"Subject ID":"Serum",
"Sample ID":"S-FMD005_003",
"Factors":{"treatment":"AL-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180601aJKsa04_1.cdf"}
},
{
"Subject ID":"Serum",
"Sample ID":"S-FMD006_004",
"Factors":{"treatment":"AL-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180601aJKsa05_1.cdf"}
},
{
"Subject ID":"Serum",
"Sample ID":"S-FMD007_005",
"Factors":{"treatment":"AL-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180601aJKsa06_1.cdf"}
},
{
"Subject ID":"Serum",
"Sample ID":"S-FMD008_006",
"Factors":{"treatment":"AL-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180601aJKsa07_1.cdf"}
},
{
"Subject ID":"Serum",
"Sample ID":"S-FMD009_007",
"Factors":{"treatment":"AL-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180601aJKsa08_1.cdf"}
},
{
"Subject ID":"Serum",
"Sample ID":"S-FMD010_008",
"Factors":{"treatment":"AL-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180601aJKsa09_1.cdf"}
},
{
"Subject ID":"Serum",
"Sample ID":"S-FMD011_009",
"Factors":{"treatment":"AL-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180601aJKsa10_1.cdf"}
},
{
"Subject ID":"Serum",
"Sample ID":"S-FMD012_010",
"Factors":{"treatment":"AL-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180601aJKsa11_1.cdf"}
},
{
"Subject ID":"Serum",
"Sample ID":"S-FMD013_011",
"Factors":{"treatment":"AL-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180601aJKsa12_1.cdf"}
},
{
"Subject ID":"Serum",
"Sample ID":"S-FMD014_012",
"Factors":{"treatment":"AL-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180601aJKsa13_1.cdf"}
},
{
"Subject ID":"Serum",
"Sample ID":"S-FMD015_013",
"Factors":{"treatment":"AL-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180601aJKsa14_1.cdf"}
},
{
"Subject ID":"Serum",
"Sample ID":"S-FMD016_014",
"Factors":{"treatment":"AL-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180601aJKsa15_1.cdf"}
},
{
"Subject ID":"Serum",
"Sample ID":"S-FMD018_015",
"Factors":{"treatment":"AL-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180601aJKsa16_1.cdf"}
},
{
"Subject ID":"serum",
"Sample ID":"S-FMD058_105",
"Factors":{"treatment":"ALHF-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180601aJKsa17_1.cdf"}
},
{
"Subject ID":"serum",
"Sample ID":"S-FMD059_106",
"Factors":{"treatment":"ALHF-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180601aJKsa18_1.cdf"}
},
{
"Subject ID":"serum",
"Sample ID":"S-FMD060_107",
"Factors":{"treatment":"ALHF-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180601aJKsa19_1.cdf"}
},
{
"Subject ID":"serum",
"Sample ID":"S-FMD061_108",
"Factors":{"treatment":"ALHF-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180601aJKsa20_1.cdf"}
},
{
"Subject ID":"serum",
"Sample ID":"S-FMD062_109",
"Factors":{"treatment":"ALHF-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180601aJKsa21_1.cdf"}
},
{
"Subject ID":"serum",
"Sample ID":"S-FMD063_110",
"Factors":{"treatment":"ALHF-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180601aJKsa22_1.cdf"}
},
{
"Subject ID":"serum",
"Sample ID":"S-FMD064_111",
"Factors":{"treatment":"ALHF-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180601aJKsa23_1.cdf"}
},
{
"Subject ID":"serum",
"Sample ID":"S-FMD065_112",
"Factors":{"treatment":"ALHF-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180601aJKsa24_1.cdf"}
},
{
"Subject ID":"serum",
"Sample ID":"S-FMD067_113",
"Factors":{"treatment":"ALHF-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180601aJKsa25_1.cdf"}
},
{
"Subject ID":"serum",
"Sample ID":"S-FMD068_114",
"Factors":{"treatment":"ALHF-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180601aJKsa26_1.cdf"}
},
{
"Subject ID":"serum",
"Sample ID":"S-FMD069_115",
