{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002287","ANALYSIS_ID":"AN003739","VERSION":"1","CREATED_ON":"September 28, 2022, 6:18 am"},

"PROJECT":{"PROJECT_TITLE":"Enhanced systemic commensal E. coli immunogenicity through minor alteration of the metabolic profile","PROJECT_SUMMARY":"LC-MS profiles of supernatant and cell pellet of bacterial culture from commensal E. coli strains with different immunogenicity.","INSTITUTE":"University of Calgary","DEPARTMENT":"Microbiology and Infectious Disease","LABORATORY":"Geuking","LAST_NAME":"Brown","FIRST_NAME":"Kirsty","ADDRESS":"HSC 1729, 3330 Hospital Dr NW","EMAIL":"kirsty.brown12@gmail.com","PHONE":"250 869 2232","FUNDING_SOURCE":"Canadian Institute of Health Research","PUBLICATIONS":"Enhanced systemic commensal E. coli immunogenicity through minor alteration of the metabolic profile","CONTRIBUTORS":"Regula Burkhard1, Mia Koegler1, Kirsty Brown2, Kirsten Wilson1, Lukas Mager2, Amanda Zucoloto2, Carolyn Thomson2, Roopa Hebbandi Nanjundappa1, Braedon McDonald1,3,4, Kathy D. McCoy2,3,4, and Markus B. Geuking1,3,4,*"},

"STUDY":{"STUDY_TITLE":"Enhanced systemic commensal E. coli immunogenicity through minor alteration of the metabolic profile","STUDY_SUMMARY":"LC-MS data from the supernatant and cell pellet of cultured commensal E. coli with and without mutations in outer membrane porin C","INSTITUTE":"University of Calgary","DEPARTMENT":"Microbiology and Infectious Disease","LABORATORY":"Geuking","LAST_NAME":"Brown","FIRST_NAME":"Kirsty","ADDRESS":"HSC 1729, 3330 Hospital Dr NW","EMAIL":"kirsty.brown1@ucalgary.ca","PHONE":"2508692232"},

