{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001368","ANALYSIS_ID":"AN002282","VERSION":"1","CREATED_ON":"April 28, 2020, 4:26 pm"},

"PROJECT":{"PROJECT_TITLE":"Malnutrition Gut microbes and Liver Metabolomics","PROJECT_SUMMARY":"Examining the role of malnutrition and gut microbes on fatty liver using the MAL-BG murine model. RP-UPLC-FTMS and HILIC-FTMS were conducted on murine livers prior and following dietary intervention. This submission contains intervention raw data.","INSTITUTE":"University of British Columbia","DEPARTMENT":"Microbiology and Immunology","LABORATORY":"Finlay","LAST_NAME":"Bauer","FIRST_NAME":"Kylynda","ADDRESS":"#301 – 2185 East Mall, University of British Columbia Vancouver, British Columbia Canada, V6T 1Z4","EMAIL":"kcbauer@msl.ubc.ca","PHONE":"(604) 822-2210","PROJECT_COMMENTS":"Intervention","CONTRIBUTORS":"B. Brett Finlay"},

"STUDY":{"STUDY_TITLE":"Malnutrition and Liver Metabolomics Intervention (part-II)","STUDY_SUMMARY":"RP-UPLC-FTMS (+/- ion detection) and HILIC-FTMS (+/- ion detection) were conducted on murine livers from healthy (CON) and malnourished model (MBG) mice. To examine the impact of dietary intervention the same untargeted metabolomics was conducted following an intervention treatment (CON, MBG, C-MBG, MBG-R groups). C-MBG = healthy to malnourished, MBG-R = malnourished model reversed on a healthy diet.","INSTITUTE":"University of British Columbia","DEPARTMENT":"Microbiology and Immunology","LABORATORY":"B. Brett Finlay","LAST_NAME":"Bauer","FIRST_NAME":"Kylynda","ADDRESS":"Michael Smith Laboratories, #301 – 2185 East Mall, University of British Columbia Vancouver, British Columbia Canada, V6T 1Z4","EMAIL":"kcbauer@msl.ubc.ca","PHONE":"(604) 822-2210","NUM_GROUPS":"4","TOTAL_SUBJECTS":"32","NUM_FEMALES":"32"},