"Factors":{"treatment":"ALHF-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180601aJKsa27_1.cdf"}
},
{
"Subject ID":"serum",
"Sample ID":"S-FMD070_116",
"Factors":{"treatment":"ALHF-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180601aJKsa28_1.cdf"}
},
{
"Subject ID":"serum",
"Sample ID":"S-FMD072_117",
"Factors":{"treatment":"ALHF-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180601aJKsa29_1.cdf"}
},
{
"Subject ID":"serum",
"Sample ID":"S-FMD073_118",
"Factors":{"treatment":"ALHF-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180601aJKsa30_1.cdf"}
},
{
"Subject ID":"serum",
"Sample ID":"S-FMD075_119",
"Factors":{"treatment":"ALHF-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180601aJKsa31_1.cdf"}
},
{
"Subject ID":"Serum",
"Sample ID":"S-FMD019_016",
"Factors":{"treatment":"FMD-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180601aJKsa32_1.cdf"}
},
{
"Subject ID":"Serum",
"Sample ID":"S-FMD020_017",
"Factors":{"treatment":"FMD-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180601aJKsa33_1.cdf"}
},
{
"Subject ID":"Serum",
"Sample ID":"S-FMD021_018",
"Factors":{"treatment":"FMD-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180601aJKsa34_1.cdf"}
},
{
"Subject ID":"Serum",
"Sample ID":"S-FMD022_019",
"Factors":{"treatment":"FMD-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180601aJKsa35_1.cdf"}
},
{
"Subject ID":"Serum",
"Sample ID":"S-FMD023_020",
"Factors":{"treatment":"FMD-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180601aJKsa36_1.cdf"}
},
{
"Subject ID":"Serum",
"Sample ID":"S-FMD024_021",
"Factors":{"treatment":"FMD-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180601aJKsa37_1.cdf"}
},
{
"Subject ID":"Serum",
"Sample ID":"S-FMD025_022",
"Factors":{"treatment":"FMD-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180601aJKsa38_1.cdf"}
},
{
"Subject ID":"Serum",
"Sample ID":"S-FMD026_023",
"Factors":{"treatment":"FMD-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180601aJKsa39_1.cdf"}
},
{
"Subject ID":"Serum",
"Sample ID":"S-FMD027_024",
"Factors":{"treatment":"FMD-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180601aJKsa40_1.cdf"}
},
{
"Subject ID":"Serum",
"Sample ID":"S-FMD028_025",
"Factors":{"treatment":"FMD-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180601aJKsa41_1.cdf"}
},
{
"Subject ID":"Serum",
"Sample ID":"S-FMD029_026",
"Factors":{"treatment":"FMD-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180601aJKsa42_1.cdf"}
},
{
"Subject ID":"Serum",
"Sample ID":"S-FMD030_027",
"Factors":{"treatment":"FMD-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180601aJKsa43_1.cdf"}
},
{
"Subject ID":"Serum",
"Sample ID":"S-FMD031_028",
"Factors":{"treatment":"FMD-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180601aJKsa44_1.cdf"}
},
{
"Subject ID":"Serum",
"Sample ID":"S-FMD032_029",
"Factors":{"treatment":"FMD-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180601aJKsa45_1.cdf"}
},
{
"Subject ID":"Serum",
"Sample ID":"S-FMD033_030",
"Factors":{"treatment":"FMD-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180601aJKsa46_1.cdf"}
},
{
"Subject ID":"Serum",
"Sample ID":"S-FMD034_031",
"Factors":{"treatment":"FMD-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180601aJKsa47_1.cdf"}
},
{
"Subject ID":"Serum",
"Sample ID":"S-FMD035_032",
"Factors":{"treatment":"FMD-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180601aJKsa48_1.cdf"}
},
{
"Subject ID":"Serum",
"Sample ID":"S-FMD036_033",
"Factors":{"treatment":"FMD-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180601aJKsa49_1.cdf"}
},
{
"Subject ID":"serum",
"Sample ID":"S-FMD094_134",
"Factors":{"treatment":"HCR-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180601aJKsa50_1.cdf"}
},
{
"Subject ID":"serum",