"SUBJECT":{"SUBJECT_TYPE":"Bacteria","SUBJECT_SPECIES":"Escherichia coli","TAXONOMY_ID":"562"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"SN_GP61_1_1",
"Factors":{"sample_site":"SN","strain":"GP61","biologial_rep":"1","technical_rep":"1"},
"Additional sample data":{"RAW_FILE_NAME":"2021_02_08_RB_HILICNeg15_GP61_SC_SN_1_1"}
},
{
"Subject ID":"-",
"Sample ID":"SN_GP61_1_2",
"Factors":{"sample_site":"SN","strain":"GP61","biologial_rep":"1","technical_rep":"2"},
"Additional sample data":{"RAW_FILE_NAME":"2021_02_08_RB_HILICNeg15_GP61_SC_SN_1_2"}
},
{
"Subject ID":"-",
"Sample ID":"SN_GP61_4_1",
"Factors":{"sample_site":"SN","strain":"GP61","biologial_rep":"4","technical_rep":"1"},
"Additional sample data":{"RAW_FILE_NAME":"2021_02_08_RB_HILICNeg15_GP61_SC_SN_4_1"}
},
{
"Subject ID":"-",
"Sample ID":"SN_GP61_4_2",
"Factors":{"sample_site":"SN","strain":"GP61","biologial_rep":"4","technical_rep":"2"},
"Additional sample data":{"RAW_FILE_NAME":"2021_02_08_RB_HILICNeg15_GP61_SC_SN_4_2"}
},
{
"Subject ID":"-",
"Sample ID":"SN_GP61_4_3",
"Factors":{"sample_site":"SN","strain":"GP61","biologial_rep":"4","technical_rep":"3"},
"Additional sample data":{"RAW_FILE_NAME":"2021_02_08_RB_HILICNeg15_GP61_SC_SN_4_3"}
},
{
"Subject ID":"-",
"Sample ID":"SN_GP61_4_4",
"Factors":{"sample_site":"SN","strain":"GP61","biologial_rep":"4","technical_rep":"4"},
"Additional sample data":{"RAW_FILE_NAME":"2021_02_08_RB_HILICNeg15_GP61_SC_SN_4_4"}
},
{
"Subject ID":"-",
"Sample ID":"SN_KO_1_1",
"Factors":{"sample_site":"SN","strain":"KO","biologial_rep":"1","technical_rep":"1"},
"Additional sample data":{"RAW_FILE_NAME":"2021_02_08_RB_HILICNeg15_KO_SC_SN_1_1"}
},
{
"Subject ID":"-",
"Sample ID":"SN_KO_1_2",
"Factors":{"sample_site":"SN","strain":"KO","biologial_rep":"1","technical_rep":"2"},
"Additional sample data":{"RAW_FILE_NAME":"2021_02_08_RB_HILICNeg15_KO_SC_SN_1_2"}
},
{
"Subject ID":"-",
"Sample ID":"SN_KO_4_1",
"Factors":{"sample_site":"SN","strain":"KO","biologial_rep":"4","technical_rep":"1"},
"Additional sample data":{"RAW_FILE_NAME":"2021_02_08_RB_HILICNeg15_KO_SC_SN_4_1"}
},
{
"Subject ID":"-",
"Sample ID":"SN_KO_4_2",
"Factors":{"sample_site":"SN","strain":"KO","biologial_rep":"4","technical_rep":"2"},
"Additional sample data":{"RAW_FILE_NAME":"2021_02_08_RB_HILICNeg15_KO_SC_SN_4_2"}
},
{
"Subject ID":"-",
"Sample ID":"SN_KO_4_3",
"Factors":{"sample_site":"SN","strain":"KO","biologial_rep":"4","technical_rep":"3"},
"Additional sample data":{"RAW_FILE_NAME":"2021_02_08_RB_HILICNeg15_KO_SC_SN_4_3"}
},
{
"Subject ID":"-",
"Sample ID":"SN_KO_4_4",
"Factors":{"sample_site":"SN","strain":"KO","biologial_rep":"4","technical_rep":"4"},
"Additional sample data":{"RAW_FILE_NAME":"2021_02_08_RB_HILICNeg15_KO_SC_SN_4_4"}
},
{
"Subject ID":"-",
"Sample ID":"SN_WT_1_1",
"Factors":{"sample_site":"SN","strain":"WT","biologial_rep":"1","technical_rep":"1"},
"Additional sample data":{"RAW_FILE_NAME":"2021_02_08_RB_HILICNeg15_WT_SC_SN_1_1"}
},
{
"Subject ID":"-",
"Sample ID":"SN_WT_1_2",
"Factors":{"sample_site":"SN","strain":"WT","biologial_rep":"1","technical_rep":"2"},
"Additional sample data":{"RAW_FILE_NAME":"2021_02_08_RB_HILICNeg15_WT_SC_SN_1_2"}
},
{
"Subject ID":"-",
"Sample ID":"SN_WT_4_1",
"Factors":{"sample_site":"SN","strain":"WT","biologial_rep":"4","technical_rep":"1"},
"Additional sample data":{"RAW_FILE_NAME":"2021_02_08_RB_HILICNeg15_WT_SC_SN_4_1"}
},
{
"Subject ID":"-",
"Sample ID":"SN_WT_4_2",
"Factors":{"sample_site":"SN","strain":"WT","biologial_rep":"4","technical_rep":"2"},
"Additional sample data":{"RAW_FILE_NAME":"2021_02_08_RB_HILICNeg15_WT_SC_SN_4_2"}
},
{
"Subject ID":"-",
"Sample ID":"SN_WT_4_3",
"Factors":{"sample_site":"SN","strain":"WT","biologial_rep":"4","technical_rep":"3"},
"Additional sample data":{"RAW_FILE_NAME":"2021_02_08_RB_HILICNeg15_WT_SC_SN_4_3"}
},
{
"Subject ID":"-",
"Sample ID":"SN_WT_4_4",
"Factors":{"sample_site":"SN","strain":"WT","biologial_rep":"4","technical_rep":"4"},
"Additional sample data":{"RAW_FILE_NAME":"2021_02_08_RB_HILICNeg15_WT_SC_SN_4_4"}
},
{
"Subject ID":"-",
"Sample ID":"Intra_GP61_1_1",
"Factors":{"sample_site":"Intra","strain":"GP61","biologial_rep":"1","technical_rep":"1"},
"Additional sample data":{"RAW_FILE_NAME":"2021_02_08_RB_HILICNeg15_GP61_SC_Intra_1_1"}
},
{
"Subject ID":"-",
"Sample ID":"Intra_GP61_1_2",
"Factors":{"sample_site":"Intra","strain":"GP61","biologial_rep":"1","technical_rep":"2"},
"Additional sample data":{"RAW_FILE_NAME":"2021_02_08_RB_HILICNeg15_GP61_SC_Intra_1_2"}
},
{
"Subject ID":"-",
"Sample ID":"Intra_GP61_4_1",
"Factors":{"sample_site":"Intra","strain":"GP61","biologial_rep":"4","technical_rep":"1"},
"Additional sample data":{"RAW_FILE_NAME":"2021_02_08_RB_HILICNeg15_GP61_SC_Intra_4_1"}
},
{
"Subject ID":"-",
"Sample ID":"Intra_GP61_4_2",
"Factors":{"sample_site":"Intra","strain":"GP61","biologial_rep":"4","technical_rep":"2"},
"Additional sample data":{"RAW_FILE_NAME":"2021_02_08_RB_HILICNeg15_GP61_SC_Intra_4_2"}
},
{
"Subject ID":"-",
"Sample ID":"Intra_GP61_4_3",
"Factors":{"sample_site":"Intra","strain":"GP61","biologial_rep":"4","technical_rep":"3"},
"Additional sample data":{"RAW_FILE_NAME":"2021_02_08_RB_HILICNeg15_GP61_SC_Intra_4_3"}
},
{
"Subject ID":"-",
"Sample ID":"Intra_GP61_4_4",
"Factors":{"sample_site":"Intra","strain":"GP61","biologial_rep":"4","technical_rep":"4"},
"Additional sample data":{"RAW_FILE_NAME":"2021_02_08_RB_HILICNeg15_GP61_SC_Intra_4_4"}
},
{
"Subject ID":"-",
"Sample ID":"Intra_KO_1_1",
"Factors":{"sample_site":"Intra","strain":"KO","biologial_rep":"1","technical_rep":"1"},
"Additional sample data":{"RAW_FILE_NAME":"2021_02_08_RB_HILICNeg15_KO_SC_Intra_1_1"}
},
{
"Subject ID":"-",
"Sample ID":"Intra_KO_1_2",
"Factors":{"sample_site":"Intra","strain":"KO","biologial_rep":"1","technical_rep":"2"},
"Additional sample data":{"RAW_FILE_NAME":"2021_02_08_RB_HILICNeg15_KO_SC_Intra_1_2"}
},
{
"Subject ID":"-",
"Sample ID":"Intra_KO_4_1",
"Factors":{"sample_site":"Intra","strain":"KO","biologial_rep":"4","technical_rep":"1"},
"Additional sample data":{"RAW_FILE_NAME":"2021_02_08_RB_HILICNeg15_KO_SC_Intra_4_1"}
},
{
"Subject ID":"-",
"Sample ID":"Intra_KO_4_2",
"Factors":{"sample_site":"Intra","strain":"KO","biologial_rep":"4","technical_rep":"2"},
"Additional sample data":{"RAW_FILE_NAME":"2021_02_08_RB_HILICNeg15_KO_SC_Intra_4_2"}
},
{
"Subject ID":"-",
"Sample ID":"Intra_KO_4_3",
"Factors":{"sample_site":"Intra","strain":"KO","biologial_rep":"4","technical_rep":"3"},
"Additional sample data":{"RAW_FILE_NAME":"2021_02_08_RB_HILICNeg15_KO_SC_Intra_4_3"}
},
{
"Subject ID":"-",
"Sample ID":"Intra_KO_4_4",
"Factors":{"sample_site":"Intra","strain":"KO","biologial_rep":"4","technical_rep":"4"},
"Additional sample data":{"RAW_FILE_NAME":"2021_02_08_RB_HILICNeg15_KO_SC_Intra_4_4"}
},
{
"Subject ID":"-",
"Sample ID":"Intra_WT_1_1",
"Factors":{"sample_site":"Intra","strain":"WT","biologial_rep":"1","technical_rep":"1"},
"Additional sample data":{"RAW_FILE_NAME":"2021_02_08_RB_HILICNeg15_WT_SC_Intra_1_1"}
},
{
"Subject ID":"-",
"Sample ID":"Intra_WT_1_2",
"Factors":{"sample_site":"Intra","strain":"WT","biologial_rep":"1","technical_rep":"2"},
"Additional sample data":{"RAW_FILE_NAME":"2021_02_08_RB_HILICNeg15_WT_SC_Intra_1_2"}
},
{
"Subject ID":"-",
"Sample ID":"Intra_WT_4_1",
"Factors":{"sample_site":"Intra","strain":"WT","biologial_rep":"4","technical_rep":"1"},
"Additional sample data":{"RAW_FILE_NAME":"2021_02_08_RB_HILICNeg15_WT_SC_Intra_4_1"}
},
{
"Subject ID":"-",
"Sample ID":"Intra_WT_4_2",
"Factors":{"sample_site":"Intra","strain":"WT","biologial_rep":"4","technical_rep":"2"},
"Additional sample data":{"RAW_FILE_NAME":"2021_02_08_RB_HILICNeg15_WT_SC_Intra_4_2"}
},
{
"Subject ID":"-",
"Sample ID":"Intra_WT_4_3",
"Factors":{"sample_site":"Intra","strain":"WT","biologial_rep":"4","technical_rep":"3"},
"Additional sample data":{"RAW_FILE_NAME":"2021_02_08_RB_HILICNeg15_WT_SC_Intra_4_3"}
},
{
"Subject ID":"-",
"Sample ID":"Intra_WT_4_4",
"Factors":{"sample_site":"Intra","strain":"WT","biologial_rep":"4","technical_rep":"4"},
"Additional sample data":{"RAW_FILE_NAME":"2021_02_08_RB_HILICNeg15_WT_SC_Intra_4_4"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"The different E. coli strains were grown in LB media and subcultured to OD600 = 0.5.","SAMPLE_TYPE":"Bacterial cells"},

