{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000307","ANALYSIS_ID":"AN000486","VERSION":"1","CREATED_ON":"January 4, 2016, 11:50 am"},

"PROJECT":{"PROJECT_TITLE":"CRBN's role in T cell activation","PROJECT_SUMMARY":"Targeting CRBN to alter CD8 T cell metabolism","INSTITUTE":"Moffitt Cancer Center","DEPARTMENT":"Immunology","LAST_NAME":"Burnette","FIRST_NAME":"Pearlie K.","ADDRESS":"-","EMAIL":"pearlie.burnette@moffitt.org","PHONE":"-"},

"STUDY":{"STUDY_TITLE":"Targeting CRBN to alter CD8 T cell metabolism","STUDY_TYPE":"T cell activation","STUDY_SUMMARY":"The purpose of this study was to evaluate the metabolic profile of different treatments of T-Cells among two separate mouse genotypes.","INSTITUTE":"University of Florida","DEPARTMENT":"SECIM","LABORATORY":"Moffitt Cancer Center - Immunology","LAST_NAME":"Swearingen","FIRST_NAME":"Rebecca","ADDRESS":"-","EMAIL":"rebecca.swearingen@moffitt.org","PHONE":"-","NUM_GROUPS":"12","TOTAL_SUBJECTS":"60"},