"Sample ID":"S-FMD095_135",
"Factors":{"treatment":"HCR-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180602aJKsa01_1.cdf"}
},
{
"Subject ID":"serum",
"Sample ID":"S-FMD098_136",
"Factors":{"treatment":"HCR-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180602aJKsa02_1.cdf"}
},
{
"Subject ID":"serum",
"Sample ID":"S-FMD099_137",
"Factors":{"treatment":"HCR-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180602aJKsa03_1.cdf"}
},
{
"Subject ID":"serum",
"Sample ID":"S-FMD100_138",
"Factors":{"treatment":"HCR-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180602aJKsa04_1.cdf"}
},
{
"Subject ID":"serum",
"Sample ID":"S-FMD101_139",
"Factors":{"treatment":"HCR-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180602aJKsa05_1.cdf"}
},
{
"Subject ID":"serum",
"Sample ID":"S-FMD102_140",
"Factors":{"treatment":"HCR-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180602aJKsa06_1.cdf"}
},
{
"Subject ID":"serum",
"Sample ID":"S-FMD103_141",
"Factors":{"treatment":"HCR-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180602aJKsa07_2.cdf"}
},
{
"Subject ID":"serum",
"Sample ID":"S-FMD104_142",
"Factors":{"treatment":"HCR-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180602aJKsa08_1.cdf"}
},
{
"Subject ID":"serum",
"Sample ID":"S-FMD105_143",
"Factors":{"treatment":"HCR-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180602aJKsa09_1.cdf"}
},
{
"Subject ID":"serum",
"Sample ID":"S-FMD106_144",
"Factors":{"treatment":"HCR-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180602aJKsa10_1.cdf"}
},
{
"Subject ID":"serum",
"Sample ID":"S-FMD107_145",
"Factors":{"treatment":"HCR-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180602aJKsa11_1.cdf"}
},
{
"Subject ID":"serum",
"Sample ID":"S-FMD108_146",
"Factors":{"treatment":"HCR-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180602aJKsa12_1.cdf"}
},
{
"Subject ID":"serum",
"Sample ID":"S-FMD109_147",
"Factors":{"treatment":"HCR-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180602aJKsa13_2.cdf"}
},
{
"Subject ID":"serum",
"Sample ID":"S-FMD110_148",
"Factors":{"treatment":"HCR-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180602aJKsa14_1.cdf"}
},
{
"Subject ID":"serum",
"Sample ID":"S-FMD111_149",
"Factors":{"treatment":"HCR-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180602aJKsa15_1.cdf"}
},
{
"Subject ID":"serum",
"Sample ID":"S-FMD077_120",
"Factors":{"treatment":"HFMD-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180602aJKsa16_1.cdf"}
},
{
"Subject ID":"serum",
"Sample ID":"S-FMD078_121",
"Factors":{"treatment":"HFMD-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180602aJKsa17_1.cdf"}
},
{
"Subject ID":"serum",
"Sample ID":"S-FMD079_122",
"Factors":{"treatment":"HFMD-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180602aJKsa18_1.cdf"}
},
{
"Subject ID":"serum",
"Sample ID":"S-FMD081_123",
"Factors":{"treatment":"HFMD-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180602aJKsa19_1.cdf"}
},
{
"Subject ID":"serum",
"Sample ID":"S-FMD083_124",
"Factors":{"treatment":"HFMD-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180602aJKsa20_1.cdf"}
},
{
"Subject ID":"serum",
"Sample ID":"S-FMD084_125",
"Factors":{"treatment":"HFMD-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180602aJKsa21_1.cdf"}
},
{
"Subject ID":"serum",
"Sample ID":"S-FMD085_126",
"Factors":{"treatment":"HFMD-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180602aJKsa22_1.cdf"}
},
{
"Subject ID":"serum",
"Sample ID":"S-FMD086_127",
"Factors":{"treatment":"HFMD-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180602aJKsa23_1.cdf"}
},
{
"Subject ID":"serum",
"Sample ID":"S-FMD088_128",
