{ "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":[] } }