"SUBJECT":{"SUBJECT_TYPE":"Animal","SUBJECT_SPECIES":"Mus musculus","ANIMAL_ANIMAL_SUPPLIER":"WT (CRBN +/+) mice are from Jackson labs and CRBN -/- mice have been bred at Moffitt Cancer Center","ANIMAL_HOUSING":"Standard bedding + cotton pads, hepa filtered air","ANIMAL_LIGHT_CYCLE":"Dark 6pm-6am","ANIMAL_FEED":"Feed from Harlan, not sterile","ANIMAL_WATER":"autoclaved H2O","ANIMAL_INCLUSION_CRITERIA":"Animals used in this experiment were sex-matched and age matched. The ages were 8-12 weeks old in both sets of experiments"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"sbs_706",
"Sample ID":"CD3 + CD28 KO1 042215",
"Factors":{"Strain":"CRBN -/-","Treatment":"anti-CD3 & anti-CD28 stimulation"},
"Additional sample data":{"Gender":"M"}
},
{
"Subject ID":"sbs_707",
"Sample ID":"CD3 + CD28 KO2 042215",
"Factors":{"Strain":"CRBN -/-","Treatment":"anti-CD3 & anti-CD28 stimulation"},
"Additional sample data":{"Gender":"M"}
},
{
"Subject ID":"sbs_708",
"Sample ID":"CD3 + CD28 KO3 042215",
"Factors":{"Strain":"CRBN -/-","Treatment":"anti-CD3 & anti-CD28 stimulation"},
"Additional sample data":{"Gender":"M"}
},
{
"Subject ID":"sbs_709",
"Sample ID":"CD3 + CD28 KO4 042215",
"Factors":{"Strain":"CRBN -/-","Treatment":"anti-CD3 & anti-CD28 stimulation"},
"Additional sample data":{"Gender":"M"}
},
{
"Subject ID":"sbs_710",
"Sample ID":"CD3 + CD28 KO5 042215",
"Factors":{"Strain":"CRBN -/-","Treatment":"anti-CD3 & anti-CD28 stimulation"},
"Additional sample data":{"Gender":"M"}
},
{
"Subject ID":"sbs_711",
"Sample ID":"CD3 KO1 042215",
"Factors":{"Strain":"CRBN -/-","Treatment":"anti-CD3 stimulation"},
"Additional sample data":{"Gender":"M"}
},
{
"Subject ID":"sbs_712",
"Sample ID":"CD3 KO2 042215",
"Factors":{"Strain":"CRBN -/-","Treatment":"anti-CD3 stimulation"},
"Additional sample data":{"Gender":"M"}
},
{
"Subject ID":"sbs_713",
"Sample ID":"CD3 KO3 042215",
"Factors":{"Strain":"CRBN -/-","Treatment":"anti-CD3 stimulation"},
"Additional sample data":{"Gender":"M"}
},
{
"Subject ID":"sbs_714",
"Sample ID":"CD3 KO4 042215",
"Factors":{"Strain":"CRBN -/-","Treatment":"anti-CD3 stimulation"},
"Additional sample data":{"Gender":"M"}
},
{
"Subject ID":"sbs_715",
"Sample ID":"CD3 KO5 042215",
"Factors":{"Strain":"CRBN -/-","Treatment":"anti-CD3 stimulation"},
"Additional sample data":{"Gender":"M"}
},
{
"Subject ID":"sbs_716",
"Sample ID":"Naive KO1 042215",
"Factors":{"Strain":"CRBN -/-","Treatment":"unstimulated"},
"Additional sample data":{"Gender":"M"}
},
{
"Subject ID":"sbs_717",
"Sample ID":"Naive KO2 042215",
"Factors":{"Strain":"CRBN -/-","Treatment":"unstimulated"},
"Additional sample data":{"Gender":"M"}
},
{
"Subject ID":"sbs_718",
"Sample ID":"Naive KO3 042215",
"Factors":{"Strain":"CRBN -/-","Treatment":"unstimulated"},
"Additional sample data":{"Gender":"M"}
},
{
"Subject ID":"sbs_719",
"Sample ID":"Naive KO4 042215",
"Factors":{"Strain":"CRBN -/-","Treatment":"unstimulated"},
"Additional sample data":{"Gender":"M"}
},
{
"Subject ID":"sbs_720",
"Sample ID":"Naive KO5 042215",
"Factors":{"Strain":"CRBN -/-","Treatment":"unstimulated"},
"Additional sample data":{"Gender":"M"}
},
{
"Subject ID":"sbs_721",
"Sample ID":"CD3 + CD28 WT1 042215",
"Factors":{"Strain":"CRBN +/+","Treatment":"anti-CD3 & anti-CD28 stimulation"},
"Additional sample data":{"Gender":"M"}
},
{
"Subject ID":"sbs_722",
"Sample ID":"CD3 + CD28 WT2 042215",
"Factors":{"Strain":"CRBN +/+","Treatment":"anti-CD3 & anti-CD28 stimulation"},
"Additional sample data":{"Gender":"M"}
},
{
"Subject ID":"sbs_723",
"Sample ID":"CD3 + CD28 WT3 042215",
"Factors":{"Strain":"CRBN +/+","Treatment":"anti-CD3 & anti-CD28 stimulation"},
"Additional sample data":{"Gender":"M"}
},
{
"Subject ID":"sbs_724",
"Sample ID":"CD3 + CD28 WT4 042215",
"Factors":{"Strain":"CRBN +/+","Treatment":"anti-CD3 & anti-CD28 stimulation"},
"Additional sample data":{"Gender":"M"}
},
{
"Subject ID":"sbs_725",
"Sample ID":"CD3 + CD28 WT5 042215",
"Factors":{"Strain":"CRBN +/+","Treatment":"anti-CD3 & anti-CD28 stimulation"},
"Additional sample data":{"Gender":"M"}
},
{
"Subject ID":"sbs_726",
"Sample ID":"CD3 WT1 042215",
"Factors":{"Strain":"CRBN +/+","Treatment":"anti-CD3 stimulation"},
"Additional sample data":{"Gender":"M"}
},
{
"Subject ID":"sbs_727",
"Sample ID":"CD3 WT2 042215",
"Factors":{"Strain":"CRBN +/+","Treatment":"anti-CD3 stimulation"},
"Additional sample data":{"Gender":"M"}
},
{
"Subject ID":"sbs_728",
"Sample ID":"CD3 WT3 042215",
"Factors":{"Strain":"CRBN +/+","Treatment":"anti-CD3 stimulation"},
"Additional sample data":{"Gender":"M"}
},
{
"Subject ID":"sbs_729",
"Sample ID":"CD3 WT4 042215",
"Factors":{"Strain":"CRBN +/+","Treatment":"anti-CD3 stimulation"},
"Additional sample data":{"Gender":"M"}
},
{
"Subject ID":"sbs_730",
"Sample ID":"CD3 WT5 042215",
"Factors":{"Strain":"CRBN +/+","Treatment":"anti-CD3 stimulation"},
"Additional sample data":{"Gender":"M"}
},
{
"Subject ID":"sbs_731",
"Sample ID":"Naive WT 1 042215",
"Factors":{"Strain":"CRBN +/+","Treatment":"unstimulated"},
"Additional sample data":{"Gender":"M"}
},
{
"Subject ID":"sbs_732",
"Sample ID":"Naive WT 2 042215",
"Factors":{"Strain":"CRBN +/+","Treatment":"unstimulated"},
"Additional sample data":{"Gender":"M"}
},
{
"Subject ID":"sbs_733",
"Sample ID":"Naive WT 3 042215",
"Factors":{"Strain":"CRBN +/+","Treatment":"unstimulated"},
"Additional sample data":{"Gender":"M"}
},
{
"Subject ID":"sbs_734",
"Sample ID":"Naive WT 4 042215",
"Factors":{"Strain":"CRBN +/+","Treatment":"unstimulated"},