"Factors":{"treatment":"HFMD-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180602aJKsa24_1.cdf"}
},
{
"Subject ID":"serum",
"Sample ID":"S-FMD089_129",
"Factors":{"treatment":"HFMD-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180602aJKsa25_1.cdf"}
},
{
"Subject ID":"serum",
"Sample ID":"S-FMD090_130",
"Factors":{"treatment":"HFMD-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180602aJKsa26_1.cdf"}
},
{
"Subject ID":"serum",
"Sample ID":"S-FMD091_131",
"Factors":{"treatment":"HFMD-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180602aJKsa27_1.cdf"}
},
{
"Subject ID":"serum",
"Sample ID":"S-FMD092_132",
"Factors":{"treatment":"HFMD-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180602aJKsa28_1.cdf"}
},
{
"Subject ID":"serum",
"Sample ID":"S-FMD093_133",
"Factors":{"treatment":"HFMD-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180602aJKsa29_1.cdf"}
},
{
"Subject ID":"Serum",
"Sample ID":"S-FMD038_034",
"Factors":{"treatment":"iFMD-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180602aJKsa30_1.cdf"}
},
{
"Subject ID":"Serum",
"Sample ID":"S-FMD039_035",
"Factors":{"treatment":"iFMD-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180602aJKsa31_1.cdf"}
},
{
"Subject ID":"Serum",
"Sample ID":"S-FMD040_036",
"Factors":{"treatment":"iFMD-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180602aJKsa32_1.cdf"}
},
{
"Subject ID":"Serum",
"Sample ID":"S-FMD041_037",
"Factors":{"treatment":"iFMD-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180602aJKsa33_1.cdf"}
},
{
"Subject ID":"Serum",
"Sample ID":"S-FMD042_038",
"Factors":{"treatment":"iFMD-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180602aJKsa34_1.cdf"}
},
{
"Subject ID":"Serum",
"Sample ID":"S-FMD043_039",
"Factors":{"treatment":"iFMD-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180602aJKsa35_1.cdf"}
},
{
"Subject ID":"Serum",
"Sample ID":"S-FMD044_040",
"Factors":{"treatment":"iFMD-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180602aJKsa36_1.cdf"}
},
{
"Subject ID":"Serum",
"Sample ID":"S-FMD045_041",
"Factors":{"treatment":"iFMD-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180602aJKsa37_1.cdf"}
},
{
"Subject ID":"Serum",
"Sample ID":"S-FMD046_042",
"Factors":{"treatment":"iFMD-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180602aJKsa38_1.cdf"}
},
{
"Subject ID":"Serum",
"Sample ID":"S-FMD047_043",
"Factors":{"treatment":"iFMD-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180602aJKsa39_1.cdf"}
},
{
"Subject ID":"Serum",
"Sample ID":"S-FMD048_044",
"Factors":{"treatment":"iFMD-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180602aJKsa40_1.cdf"}
},
{
"Subject ID":"Serum",
"Sample ID":"S-FMD049_045",
"Factors":{"treatment":"iFMD-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180602aJKsa41_1.cdf"}
},
{
"Subject ID":"Serum",
"Sample ID":"S-FMD050_046",
"Factors":{"treatment":"iFMD-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180602aJKsa42_1.cdf"}
},
{
"Subject ID":"Serum",
"Sample ID":"S-FMD051_047",
"Factors":{"treatment":"iFMD-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180602aJKsa43_1.cdf"}
},
{
"Subject ID":"Serum",
"Sample ID":"S-FMD052_048",
"Factors":{"treatment":"iFMD-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180602aJKsa44_1.cdf"}
},
{
"Subject ID":"Serum",
"Sample ID":"S-FMD054_049",
"Factors":{"treatment":"iFMD-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180602aJKsa45_1.cdf"}
},
{
"Subject ID":"Serum",
"Sample ID":"S-FMD055_050",
"Factors":{"treatment":"iFMD-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180602aJKsa46_1.cdf"}
},
{
"Subject ID":"Serum",
"Sample ID":"S-FMD056_051",
"Factors":{"treatment":"iFMD-Serum"},