"TREATMENT":{"TREATMENT_SUMMARY":"E.coli strains were either wild type (MG1655), were deficient in outer membrane porin (OmpC KO) or had a viral epitope from LCMV in place of the OmpC (GP61)"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Metabolites from supernatant were extracted in 100% methanol, precipitated at -20°C for 1 hour, centrifuged and diluted into a linear range (1:20 final dilution) with 50% methanol. To extract intracellular metabolites, bacterial pellet was snap-frozen in liquid nitrogen, resuspended in cell lysis buffer (1M Tris, 5M NaCL, 0.5M EDTA, 10% SDS in H2O) and sonicated. Metabolites were extracted as described above"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"HILIC","INSTRUMENT_NAME":"Thermo Vanquish","COLUMN_NAME":"Thermo Syncronis HILIC (100 x 2.1mm, 1.7um)","FLOW_GRADIENT":"2 stage linear gradient","FLOW_RATE":"600uL/min","COLUMN_TEMPERATURE":"30C","METHODS_FILENAME":"protocol.docx","SOLVENT_A":"20mM ammonium formate pH 3 in H20","SOLVENT_B":"MS Grade Acetonitrile with 0.1% formic acid"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS","LABORATORY_NAME":"Lewis, IA","OPERATOR_NAME":"Drikic, M","SOFTWARE_VERSION":"Xcalibur","ACQUISITION_DATE":"2021_02"},