"Additional sample data":{"Gender":"M"}
},
{
"Subject ID":"sbs_735",
"Sample ID":"Naive WT 5 042215",
"Factors":{"Strain":"CRBN +/+","Treatment":"unstimulated"},
"Additional sample data":{"Gender":"M"}
},
{
"Subject ID":"sbs_736",
"Sample ID":"CD3 + CD28 KO1",
"Factors":{"Strain":"CRBN -/-","Treatment":"anti-CD3 & anti-CD28 stimulation"},
"Additional sample data":{"Gender":"M"}
},
{
"Subject ID":"sbs_737",
"Sample ID":"CD3 + CD28 KO2",
"Factors":{"Strain":"CRBN -/-","Treatment":"anti-CD3 & anti-CD28 stimulation"},
"Additional sample data":{"Gender":"M"}
},
{
"Subject ID":"sbs_738",
"Sample ID":"CD3 + CD28 KO3",
"Factors":{"Strain":"CRBN -/-","Treatment":"anti-CD3 & anti-CD28 stimulation"},
"Additional sample data":{"Gender":"M"}
},
{
"Subject ID":"sbs_739",
"Sample ID":"CD3 + CD28 KO4",
"Factors":{"Strain":"CRBN -/-","Treatment":"anti-CD3 & anti-CD28 stimulation"},
"Additional sample data":{"Gender":"M"}
},
{
"Subject ID":"sbs_740",
"Sample ID":"CD3 + CD28 KO5",
"Factors":{"Strain":"CRBN -/-","Treatment":"anti-CD3 & anti-CD28 stimulation"},
"Additional sample data":{"Gender":"M"}
},
{
"Subject ID":"sbs_741",
"Sample ID":"CD3 KO1",
"Factors":{"Strain":"CRBN -/-","Treatment":"anti-CD3 stimulation"},
"Additional sample data":{"Gender":"M"}
},
{
"Subject ID":"sbs_742",
"Sample ID":"CD3 KO2",
"Factors":{"Strain":"CRBN -/-","Treatment":"anti-CD3 stimulation"},
"Additional sample data":{"Gender":"M"}
},
{
"Subject ID":"sbs_743",
"Sample ID":"CD3 KO3",
"Factors":{"Strain":"CRBN -/-","Treatment":"anti-CD3 stimulation"},
"Additional sample data":{"Gender":"M"}
},
{
"Subject ID":"sbs_744",
"Sample ID":"CD3 KO4",
"Factors":{"Strain":"CRBN -/-","Treatment":"anti-CD3 stimulation"},
"Additional sample data":{"Gender":"M"}
},
{
"Subject ID":"sbs_745",
"Sample ID":"CD3 KO5",
"Factors":{"Strain":"CRBN -/-","Treatment":"anti-CD3 stimulation"},
"Additional sample data":{"Gender":"M"}
},
{
"Subject ID":"sbs_746",
"Sample ID":"Naive KO1",
"Factors":{"Strain":"CRBN -/-","Treatment":"unstimulated"},
"Additional sample data":{"Gender":"M"}
},
{
"Subject ID":"sbs_747",
"Sample ID":"Naive KO2",
"Factors":{"Strain":"CRBN -/-","Treatment":"unstimulated"},
"Additional sample data":{"Gender":"M"}
},
{
"Subject ID":"sbs_748",
"Sample ID":"Naive KO3",
"Factors":{"Strain":"CRBN -/-","Treatment":"unstimulated"},
"Additional sample data":{"Gender":"M"}
},
{
"Subject ID":"sbs_749",
"Sample ID":"Naive KO4",
"Factors":{"Strain":"CRBN -/-","Treatment":"unstimulated"},
"Additional sample data":{"Gender":"M"}
},
{
"Subject ID":"sbs_750",
"Sample ID":"Naive KO5",
"Factors":{"Strain":"CRBN -/-","Treatment":"unstimulated"},
"Additional sample data":{"Gender":"M"}
},
{
"Subject ID":"sbs_751",
"Sample ID":"CD3 + CD28 WT1",
"Factors":{"Strain":"CRBN +/+","Treatment":"anti-CD3 & anti-CD28 stimulation"},
"Additional sample data":{"Gender":"M"}
},
{
"Subject ID":"sbs_752",
"Sample ID":"CD3 + CD28 WT2",
"Factors":{"Strain":"CRBN +/+","Treatment":"anti-CD3 & anti-CD28 stimulation"},
"Additional sample data":{"Gender":"M"}
},
{
"Subject ID":"sbs_753",
"Sample ID":"CD3 + CD28 WT3",
"Factors":{"Strain":"CRBN +/+","Treatment":"anti-CD3 & anti-CD28 stimulation"},
"Additional sample data":{"Gender":"M"}
},
{
"Subject ID":"sbs_754",
"Sample ID":"CD3 + CD28 WT4",
"Factors":{"Strain":"CRBN +/+","Treatment":"anti-CD3 & anti-CD28 stimulation"},
"Additional sample data":{"Gender":"M"}
},
{
"Subject ID":"sbs_755",
"Sample ID":"CD3 + CD28 WT5",
"Factors":{"Strain":"CRBN +/+","Treatment":"anti-CD3 & anti-CD28 stimulation"},
"Additional sample data":{"Gender":"M"}
},
{
"Subject ID":"sbs_756",
"Sample ID":"CD3 WT1",
"Factors":{"Strain":"CRBN +/+","Treatment":"anti-CD3 stimulation"},
"Additional sample data":{"Gender":"M"}
},
{
"Subject ID":"sbs_757",
"Sample ID":"CD3 WT2",
"Factors":{"Strain":"CRBN +/+","Treatment":"anti-CD3 stimulation"},
"Additional sample data":{"Gender":"M"}
},
{
"Subject ID":"sbs_758",
"Sample ID":"CD3 WT3",
"Factors":{"Strain":"CRBN +/+","Treatment":"anti-CD3 stimulation"},
"Additional sample data":{"Gender":"M"}
},
{
"Subject ID":"sbs_759",
"Sample ID":"CD3 WT4",
"Factors":{"Strain":"CRBN +/+","Treatment":"anti-CD3 stimulation"},
"Additional sample data":{"Gender":"M"}
},
{
"Subject ID":"sbs_760",
"Sample ID":"CD3 WT5",
"Factors":{"Strain":"CRBN +/+","Treatment":"anti-CD3 stimulation"},
"Additional sample data":{"Gender":"M"}
},
{
"Subject ID":"sbs_761",
"Sample ID":"Naive WT 1",
"Factors":{"Strain":"CRBN +/+","Treatment":"unstimulated"},
"Additional sample data":{"Gender":"M"}
},
{
"Subject ID":"sbs_762",
"Sample ID":"Naive WT 2",
"Factors":{"Strain":"CRBN +/+","Treatment":"unstimulated"},
"Additional sample data":{"Gender":"M"}
},
{
"Subject ID":"sbs_763",
"Sample ID":"Naive WT 3",
"Factors":{"Strain":"CRBN +/+","Treatment":"unstimulated"},
"Additional sample data":{"Gender":"M"}
},
{
"Subject ID":"sbs_764",
"Sample ID":"Naive WT 4",
"Factors":{"Strain":"CRBN +/+","Treatment":"unstimulated"},
"Additional sample data":{"Gender":"M"}
},
{
"Subject ID":"sbs_765",
"Sample ID":"Naive WT 5",
"Factors":{"Strain":"CRBN +/+","Treatment":"unstimulated"},
"Additional sample data":{"Gender":"M"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"-","SAMPLE_TYPE":"cell","COLLECTION_METHOD":"centrifuged in ficoll-gradient to remove debris, then washed in PBS","COLLECTION_TIME":"0 or 24 hours after stimulation","STORAGE_CONDITIONS":"-80°C","COLLECTION_VIALS":"15mL conical tubes","STORAGE_VIALS":"microfuge tubes"},