"Additional sample data":{"RAW_FILE_NAME":"180602aJKsa47_1.cdf"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Mice were euthanized and serum was collected thereafter. Liver was perfused in PBS, frozen in LN2 and pulverized thereafter.","SAMPLE_TYPE":"Blood (serum)"},

"TREATMENT":{"TREATMENT_SUMMARY":"6, 5-8 All mice were identified with FMD followed by a 3 digit number SD - day SD - night FMD - fed iFMD - fed FMD - fast iFMD - fast FMD - refed iFMD - refed"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Extraction of Mammalian Tissue Samples: Liver 1. References: Fiehn O, Kind T (2006) Metabolite profiling in blood plasma. In: Metabolomics: Methods and Protocols. Weckwerth W (ed.), Humana Press, Totowa NJ (in press) 2.Starting material: Liver sample: weigh 4mg per sample into 2mL Eppendorf tubes. 3. Equipment: Centrifuge (Eppendorf 5415 D) Calibrated pipettes 1-200?l and 100-1000?l Eppendorf tubes 2mL, clear (Cat. No. 022363204) Centrifuge tubes 50mL, polypropylene Eppendorff Tabletop Centrifuge (Proteomics core Lab.) ThermoElectron Neslab RTE 740 cooling bath at –20°C MiniVortexer (VWR) Orbital Mixing Chilling/Heating Plate (Torrey Pines Scientific Instruments) Speed vacuum concentration system (Labconco Centrivap cold trap) Turex mini homogenizer 4. Chemicals Acetonitrile, LCMS grade (JT Baker; Cat. No.9829-02) Isopropanol, HPLC grade (JT Baker; Cat. No. 9095-02) Methanol Acetone Crushed ice 18 M? pure water (Millipore) Nitrogen line with pipette tip pH paper 5-10 (EMD Chem. Inc.) 5. Procedure Preparation of extraction mix and material before experiment: Switch on bath to pre-cool at –20°C (±2°C validity temperature range) Check pH of acetonitrile and isopropanol (pH7) using wetted pH paper Make the extraction solution by mixing acetonitrile, isopropanol and water in proportions 3 : 3 : 2 De-gas the extraction solution for 5 min with nitrogen. Make sure that the nitrogen line was flushed out of air before using it for degassing the extraction solvent solution Sample Preparation Weigh 4mg tissue sample in to a 2mL Eppendorf tube. Add 1mL extraction solvent to the tissue sample and homogenize for 45 seconds ensuring that sample resembles a powder. In between samples, clean the homogenizer in solutions of methanol, acetone, water, and the extraction solvent in the order listed. Vortex samples for 10 seconds, then 5 minutes on 4°C shaker. Centrifuge the samples for 2 minutes at 14,000 rcf. Aliquot 500µL supernatant for analysis, and 500µL for a backup. Store backup aliquots in the -20°C freezer. Evaporate one 500µl analysis aliquot in the Labconco Centrivap cold trap concentrator to complete dryness (typically overnight). The dried aliquot is then re-suspended with 500?l 50% acetonitrile (degassed as given) Centrifuge for 2 minutes at 14,000 rcf using the centrifuge Eppendorf 5415. Remove supernatant to a new Eppendorf tube. Evaporate the supernatant to dryness in the the Labconco Centrivap cold trap concentrator. Submit to derivatization. The residue should contain membrane lipids because these are supposedly not soluble enough to be found in the 50% acetonitrile solution. Therefore, this ‘membrane residue’ is now taken for membrane lipidomic fingerprinting using the nanomate LTQ ion trap mass spectrometer. Likely, a good solvent to redissolve the membrane lipids is e.g. 75% isopropanol (degassed as given above). If the ‘analysis’ aliquot is to be used for semi lipophilic compounds such as tyrosine pathway intermediates (incl. dopamine, serotonine etc, i.e. polar aromatic compounds), then these are supposedly to be found together with the ‘GCTOF’ aliquot. We can assume that this mixture is still too complex for Agilent chipLCMS. Therefore, in order to develop and validate target analysis for such aromatic compounds, we