{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001044","ANALYSIS_ID":"AN001708","VERSION":"1","CREATED_ON":"September 4, 2018, 11:37 am"},

"PROJECT":{"PROJECT_TITLE":"PGC1-A induces TCA enzymes","PROJECT_SUMMARY":"Demonstrate the experimental protocol of stable isotope tracer based metabolomic investigation of cell metabolism","INSTITUTE":"Univ. of Alabama at Birmingham","DEPARTMENT":"Urology","LAST_NAME":"Sudarshan","FIRST_NAME":"Sunil","ADDRESS":"NA","EMAIL":"sudarshan@uab.edu","PHONE":"000-000-0000"},

"STUDY":{"STUDY_TITLE":"PGC1-A effect on TCA enzymes","STUDY_TYPE":"Tracer time course in medium","STUDY_SUMMARY":"13C6-glucose used to track the effects of PGC1-A on RCC4 and Caki-1 metabolism","INSTITUTE":"University of Alabama, Birmingham","DEPARTMENT":"Urology","LAST_NAME":"Sudarshan","FIRST_NAME":"Sunil","ADDRESS":"NA","EMAIL":"sudarshan@uab.edu","PHONE":"000-000-0000"},

"SUBJECT":{"SUBJECT_TYPE":"Animal","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"10_Caki-1_adGFP_13CGlc_rep2-cells-polar_GCMS_A",
"Factors":{"cell_type":"Caki-1","protocol.id":"adGFP_13CGlc"},
"Additional sample data":{"lineage_1":"10_Caki-1_adGFP_13CGlc_rep2","cell_type":"Caki-1","plate_media_tare":"-1","plate_media_tare%units":"g","protocol.id":"adGFP_13CGlc","replicate":"2","replicate%type":"biological","species":"Mus musculus","species_type":"Animal","taxonomy_id":"10090","lineage_2":"10_Caki-1_adGFP_13CGlc_rep2-cells","cell_type":"Caki-1","protocol.id":"cell_quench_collection","lineage_3":"10_Caki-1_adGFP_13CGlc_rep2-cells-polar_GCMS_A","protocol.id":"polar_extraction","replicate":"1","replicate%type":"analytical","type":"polar","weight":"0.2187","weight%units":"g"}
},
{
"Subject ID":"-",
"Sample ID":"11_Caki-1_adPGC1A_13CGlc_rep1-cells-polar_GCMS_A",
"Factors":{"cell_type":"Caki-1","protocol.id":"adPGC1A_13CGlc"},
"Additional sample data":{"lineage_1":"11_Caki-1_adPGC1A_13CGlc_rep1","cell_type":"Caki-1","plate_media_tare":"-1","plate_media_tare%units":"g","protocol.id":"adPGC1A_13CGlc","replicate":"1","replicate%type":"biological","species":"Mus musculus","species_type":"Animal","taxonomy_id":"10090","lineage_2":"11_Caki-1_adPGC1A_13CGlc_rep1-cells","cell_type":"Caki-1","protocol.id":"cell_quench_collection","lineage_3":"11_Caki-1_adPGC1A_13CGlc_rep1-cells-polar_GCMS_A","protocol.id":"polar_extraction","replicate":"1","replicate%type":"analytical","type":"polar","weight":"0.2178","weight%units":"g"}
},
{
"Subject ID":"-",
"Sample ID":"12_Caki-1_adPGC1A_13CGlc_rep2-cells-polar_GCMS_A",
"Factors":{"cell_type":"Caki-1","protocol.id":"adPGC1A_13CGlc"},