"MS":{"INSTRUMENT_NAME":"Thermo Q Exactive HF hybrid Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","ION_MODE":"NEGATIVE","MS_COMMENTS":"50-750 m/z, peak integration and assignment using El-Maven software matching to authentic standard library (~150 compounds)."},

"MS_METABOLITE_DATA":{
"Units":"AUC",

"Data":[{"Metabolite":"Glycine","SN_GP61_1_1":"0","SN_GP61_1_2":"0","SN_GP61_4_1":"0","SN_GP61_4_2":"0","SN_GP61_4_3":"0","SN_GP61_4_4":"0","SN_KO_1_1":"0","SN_KO_1_2":"0","SN_KO_4_1":"0","SN_KO_4_2":"0","SN_KO_4_3":"0","SN_KO_4_4":"0","SN_WT_1_1":"0","SN_WT_1_2":"0","SN_WT_4_1":"0","SN_WT_4_2":"0","SN_WT_4_3":"0","SN_WT_4_4":"0","Intra_GP61_1_1":"6289.11","Intra_GP61_1_2":"36142.47","Intra_GP61_4_1":"10988.68","Intra_GP61_4_2":"0","Intra_GP61_4_3":"0","Intra_GP61_4_4":"0","Intra_KO_1_1":"101382.2","Intra_KO_1_2":"39976.43","Intra_KO_4_1":"16829.46","Intra_KO_4_2":"47025.01","Intra_KO_4_3":"63429.63","Intra_KO_4_4":"47985.88","Intra_WT_1_1":"86457.1","Intra_WT_1_2":"65015.85","Intra_WT_4_1":"28007.77","Intra_WT_4_2":"12072.55","Intra_WT_4_3":"45035.75","Intra_WT_4_4":"80635.98"},{"Metabolite":"Isobutyric 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}