{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001367","ANALYSIS_ID":"AN002275","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 prior 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":"Pre-Intervention","CONTRIBUTORS":"B. Brett Finlay"},

"STUDY":{"STUDY_TITLE":"Malnutrition and Liver Metabolomics Pre-Intervention (part-I)","STUDY_SUMMARY":"RP-UPLC-FTMS (+/- ion detection) and HILIC-FTMS (+/- ion detection) were conducted on murine livers from healthy (CON) and malnourished (MAL) mice. To examine the impact of gut microbes and malnutrition, data was also collected from a third group (MBG).","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":"3","TOTAL_SUBJECTS":"12","NUM_FEMALES":"12"},

"SUBJECT":{"SUBJECT_TYPE":"Mammal","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090","GENOTYPE_STRAIN":"C57BL/6J","AGE_OR_AGE_RANGE":"~7 weeks (Pre-intervention)","GENDER":"Female","ANIMAL_ANIMAL_SUPPLIER":"Jackson Laboratories"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"CONA_1",
"Factors":{"Treatment":"CON","Start Diet":"Healthy","Final Diet":"Healthy"},
"Additional sample data":{"Study":"Pre-Intervention"}
},
{
"Subject ID":"-",
"Sample ID":"CONA_2",
"Factors":{"Treatment":"CON","Start Diet":"Healthy","Final Diet":"Healthy"},
"Additional sample data":{"Study":"Pre-Intervention"}
},
{
"Subject ID":"-",
"Sample ID":"CONA_3",
"Factors":{"Treatment":"CON","Start Diet":"Healthy","Final Diet":"Healthy"},
"Additional sample data":{"Study":"Pre-Intervention"}
},
{
"Subject ID":"-",
"Sample ID":"CONA_4",
"Factors":{"Treatment":"CON","Start Diet":"Healthy","Final Diet":"Healthy"},
"Additional sample data":{"Study":"Pre-Intervention"}
},
{
"Subject ID":"-",
"Sample ID":"MALA_1",
"Factors":{"Treatment":"MAL","Start Diet":"Malnourished","Final Diet":"Malnourished"},
"Additional sample data":{"Study":"Pre-Intervention"}
},
{
"Subject ID":"-",
"Sample ID":"MALA_2",
"Factors":{"Treatment":"MAL","Start Diet":"Malnourished","Final Diet":"Malnourished"},
"Additional sample data":{"Study":"Pre-Intervention"}
},
{
"Subject ID":"-",
"Sample ID":"MALA_3",
"Factors":{"Treatment":"MAL","Start Diet":"Malnourished","Final Diet":"Malnourished"},
"Additional sample data":{"Study":"Pre-Intervention"}
},
{
"Subject ID":"-",
"Sample ID":"MALA_4",
"Factors":{"Treatment":"MAL","Start Diet":"Malnourished","Final Diet":"Malnourished"},
"Additional sample data":{"Study":"Pre-Intervention"}
},
{
"Subject ID":"-",
"Sample ID":"MBGA_1",
"Factors":{"Treatment":"MBG","Start Diet":"Malnourished","Final Diet":"Malnourished"},
"Additional sample data":{"Study":"Pre-Intervention"}
},
{
"Subject ID":"-",
"Sample ID":"MBGA_2",
"Factors":{"Treatment":"MBG","Start Diet":"Malnourished","Final Diet":"Malnourished"},
"Additional sample data":{"Study":"Pre-Intervention"}
},
{
"Subject ID":"-",
"Sample ID":"MBGA_3",
"Factors":{"Treatment":"MBG","Start Diet":"Malnourished","Final Diet":"Malnourished"},
"Additional sample data":{"Study":"Pre-Intervention"}
},
{
"Subject ID":"-",
"Sample ID":"MBGA_4",
"Factors":{"Treatment":"MBG","Start Diet":"Malnourished","Final Diet":"Malnourished"},
"Additional sample data":{"Study":"Pre-Intervention"}
}
],
"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), MAL = mice placed on an isocaloric malnourished diet (protein/fat deficient), MBG = MAL mice with repeated exposure to fecal microbes, mice were placed on the respective treatments for one month following weaning."},

"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":"Reversed phase","INSTRUMENT_NAME":"Thermo Dionex Ultimate 3000","COLUMN_NAME":"Waters BEH C8 (2.1 x 50 mm, 1.7 µm)"},

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

"MS":{"INSTRUMENT_NAME":"Thermo LTQ-Orbitrap Velos Pro","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","ION_MODE":"POSITIVE","MS_COMMENTS":"For relative quantitation, 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. The mass scan range was m/z 80 to 1800, with a reference lock-mass for real-time calibration. Two UPLC-FTMS datasets were acquired for each sample, one with positive-ion detection and the other with negative-ion detection. LC-MS/MS data was also acquired from each sample set with collision induced dissociation (CID) at different levels of normalized collision energy (from publication methods).","MS_RESULTS_FILE":"ST001367_AN002275_Results.txt UNITS:Abundance Has m/z:Yes Has RT:Yes RT units:Minutes"}

}