"Additional sample data":{"lineage_1":"12_Caki-1_adPGC1A_13CGlc_rep2","cell_type":"Caki-1","plate_media_tare":"-1","plate_media_tare%units":"g","protocol.id":"adPGC1A_13CGlc","replicate":"2","replicate%type":"biological","species":"Mus musculus","species_type":"Animal","taxonomy_id":"10090","lineage_2":"12_Caki-1_adPGC1A_13CGlc_rep2-cells","cell_type":"Caki-1","protocol.id":"cell_quench_collection","lineage_3":"12_Caki-1_adPGC1A_13CGlc_rep2-cells-polar_GCMS_A","protocol.id":"polar_extraction","replicate":"1","replicate%type":"analytical","type":"polar","weight":"0.2149","weight%units":"g"}
},
{
"Subject ID":"-",
"Sample ID":"3_RCC4_adGFP_13CGlc_rep1-cells-polar_GCMS_A",
"Factors":{"cell_type":"RCC4","protocol.id":"adGFP_13CGlc"},
"Additional sample data":{"lineage_1":"3_RCC4_adGFP_13CGlc_rep1","cell_type":"RCC4","plate_media_tare":"-1","plate_media_tare%units":"g","protocol.id":"adGFP_13CGlc","replicate":"1","replicate%type":"biological","species":"Mus musculus","species_type":"Animal","taxonomy_id":"10090","lineage_2":"3_RCC4_adGFP_13CGlc_rep1-cells","cell_type":"RCC4","protocol.id":"cell_quench_collection","lineage_3":"3_RCC4_adGFP_13CGlc_rep1-cells-polar_GCMS_A","protocol.id":"polar_extraction","replicate":"1","replicate%type":"analytical","type":"polar","weight":"0.227","weight%units":"g"}
},
{
"Subject ID":"-",
"Sample ID":"4_RCC4_adGFP_13CGlc_rep2-cells-polar_GCMS_A",
"Factors":{"cell_type":"RCC4","protocol.id":"adGFP_13CGlc"},
"Additional sample data":{"lineage_1":"4_RCC4_adGFP_13CGlc_rep2","cell_type":"RCC4","plate_media_tare":"-1","plate_media_tare%units":"g","protocol.id":"adGFP_13CGlc","replicate":"2","replicate%type":"biological","species":"Mus musculus","species_type":"Animal","taxonomy_id":"10090","lineage_2":"4_RCC4_adGFP_13CGlc_rep2-cells","cell_type":"RCC4","protocol.id":"cell_quench_collection","lineage_3":"4_RCC4_adGFP_13CGlc_rep2-cells-polar_GCMS_A","protocol.id":"polar_extraction","replicate":"1","replicate%type":"analytical","type":"polar","weight":"0.2295","weight%units":"g"}
},
{
"Subject ID":"-",
"Sample ID":"5_RCC4_adPGC1A_13CGlc_rep1-cells-polar_GCMS_A",
"Factors":{"cell_type":"RCC4","protocol.id":"adPGC1A_13CGlc"},
"Additional sample data":{"lineage_1":"5_RCC4_adPGC1A_13CGlc_rep1","cell_type":"RCC4","plate_media_tare":"-1","plate_media_tare%units":"g","protocol.id":"adPGC1A_13CGlc","replicate":"1","replicate%type":"biological","species":"Mus musculus","species_type":"Animal","taxonomy_id":"10090","lineage_2":"5_RCC4_adPGC1A_13CGlc_rep1-cells","cell_type":"RCC4","protocol.id":"cell_quench_collection","lineage_3":"5_RCC4_adPGC1A_13CGlc_rep1-cells-polar_GCMS_A","protocol.id":"polar_extraction","replicate":"1","replicate%type":"analytical","type":"polar","weight":"0.2317","weight%units":"g"}
},
{
"Subject ID":"-",
"Sample ID":"6_RCC4_adPGC1A_13CGlc_rep2-cells-polar_GCMS_A",