"SUBJECT":{"SUBJECT_TYPE":"Mammal","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090","GENOTYPE_STRAIN":"C57BL/6J","AGE_OR_AGE_RANGE":"~11 weeks (Intervention)","GENDER":"Female","ANIMAL_ANIMAL_SUPPLIER":"Jackson Laboratories"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"CON_1",
"Factors":{"Study":"Intervention","Treatment":"CON","Start Diet":"Healthy","Final Diet":"Healthy"}
},
{
"Subject ID":"-",
"Sample ID":"CON_2",
"Factors":{"Study":"Intervention","Treatment":"CON","Start Diet":"Healthy","Final Diet":"Healthy"}
},
{
"Subject ID":"-",
"Sample ID":"CON_3",
"Factors":{"Study":"Intervention","Treatment":"CON","Start Diet":"Healthy","Final Diet":"Healthy"}
},
{
"Subject ID":"-",
"Sample ID":"CON_4",
"Factors":{"Study":"Intervention","Treatment":"CON","Start Diet":"Healthy","Final Diet":"Healthy"}
},
{
"Subject ID":"-",
"Sample ID":"CON_5",
"Factors":{"Study":"Intervention","Treatment":"CON","Start Diet":"Healthy","Final Diet":"Healthy"}
},
{
"Subject ID":"-",
"Sample ID":"CON_6",
"Factors":{"Study":"Intervention","Treatment":"CON","Start Diet":"Healthy","Final Diet":"Healthy"}
},
{
"Subject ID":"-",
"Sample ID":"CON_7",
"Factors":{"Study":"Intervention","Treatment":"CON","Start Diet":"Healthy","Final Diet":"Healthy"}
},
{
"Subject ID":"-",
"Sample ID":"CON_8",
"Factors":{"Study":"Intervention","Treatment":"CON","Start Diet":"Healthy","Final Diet":"Healthy"}
},
{
"Subject ID":"-",
"Sample ID":"C-MBG_1",
"Factors":{"Study":"Intervention","Treatment":"C-MBG","Start Diet":"Healthy","Final Diet":"Malnourished"}
},
{
"Subject ID":"-",
"Sample ID":"C-MBG_2",
"Factors":{"Study":"Intervention","Treatment":"C-MBG","Start Diet":"Healthy","Final Diet":"Malnourished"}
},
{
"Subject ID":"-",
"Sample ID":"C-MBG_3",
"Factors":{"Study":"Intervention","Treatment":"C-MBG","Start Diet":"Healthy","Final Diet":"Malnourished"}
},
{
"Subject ID":"-",
"Sample ID":"C-MBG_4",
"Factors":{"Study":"Intervention","Treatment":"C-MBG","Start Diet":"Healthy","Final Diet":"Malnourished"}
},
{
"Subject ID":"-",
"Sample ID":"C-MBG_5",
"Factors":{"Study":"Intervention","Treatment":"C-MBG","Start Diet":"Healthy","Final Diet":"Malnourished"}
},
{
"Subject ID":"-",
"Sample ID":"C-MBG_6",
"Factors":{"Study":"Intervention","Treatment":"C-MBG","Start Diet":"Healthy","Final Diet":"Malnourished"}
},
{
"Subject ID":"-",
"Sample ID":"C-MBG_7",
"Factors":{"Study":"Intervention","Treatment":"C-MBG","Start Diet":"Healthy","Final Diet":"Malnourished"}
},
{
"Subject ID":"-",
"Sample ID":"C-MBG_8",
"Factors":{"Study":"Intervention","Treatment":"C-MBG","Start Diet":"Healthy","Final Diet":"Malnourished"}
},
{
"Subject ID":"-",
"Sample ID":"MBG_1",
"Factors":{"Study":"Intervention","Treatment":"MBG","Start Diet":"Malnourished","Final Diet":"Malnourished"}
},
{
"Subject ID":"-",
"Sample ID":"MBG_2",
"Factors":{"Study":"Intervention","Treatment":"MBG","Start Diet":"Malnourished","Final Diet":"Malnourished"}
},
{
"Subject ID":"-",
"Sample ID":"MBG_3",
"Factors":{"Study":"Intervention","Treatment":"MBG","Start Diet":"Malnourished","Final Diet":"Malnourished"}
},
{
"Subject ID":"-",
"Sample ID":"MBG_4",
"Factors":{"Study":"Intervention","Treatment":"MBG","Start Diet":"Malnourished","Final Diet":"Malnourished"}
},
{
"Subject ID":"-",
"Sample ID":"MBG_5",
"Factors":{"Study":"Intervention","Treatment":"MBG","Start Diet":"Malnourished","Final Diet":"Malnourished"}
},
{
"Subject ID":"-",
"Sample ID":"MBG_6",
"Factors":{"Study":"Intervention","Treatment":"MBG","Start Diet":"Malnourished","Final Diet":"Malnourished"}
},
{
"Subject ID":"-",
"Sample ID":"MBG_7",
"Factors":{"Study":"Intervention","Treatment":"MBG","Start Diet":"Malnourished","Final Diet":"Malnourished"}
},
{
"Subject ID":"-",
"Sample ID":"MBG_8",
"Factors":{"Study":"Intervention","Treatment":"MBG","Start Diet":"Malnourished","Final Diet":"Malnourished"}
},
{
"Subject ID":"-",
"Sample ID":"MBG-R_1",
"Factors":{"Study":"Intervention","Treatment":"MBG-R","Start Diet":"Malnourished","Final Diet":"Healthy"}
},
{
"Subject ID":"-",
"Sample ID":"MBG-R_2",
"Factors":{"Study":"Intervention","Treatment":"MBG-R","Start Diet":"Malnourished","Final Diet":"Healthy"}
},
{
"Subject ID":"-",
"Sample ID":"MBG-R_3",
"Factors":{"Study":"Intervention","Treatment":"MBG-R","Start Diet":"Malnourished","Final Diet":"Healthy"}
},
{
"Subject ID":"-",
"Sample ID":"MBG-R_4",
"Factors":{"Study":"Intervention","Treatment":"MBG-R","Start Diet":"Malnourished","Final Diet":"Healthy"}
},
{
"Subject ID":"-",
"Sample ID":"MBG-R_5",
"Factors":{"Study":"Intervention","Treatment":"MBG-R","Start Diet":"Malnourished","Final Diet":"Healthy"}
},
{
"Subject ID":"-",
"Sample ID":"MBG-R_6",
"Factors":{"Study":"Intervention","Treatment":"MBG-R","Start Diet":"Malnourished","Final Diet":"Healthy"}
},
{
"Subject ID":"-",
"Sample ID":"MBG-R_7",
"Factors":{"Study":"Intervention","Treatment":"MBG-R","Start Diet":"Malnourished","Final Diet":"Healthy"}
},
{
"Subject ID":"-",
"Sample ID":"MBG-R_8",
"Factors":{"Study":"Intervention","Treatment":"MBG-R","Start Diet":"Malnourished","Final Diet":"Healthy"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Following sacrifice, murine liver lobes were isolated and stored at -70/80 C prior to untargeted metabolomics.","SAMPLE_TYPE":"Liver"},