"TREATMENT":{"TREATMENT_SUMMARY":"-","ANIMAL_ANESTHESIA":"CO2 asphyxiation","ANIMAL_ACCLIMATION_DURATION":"Mice from Jackson are subjected to a week-long acclimation period in our facility prior to experimental use.","ANIMAL_ENDP_TISSUE_COLL_LIST":"Spleen into cell culture media","CELL_GROWTH_CONTAINER":"96-well round-bottom plate that was coated with anti-CD3 antibody","CELL_GROWTH_RATE":"Murine T cells generally divide after 48-72 hours of stimulation.","CELL_MEDIA":"RPMI 1640 with 10% FBS, pen/strep, gentamycin, NEAA, Sodium pyruvate, fungizone (Amphotericin B), 2-mercaptoethanol","CELL_ENVIR_COND":"37°C, normoxic conditions"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"-","SAMPLEPREP_PROTOCOL_FILENAME":"Consolidated Cellular Metabolomics with DNA quant.pdf","SAMPLE_SPIKING":"Appendix A - Internal Standard Prep GLCMS.pdf"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Thermo Scientific-Dionex Ultimate 3000","COLUMN_NAME":"ACE Excel 2 C18-PFP (100 x 2.1mm, 2um)","METHODS_FILENAME":"Metabolomics_LCMSProtocol.pdf"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS","LABORATORY_NAME":"Garrett Lab","ANALYSIS_PROTOCOL_FILE":"Metabolomics_LCMSProtocol.pdf"},

"MS":{"MS_COMMENTS":"-","INSTRUMENT_NAME":"Thermo Q Exactive Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","ION_MODE":"POSITIVE"},

"MS_METABOLITE_DATA":{
"Units":"Peak area",

"Data":[],

"Metabolites":[]
}

}