"Factors":{"cell_type":"RCC4","protocol.id":"adPGC1A_13CGlc"},
"Additional sample data":{"lineage_1":"6_RCC4_adPGC1A_13CGlc_rep2","cell_type":"RCC4","plate_media_tare":"-1","plate_media_tare%units":"g","protocol.id":"adPGC1A_13CGlc","replicate":"2","replicate%type":"biological","species":"Mus musculus","species_type":"Animal","taxonomy_id":"10090","lineage_2":"6_RCC4_adPGC1A_13CGlc_rep2-cells","cell_type":"RCC4","protocol.id":"cell_quench_collection","lineage_3":"6_RCC4_adPGC1A_13CGlc_rep2-cells-polar_GCMS_A","protocol.id":"polar_extraction","replicate":"1","replicate%type":"analytical","type":"polar","weight":"0.2302","weight%units":"g"}
},
{
"Subject ID":"-",
"Sample ID":"9_Caki-1_adGFP_13CGlc_rep1-cells-polar_GCMS_A",
"Factors":{"cell_type":"Caki-1","protocol.id":"adGFP_13CGlc"},
"Additional sample data":{"lineage_1":"9_Caki-1_adGFP_13CGlc_rep1","cell_type":"Caki-1","plate_media_tare":"-1","plate_media_tare%units":"g","protocol.id":"adGFP_13CGlc","replicate":"1","replicate%type":"biological","species":"Mus musculus","species_type":"Animal","taxonomy_id":"10090","lineage_2":"9_Caki-1_adGFP_13CGlc_rep1-cells","cell_type":"Caki-1","protocol.id":"cell_quench_collection","lineage_3":"9_Caki-1_adGFP_13CGlc_rep1-cells-polar_GCMS_A","protocol.id":"polar_extraction","replicate":"1","replicate%type":"analytical","type":"polar","weight":"0.23","weight%units":"g"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Collection and quench of cells in tissue culture Media is extracted from plate.","COLLECTION_PROTOCOL_ID":"cell_quench_collection cells_media","COLLECTION_PROTOCOL_FILENAME":"WS_Fan_Quench_cell_tissue.pdf","SAMPLE_TYPE":"Cultured cells"},

"TREATMENT":{"TREATMENT_SUMMARY":"Grown in unlabeled glucose and infected with adGFP. Grown in labeled glucose and infected with adGFP. Grown in unlabeled glucose and infected with adPGC1A. Grown in labeled glucose and infected with adPGC1A.","TREATMENT_PROTOCOL_ID":"adGFP_12CGlc adGFP_13CGlc adPGC1A_12CGlc adPGC1A_13CGlc"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Lipid extraction from cells. Polar extraction from cells. Protein extraction and quantification.","SAMPLEPREP_PROTOCOL_ID":"lipid_extraction polar_extraction protein_extraction","SAMPLEPREP_PROTOCOL_FILENAME":"WS_Fan_Extract_Polar_Lipid_Prot.pdf;WS_Fan_Prot_Quant.pdf"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"Targeted GC","CHROMATOGRAPHY_TYPE":"GC","INSTRUMENT_NAME":"GC-EI-MS, Thermo ITQ","COLUMN_NAME":"SGE 0.15 mm i.d. x 50 m fused silica open-tubular column, coated with 0.25 µm BPX-5 (5% phenylmethyl- phenylsiloxane) BPX-5 (5% phenylmethyl- phenylsiloxane)"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS"},