should use some sort of Solid Phase purification. We re-suspend the dried ‘GCTOF’ aliquot in 300 l water (degassed as before) to take out sugars, aliphatic amino acids, hydroxyl acids and similar logP compounds. The residue should contain our target aromatics .We could also try to adjust pH by using low concentration acetate or phosphate buffer. The residue could then be taken up in 50% acetonitrile and used for GCTOF and Agilent chipMS experiments. The other aliquot should be checked how much of our target compounds would actually be found in the ‘sugar’ fraction. 6. Problems To prevent contamination disposable material is used. Control pH from extraction mix. 7. Quality assurance For each sequence of sample extractions, perform one blank negative control extraction by applying the total procedure (i.e. all materials and plastic ware) without biological sample. 8. Disposal of waste Collect all chemicals in appropriate bottles and follow the disposal rules. Sample preparation of blood plasma or serum samples for GCTOF analysis Purpose: This SOP describes sample extraction and sample preparation for primary metabolism profiling by gas chromatography/time-of-flight mass spectrometry (GCTOF). References: Fiehn O, Kind T (2006) Metabolite profiling in blood plasma. In: Metabolomics: Methods and Protocols. Weckwerth W (ed.), Humana Press, Totowa NJ. Fiehn, O. Metabolomics by gas chromatography - mass spectrometry: combined targeted and untargeted profiling. 2016. Curr. Protoc. Mol. Biol. 114:30.4.1-30.4.32. doi: 10.1002/0471142727.mb3004s114. Starting material: Plasma/serum: 30 µL sample volume or aliquot Equipment: Centrifuge Eppendorf 5415 D Calibrated pipettes 1-200µL and 100-1000µL Multi-Tube Vortexer (VWR VX-2500) Orbital Mixing Chilling/Heating Plate (Torrey Pines Scientific Instruments) Speed vacuum concentration system (Labconco Centrivap cold trap) Nitrogen line with Pasteur pipette Chemicals and consumables: Product Manufacturer & Part Number Eppendorf tubes 1.5 mL, uncolored Eppendorf 022363204 Crushed ice UC Davis Water, LC/MS Grade Fisher Optima W6-4 Acetonitrile, LC/MS Grade Fisher Optima A955-4 Isopropanol, LC/MS Grade Fisher A461-4 pH paper 5-10 Millipore Sigma 1095330001 Bioreclamation human plasma (disodium EDTA) Bioreclamation HMPLEDTA Sample Preparation: Preparation of extraction solvent For 1 L of extraction solvent, combine 375 mL of acetonitrile, 375 mL of isopropanol, and 250 mL water in a 1 L bottle conditioned with the aforementioned chemicals. If a different total volume of extraction solvent is needed, simply mix acetonitrile, isopropanol, and water in volumes in proportion 3:3:2. Purge the extraction solution mix for 5 min with nitrogen with small bubbles. Make sure that the nitrogen line is flushed out of air before using it for degassing the extraction solvent solution. Store at -20°C until use. Note: if solvent freezes, sonicate until thawed and mix before use. Extraction Thaw raw samples at room temperature (or in the refrigerator at 4?C) and vortex 10 sec at low speed to homogenize. Aliquot 30 ?L of plasma sample into a 1.5 mL Eppendorf tube. Keep all samples on ice. Add 1 mL 3:3:2 (v/v/v) ACN:IPA:H2O extraction solvent (prechilled in a -20°C freezer). Vortex the sample for 10 sec. Shake for 5 min at 4°C using the Orbital Mixing Chilling/Heating Plate. Continue to keep all extracted samples on ice. Centrifuge samples for 2 min at 14000 rcf. Aliquot two 450 ?L portions of the supernatant into 1.5 mL Eppendorf tubes (one for analysis and one as a backup sample). Transfer 100 ?L of the remaining supernatant from each sample to a 2, 15, or 50 mL tube for pools, depending on number of samples in the study. Evaporate one 450 ?L aliquot