{ "METABOLOMICS WORKBENCH":{"STUDY_ID":"ST000262","ANALYSIS_ID":"AN000418","VERSION":"1","CREATED_ON":"02-08-2024"}, "PROJECT":{"PROJECT_TITLE":"FLUTE: Functionalizing Lists of Unknown TB Entities","PROJECT_TYPE":"NIH U19","PROJECT_SUMMARY":"functional genomics of proteins of unknown function in M. tuberculosis","INSTITUTE":"Weill Cornell Medicine","DEPARTMENT":"Microbiology and Immunology","LAST_NAME":"Rhee","FIRST_NAME":"Kyu","ADDRESS":"#N/A","EMAIL":"kyr9001@med.cornell.edu","DOI":"http://dx.doi.org/10.21228/M8388M"}, "STUDY":{"STUDY_TITLE":"Activity-Based Metabolic Profiling of M. tuberculosis H37Rv Rv1713","STUDY_TYPE":"timecourse","STUDY_SUMMARY":"These experiments involve incubating various proteins of unknown function in the M. tuberculosis genome with whole-cell lysate and assaying changes in metabolite levels over time (e.g. 0, 15, 30min) to try to infer what reaction they might catalyze.","INSTITUTE":"Weill Cornell Medicine","DEPARTMENT":"Microbiology and Immunology","LAST_NAME":"Rhee","FIRST_NAME":"Kyu","ADDRESS":"Department of Microbiology and Immunology, Weill Cornell Medical College, 1300 York Avenue, New York, NY","EMAIL":"kyr9001@med.cornell.edu","SUBMIT_DATE":"2015-11-13"}, "SUBJECT":{"SUBJECT_TYPE":"Bacterial cells","SUBJECT_SPECIES":"Mycobacterium tuberculosis H37Rv","TAXONOMY_ID":"83332","GENOTYPE_STRAIN":"Mycobacterium tuberculosis H37Rv, taxid:","SPECIES_GROUP":"Microorganism"}, "SUBJECT_SAMPLE_FACTORS":[ { "Subject ID":"Rv1713", "Sample ID":"1mMGTP1713_A_0", "Factors":{"timepoint (min)":"0","co-factor added to lysate":"1mM GTP"} }, { "Subject ID":"Rv1713", "Sample ID":"1mMGTP1713_B_0", "Factors":{"timepoint (min)":"0","co-factor added to lysate":"1mM GTP"} }, { "Subject ID":"Rv1713", "Sample ID":"1mMGTP1713_C_0", "Factors":{"timepoint (min)":"0","co-factor added to lysate":"1mM GTP"} }, { "Subject ID":"Rv1713", "Sample ID":"1713_A_0", "Factors":{"timepoint (min)":"0","co-factor added to lysate":"None"} }, { "Subject ID":"Rv1713", "Sample ID":"1713_B_0", "Factors":{"timepoint (min)":"0","co-factor added to lysate":"None"} }, { "Subject ID":"Rv1713", "Sample ID":"1713_C_0", "Factors":{"timepoint (min)":"0","co-factor added to lysate":"None"} }, { "Subject ID":"Rv1713", "Sample ID":"1mMGTP1713_A_15", "Factors":{"timepoint (min)":"15","co-factor added to lysate":"1mM GTP"} }, { "Subject ID":"Rv1713", "Sample ID":"1mMGTP1713_B_15", "Factors":{"timepoint (min)":"15","co-factor added to lysate":"1mM GTP"} }, { "Subject ID":"Rv1713", "Sample ID":"1mMGTP1713_C_15", "Factors":{"timepoint (min)":"15","co-factor added to lysate":"1mM GTP"} }, { "Subject ID":"Rv1713", "Sample ID":"1713_A_15", "Factors":{"timepoint (min)":"15","co-factor added to lysate":"None"} }, { "Subject