"MS":{"INSTRUMENT_NAME":"Thermo ITQ","INSTRUMENT_TYPE":"GC-ITQ","MS_TYPE":"EI","ION_MODE":"POSITIVE","MS_COMMENTS":"GCMS Analytical Experiment with detection of compounds by comparison to standards. Derivitization is done with MTBSTFA (N-methyl-N-[tert-butyldimethylsilyl]trifluoroacetamide)."},

"MS_METABOLITE_DATA":{
"Units":"normalized peak area",

"Data":[{"Metabolite":"Ala-13C0","10_Caki-1_adGFP_13CGlc_rep2-cells-polar_GCMS_A":"6.4241897825466925","11_Caki-1_adPGC1A_13CGlc_rep1-cells-polar_GCMS_A":"7.8984270757927995","12_Caki-1_adPGC1A_13CGlc_rep2-cells-polar_GCMS_A":"6.477316580437009","3_RCC4_adGFP_13CGlc_rep1-cells-polar_GCMS_A":"2.606917612615109","4_RCC4_adGFP_13CGlc_rep2-cells-polar_GCMS_A":"2.732416528959684","5_RCC4_adPGC1A_13CGlc_rep1-cells-polar_GCMS_A":"3.8906340687749443","6_RCC4_adPGC1A_13CGlc_rep2-cells-polar_GCMS_A":"3.4772305246282134","9_Caki-1_adGFP_13CGlc_rep1-cells-polar_GCMS_A":"6.100082394400357"},{"Metabolite":"Ala-13C1","10_Caki-1_adGFP_13CGlc_rep2-cells-polar_GCMS_A":"0.5415827848124741","11_Caki-1_adPGC1A_13CGlc_rep1-cells-polar_GCMS_A":"0.5052095885206913","12_Caki-1_adPGC1A_13CGlc_rep2-cells-polar_GCMS_A":"0.4013179790110141","3_RCC4_adGFP_13CGlc_rep1-cells-polar_GCMS_A":"0.07271960083128713","4_RCC4_adGFP_13CGlc_rep2-cells-polar_GCMS_A":"0.17115011688621878","5_RCC4_adPGC1A_13CGlc_rep1-cells-polar_GCMS_A":"0.26834066137804624","6_RCC4_adPGC1A_13CGlc_rep2-cells-polar_GCMS_A":"0.17142532181227485","9_Caki-1_adGFP_13CGlc_rep1-cells-polar_GCMS_A":"0.3321264297940224"},{"Metabolite":"Ala-13C2","10_Caki-1_adGFP_13CGlc_rep2-cells-polar_GCMS_A":"0.5481474487242058","11_Caki-1_adPGC1A_13CGlc_rep1-cells-polar_GCMS_A":"0.8555650402577313","12_Caki-1_adPGC1A_13CGlc_rep2-cells-polar_GCMS_A":"0.6604617654147859","3_RCC4_adGFP_13CGlc_rep1-cells-polar_GCMS_A":"0.20206167288490154","4_RCC4_adGFP_13CGlc_rep2-cells-polar_GCMS_A":"0.24876109072182162","5_RCC4_adPGC1A_13CGlc_rep1-cells-polar_GCMS_A":"0.510354490949757","6_RCC4_adPGC1A_13CGlc_rep2-cells-polar_GCMS_A":"0.3328981764180146","9_Caki-1_adGFP_13CGlc_rep1-cells-polar_GCMS_A":"0.5745610421486419"},{"Metabolite":"Ala-13C3","10_Caki-1_adGFP_13CGlc_rep2-cells-polar_GCMS_A":"7.071030370347523","11_Caki-1_adPGC1A_13CGlc_rep1-cells-polar_GCMS_A":"9.391343353938804","12_Caki-1_adPGC1A_13CGlc_rep2-cells-polar_GCMS_A":"8.503726311322726","3_RCC4_adGFP_13CGlc_rep1-cells-polar_GCMS_A":"1.2315921845199949","4_RCC4_adGFP_13CGlc_rep2-cells-polar_GCMS_A":"1.3012762865580982","5_RCC4_adPGC1A_13CGlc_rep1-cells-polar_GCMS_A":"2.0189998407601433","6_RCC4_adPGC1A_13CGlc_rep2-cells-polar_GCMS_A":"1.8366556948717396","9_Caki-1_adGFP_13CGlc_rep1-cells-polar_GCMS_A":"6.696928163785559"},{"Metabolite":"Ala-ALL