"TREATMENT":{"TREATMENT_SUMMARY":"CON = control mice placed on a healthy (standard mouse chow) for 2 months, MBG = malnourished model for 2 months, C-MBG = control diet one month and then malnourished model for one month, MBG-R = malnourished model for one month and then reversed on the healthy diet"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"RP-UPLC-FTMS: Individual mouse liver samples were mixed with water, 5 μL per mg of the tissue, and two 4-mm metal balls were added to an Eppendorf tube. The tissue was homogenized on a MM 400 mill mixer at a vibrating frequency of 30 Hz for 1 min twice. After 5-s spin-down, a mixture of methanol-chloroform (4:1) was added, at 25 μL per mg tissue, to each tube. The sample was homogenized again for metabolite extraction using the same setup for 1 min twice, followed by sonication in an ice-water bath for 5 min. The tube was centrifuged at 15,000 rpm and at 10 0C for 20 min. The clear supernatant was transferred to a 1.5-mL Eppendorf tube. A 60-μL aliquot from each sample was dried down inside the same nitrogen evaporator and the residue was reconstituted in 40 μL of 80% methanol. 10 μL was injected for reversed-phase RP-UPLC-FTMS. HILIC-FTMS: Individual sample supernatants were mixed with 120 μL of water, 180 μL of methanol and 195 μL of chloroform. The mixture was vortex mixed at 3000 rpm for 30 s before centrifugal clarification. 300 μL of the upper, aqueous phase was precisely taken out and transferred to a “V”-shape LC injection microvial and was dried down under a gentle nitrogen gas flow in the nitrogen evaporator. The residue was reconstituted in 50 μL of 80% acetonitrile. 10 μL was injected for HILIC-FTMS. *See Methods"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"HILIC","INSTRUMENT_NAME":"Thermo Dionex Ultimate 3000","COLUMN_NAME":"Waters HILIC column (2.1 x 100 mm, 1.8 µm)"},

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

"MS":{"INSTRUMENT_NAME":"Thermo LTQ-Orbitrap Velos Pro","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","ION_MODE":"NEGATIVE","MS_COMMENTS":"The MS instrument was run in the survey scan mode with FTMS detection at a mass resolution of 60,000 FWHM at m/z 400. Two HILIC-FTMS datasets were acquired for each sample, one with positive-ion detection and the other with negative-ion detection. The mass scan range was m/z 80 to 800 (from publication methods).","MS_RESULTS_FILE":"ST001368_AN002282_Results.txt UNITS:abundance Has m/z:Yes Has RT:Yes RT units:Minutes"}

}