{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001366","ANALYSIS_ID":"AN002274","VERSION":"1","CREATED_ON":"April 27, 2020, 10:54 am"},

"PROJECT":{"PROJECT_TITLE":"Malnutrition, Microbes, and Hippocampal Metabolomics","PROJECT_SUMMARY":"Examining the role of malnutrition and gut microbes on CNS function using the MAL-BG murine model. RP-UPLC-FTMS was conducted on murine hippocampal tissue.","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","CONTRIBUTORS":"B. Brett Finlay"},

"STUDY":{"STUDY_TITLE":"Malnutrition and Liver Metabolomics","STUDY_SUMMARY":"RP-UPLC-FTMS (+/- ion detection) were conducted on hippocampi from healthy (CON) and malnourished (MAL) mice, and MAL-BG (malnutrition plus E.coli/Bacteroidales exposure) mice.","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":"15","NUM_FEMALES":"15"},

"SUBJECT":{"SUBJECT_TYPE":"Mammal","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090","GENOTYPE_STRAIN":"C57BL/6J","AGE_OR_AGE_RANGE":"7 weeks","GENDER":"Female","ANIMAL_ANIMAL_SUPPLIER":"Jackson Laboratories"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"CON_1",
"Factors":{"Treatment":"CON","Diet":"Healthy","Bacterial Exposure":"No"}
},
{
"Subject ID":"-",
"Sample ID":"CON_2",
"Factors":{"Treatment":"CON","Diet":"Healthy","Bacterial Exposure":"No"}
},
{
"Subject ID":"-",
"Sample ID":"CON_3",
"Factors":{"Treatment":"CON","Diet":"Healthy","Bacterial Exposure":"No"}
},
{
"Subject ID":"-",
"Sample ID":"CON_4",
"Factors":{"Treatment":"CON","Diet":"Healthy","Bacterial Exposure":"No"}
},
{
"Subject ID":"-",
"Sample ID":"CON_5",
"Factors":{"Treatment":"CON","Diet":"Healthy","Bacterial Exposure":"No"}
},
{
"Subject ID":"-",
"Sample ID":"MAL_1",
"Factors":{"Treatment":"MAL","Diet":"Malnourished","Bacterial Exposure":"No"}
},
{
"Subject ID":"-",
"Sample ID":"MAL_2",
"Factors":{"Treatment":"MAL","Diet":"Malnourished","Bacterial Exposure":"No"}
},
{
"Subject ID":"-",
"Sample ID":"MAL_3",
"Factors":{"Treatment":"MAL","Diet":"Malnourished","Bacterial Exposure":"No"}
},
{
"Subject ID":"-",
"Sample ID":"MAL_4",
"Factors":{"Treatment":"MAL","Diet":"Malnourished","Bacterial Exposure":"No"}
},
{
"Subject ID":"-",
"Sample ID":"MAL_5",
"Factors":{"Treatment":"MAL","Diet":"Malnourished","Bacterial Exposure":"No"}
},
{
"Subject ID":"-",
"Sample ID":"MALBG_1",
"Factors":{"Treatment":"MAL-BG","Diet":"Malnourished","Bacterial Exposure":"Yes"}
},
{
"Subject ID":"-",
"Sample ID":"MALBG_2",
"Factors":{"Treatment":"MAL-BG","Diet":"Malnourished","Bacterial Exposure":"Yes"}
},
{
"Subject ID":"-",
"Sample ID":"MALBG_3",
"Factors":{"Treatment":"MAL-BG","Diet":"Malnourished","Bacterial Exposure":"Yes"}
},
{
"Subject ID":"-",
"Sample ID":"MALBG_4",
"Factors":{"Treatment":"MAL-BG","Diet":"Malnourished","Bacterial Exposure":"Yes"}
},
{
"Subject ID":"-",
"Sample ID":"MALBG_5",
"Factors":{"Treatment":"MAL-BG","Diet":"Malnourished","Bacterial Exposure":"Yes"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Following sacrifice, murine liver lobes were isolated and stored at -70/80 C prior to untargeted metabolomics.","SAMPLE_TYPE":"Hippocampus"},

"TREATMENT":{"TREATMENT_SUMMARY":"CON = control mice on healthy diet, MAL = mice placed on a protein/fat deficient diet (malnourished), MAL-BG = MAL mice plus iterative E.coli/Bacteroidales exposure"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Methods reported in methodology .zip folder / Metabolomics were completed by TMIC (The Metabolomics Innovation Centre). Each mouse hippocampal sample in an Eppendorf tube was mixed with water, 5 μL per mg of the tissue, and two 4-mm metal balls were added. 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. Two rounds of sample injections were made, with positive- and negative-ion detection, respectively."},

"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":"NEGATIVE","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":"ST001366_AN002274_Results.txt UNITS:m/z values Has m/z:Yes Has RT:Yes RT units:Minutes"}

}