","10_Caki-1_adGFP_13CGlc_rep2-cells-polar_GCMS_A":"14.584950386430895","11_Caki-1_adPGC1A_13CGlc_rep1-cells-polar_GCMS_A":"18.650545058510026","12_Caki-1_adPGC1A_13CGlc_rep2-cells-polar_GCMS_A":"16.042822636185534","3_RCC4_adGFP_13CGlc_rep1-cells-polar_GCMS_A":"4.113291070851293","4_RCC4_adGFP_13CGlc_rep2-cells-polar_GCMS_A":"4.4536040231258225","5_RCC4_adPGC1A_13CGlc_rep1-cells-polar_GCMS_A":"6.68832906186289","6_RCC4_adPGC1A_13CGlc_rep2-cells-polar_GCMS_A":"5.818209717730243","9_Caki-1_adGFP_13CGlc_rep1-cells-polar_GCMS_A":"13.703698030128582"},{"Metabolite":"Arg-13C0","10_Caki-1_adGFP_13CGlc_rep2-cells-polar_GCMS_A":"3.505529135957547","11_Caki-1_adPGC1A_13CGlc_rep1-cells-polar_GCMS_A":"2.2474615951404275","12_Caki-1_adPGC1A_13CGlc_rep2-cells-polar_GCMS_A":"3.451258443992942","3_RCC4_adGFP_13CGlc_rep1-cells-polar_GCMS_A":"8.752813466570425","4_RCC4_adGFP_13CGlc_rep2-cells-polar_GCMS_A":"10.793528680847086","5_RCC4_adPGC1A_13CGlc_rep1-cells-polar_GCMS_A":"9.856335019614388","6_RCC4_adPGC1A_13CGlc_rep2-cells-polar_GCMS_A":"7.309463946820814","9_Caki-1_adGFP_13CGlc_rep1-cells-polar_GCMS_A":"3.7556172992241352"},{"Metabolite":"Arg-13C1","10_Caki-1_adGFP_13CGlc_rep2-cells-polar_GCMS_A":"1.174582637600387","11_Caki-1_adPGC1A_13CGlc_rep1-cells-polar_GCMS_A":"0.8022578815379406","12_Caki-1_adPGC1A_13CGlc_rep2-cells-polar_GCMS_A":"1.5225215256790112","3_RCC4_adGFP_13CGlc_rep1-cells-polar_GCMS_A":"4.377409610675915","4_RCC4_adGFP_13CGlc_rep2-cells-polar_GCMS_A":"3.244813222223054","5_RCC4_adPGC1A_13CGlc_rep1-cells-polar_GCMS_A":"3.7312286016530067","6_RCC4_adPGC1A_13CGlc_rep2-cells-polar_GCMS_A":"2.5566195151104596","9_Caki-1_adGFP_13CGlc_rep1-cells-polar_GCMS_A":"1.0694695175332167"},{"Metabolite":"Arg-13C2","10_Caki-1_adGFP_13CGlc_rep2-cells-polar_GCMS_A":"0.04095235031058458","11_Caki-1_adPGC1A_13CGlc_rep1-cells-polar_GCMS_A":"0.13184586585958774","12_Caki-1_adPGC1A_13CGlc_rep2-cells-polar_GCMS_A":"0.05999809320207791","3_RCC4_adGFP_13CGlc_rep1-cells-polar_GCMS_A":"0.2859380816782349","4_RCC4_adGFP_13CGlc_rep2-cells-polar_GCMS_A":"0.14865559019309812","5_RCC4_adPGC1A_13CGlc_rep1-cells-polar_GCMS_A":"0.1963506708953054","6_RCC4_adPGC1A_13CGlc_rep2-cells-polar_GCMS_A":"0","9_Caki-1_adGFP_13CGlc_rep1-cells-polar_GCMS_A":"0.1286677876427191"},{"Metabolite":"Arg-13C3","10_Caki-1_adGFP_13CGlc_rep2-cells-polar_GCMS_A":"0","11_Caki-1_adPGC1A_13CGlc_rep1-cells-polar_GCMS_A":"0","12_Caki-1_adPGC1A_13CGlc_rep2-cells-polar_GCMS_A":"0","3_RCC4_adGFP_13CGlc_rep1-cells-polar_GCMS_A":"0.6350448065421972","4_RCC4_adGFP_13CGlc_rep2-cells-polar_GCMS_A":"0.29032729791652867","5_RCC4_adPGC1A_13CGlc_rep1-cells-polar_GCMS_A":"0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}

}