of the sample in the Labconco Centrivap cold trap concentrator to complete dryness. Proceed with cleanup or store tubes at -20°C until cleanup. Pooling Transfer multiple 475 µL aliquots of pooled samples to 1.5 mL Eppendorf tubes, one aliquot for every 10 samples in the study. If there is still pool remaining, prepare additional aliquots for backup. Centrifuge pool samples for 2 min at 14000 rcf. Remove 450 µL supernatant to new 1.5 mL Eppendorf tube. Evaporate to complete dryness in the Labconco Centrivap cold trap concentrator. Proceed with cleanup or store tubes at -20°C until cleanup. Cleanup Resuspend the dried aliquot with 500 ?L 50:50 (v/v) ACN:H2O (degassed as given above) and vortex for about 10 sec. Centrifuge for 2 min at 14000 rcf. Remove 475 ?L supernatant to a new 1.5 mL Eppendorf tube. Evaporate the transferred supernatant to complete dryness in the Labconco Centrivap cold trap concentrator. Submit to derivatization (see SOP “Derivatization of GC Samples & Standards”) or store at -20°C until ready for analysis. Quality assurance For every 50 samples, perform one method blank negative control extraction by applying the total procedure (i.e. all materials and plastic ware) without biological sample. If no combined pool was made from the extracted samples, use one commercial plasma/serum pool sample per 10 authentic subject samples as control instead. Disposal of waste Collect all chemicals in appropriate bottles and follow the disposal rules. Collect residual plasma/serum samples in specifically designed red ‘biohazard’ waste bags."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"Primary metabolism by GCTOF","CHROMATOGRAPHY_TYPE":"GC","INSTRUMENT_NAME":"LECO Pegasus IV GC-time of flight mass spectrometers","COLUMN_NAME":"Rtx-5Sil MS column"},

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

"MS":{"INSTRUMENT_NAME":"Leco Pegasus IV TOF","INSTRUMENT_TYPE":"GC-TOF","MS_TYPE":"EI","ION_MODE":"UNSPECIFIED","MS_COMMENTS":"GC-TOF Method: Instruments: Gerstel CIS4 –with dual MPS Injector/ Agilent 6890 GC- Pegasus III TOF MS Injector conditions: Agilent 6890 GC is equipped with a Gerstel automatic liner exchange system (ALEX) that includes a multipurpose sample (MPS2) dual rail, and a Gerstel CIS cold injection system (Gerstel, Muehlheim, Germany) with temperature program as follows: 50°C to 275°C final temperature at a rate of 12 °C/s and hold for 3 minutes. Injection volume is 0.5 ?l with 10 ?l/s injection speed on a splitless injector with purge time of 25 seconds. Liner (Gerstel #011711-010-00) is changed after every 10 samples, (using the Maestro1 Gerstel software vs. 1.1.4.18). Before and after each injection, the 10 ?l injection syringe is washed three times with 10 ?l ethyl acetate. Gas Chromatography conditions: A 30 m long, 0.25 mm i.d. Rtx-5Sil MS column (0.25 ?m 95% dimethyl 5% diphenyl polysiloxane film) with additional 10 m integrated guard column is used (Restek, Bellefonte PA). 99.9999% pure Helium with built-in purifier (Airgas, Radnor PA) is set at constant flow of 1 ml/min. The oven temperature is held constant at 50°C for 1 min and then ramped at 20°C/min to 330°C at which it is held constant for 5 min. Mass spectrometer settings: A Leco Pegasus IV time of flight mass spectrometer is controlled by the Leco ChromaTOF software vs. 2.32 (St. Joseph, MI). The transfer line temperature between gas chromatograph and mass spectrometer is set to 280°C. Electron impact ionization at 70V is employed with an ion source temperature of 250°C. Acquisition rate is 17 spectra/second, with a scan mass range of 85-500 Da."},

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

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}

}