ID":"Rv1713", "Sample ID":"1713_B_15", "Factors":{"timepoint (min)":"15","co-factor added to lysate":"None"} }, { "Subject ID":"Rv1713", "Sample ID":"1713_C_15", "Factors":{"timepoint (min)":"15","co-factor added to lysate":"None"} }, { "Subject ID":"Rv1713", "Sample ID":"1mMGTP1713_A_30", "Factors":{"timepoint (min)":"30","co-factor added to lysate":"1mM GTP"} }, { "Subject ID":"Rv1713", "Sample ID":"1mMGTP1713_B_30", "Factors":{"timepoint (min)":"30","co-factor added to lysate":"1mM GTP"} }, { "Subject ID":"Rv1713", "Sample ID":"1mMGTP1713_C_30", "Factors":{"timepoint (min)":"30","co-factor added to lysate":"1mM GTP"} }, { "Subject ID":"Rv1713", "Sample ID":"1713_A_30", "Factors":{"timepoint (min)":"30","co-factor added to lysate":"None"} }, { "Subject ID":"Rv1713", "Sample ID":"1713_B_30", "Factors":{"timepoint (min)":"30","co-factor added to lysate":"None"} }, { "Subject ID":"Rv1713", "Sample ID":"1713_C_30", "Factors":{"timepoint (min)":"30","co-factor added to lysate":"None"} } ], "COLLECTION":{"COLLECTION_SUMMARY":"protein expression","COLLECTION_PROTOCOL_ID":"Rv1713 from M. tuberculosis H37Rv was expressed in E. coli cells and purified...","SAMPLE_TYPE":"Bacterial cells","COLLECTION_VIALS":"polypropylene microfuge tubes","STORAGE_VIALS":"Agilent polypropylene conical bottom vials"}, "TREATMENT":[], "SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"10 uM enzyme incubated at 25C in M. bovis whole-cell extract","PROCESSING_METHOD":"extract was lyophilized and resuspended in 20 mM Tris-HCL pH 8.0","PROCESSING_STORAGE_CONDITIONS":"cell pellet frozen at -80C","EXTRACTION_METHOD":"70% acetonitrile","EXTRACT_CLEANUP":"centrifugation followed by aspiration of supernatant and lyophilization","EXTRACT_STORAGE":"frozen at -80C"}, "CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"Aqueous normal phase diamond hydride","METHODS_FILENAME":"ANPpos/ANP_neg","INSTRUMENT_NAME":"Agilent 1290","COLUMN_NAME":"Microsolv Diamond hydride (150mm,4um)","FLOW_RATE":"0.4 ml/min","SOLVENT_A":"100% water; 0.2% formic acid","SOLVENT_B":"100% acetonitrile; 0.2% formic acid","ANALYTICAL_TIME":"24 minutes","WASHING_BUFFER":"50% methanol","CHROMATOGRAPHY_TYPE":"Normal phase"}, "ANALYSIS":{"LABORATORY_NAME":"Rhee Lab","ANALYSIS_TYPE":"MS","ANALYSIS_COMMENTS":"NEGATIVE","SOFTWARE_VERSION":"XCMS online","PROCESSED_FILE":"Rv1713.xlsx","DETECTOR_TYPE":"Agilent 6220 ToF MS"}, "MS":{"INSTRUMENT_NAME":"Agilent 6220 TOF","INSTRUMENT_TYPE":"TOF","MS_TYPE":"ESI","ION_MODE":"NEGATIVE","CAPILLARY_VOLTAGE":"3500","DRY_GAS_FLOW":"10 l/min","DRY_GAS_TEMP":"250","FRAGMENT_VOLTAGE":"135V","MASS_ACCURACY":"5 ppm","NEBULIZER":"35","OCTPOLE_VOLTAGE":"400","SCAN_RANGE_MOVERZ":"50-1200","SCANNING_CYCLE":"1.4","SKIMMER_VOLTAGE":"65"} }