{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001049","ANALYSIS_ID":"AN001864","VERSION":"1","CREATED_ON":"February 19, 2019, 9:19 pm"},

"PROJECT":{"PROJECT_TITLE":"P4HA1 knockdown in the breast cell line MDA231","PROJECT_SUMMARY":"Determine the effect of knocking down P4HA1 in the MDA231 cell line (including alterations to metabolic pathways).","INSTITUTE":"University of Kentucky","DEPARTMENT":"Markey Cancer Center","LAST_NAME":"Xu","FIRST_NAME":"Ren","ADDRESS":"BBSRC361, 741 South Limestone, Lexington, KY 40536, USA","EMAIL":"ren.xu2010@uky.edu","PHONE":"000-000-0000"},

"STUDY":{"STUDY_TITLE":"P4HA1 knockdown in the breast cell line MDA231 (part I)","STUDY_TYPE":"isotope tracer","STUDY_SUMMARY":"Determine the effect of knocking down P4HA1 in the MDA231 cell line (including alterations to metabolic pathways). Control versus knockdown","INSTITUTE":"University of Kentucky","DEPARTMENT":"Markey Cancer Center","LAST_NAME":"Xiong","FIRST_NAME":"Gaofeng","ADDRESS":"BBSRC361, 741 South Limestone, Lexington, KY 40536, USA","EMAIL":"gaofeng.xiong@uky.edu","PHONE":"000-000-0000","STUDY_COMMENTS":"For additional comments about the study, like listing a publication."},

"SUBJECT":{"SUBJECT_TYPE":"Animal","SUBJECT_SPECIES":"Homo sapiens","TAXONOMY_ID":"9606"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"1_MDA231_12CGlc_shCTL_rep1-cells-polar_GCMS_A",
"Factors":{"protocol.id":"12CGlc_shCTL"},
"Additional sample data":{"lineage_1":"1_MDA231_12CGlc_shCTL_rep1","cell_type":"MDA231","plate_with_media_weight":"19.2778","plate_with_media_weight%units":"g","protocol.id":"12CGlc_shCTL","replicate":"1","lineage_2":"1_MDA231_12CGlc_shCTL_rep1-cells","cell_type":"MDA231","protocol.id":"cell_quench_collection","lineage_3":"1_MDA231_12CGlc_shCTL_rep1-cells-polar_GCMS_A","protocol.id":"['polar_extraction', 'GCMS_file_storage1']","replicate":"1","replicate%type":"analytical","sample_split_ratio":"0.11677828270748629","type":"polar","weight":"0.19530000000000003","weight%units":"g","lineage_4":"1_MDA231_12CGlc_shCTL_rep1-cells-protein","dry_weight":"0.00039999999999995595","dry_weight%units":"g","protein_weight":"0.3296","protein_weight%units":"mg","protocol.id":"protein_extraction","type":"protein"}
},
{
"Subject ID":"-",
"Sample ID":"2_MDA231_13CGlc_shCTL_rep1-cells-polar_GCMS_A",
"Factors":{"protocol.id":"13CGlc_shCTL"},
"Additional sample data":{"lineage_1":"2_MDA231_13CGlc_shCTL_rep1","cell_type":"MDA231","plate_with_media_weight":"19.2007","plate_with_media_weight%units":"g","protocol.id":"13CGlc_shCTL","replicate":"1","lineage_2":"2_MDA231_13CGlc_shCTL_rep1-cells","cell_type":"MDA231","protocol.id":"cell_quench_collection","lineage_3":"2_MDA231_13CGlc_shCTL_rep1-cells-polar_GCMS_A","protocol.id":"['polar_extraction', 'GCMS_file_storage2']","replicate":"1","replicate%type":"analytical","sample_split_ratio":"0.11709869489384735","type":"polar","weight":"0.1947000000000001","weight%units":"g","lineage_4":"2_MDA231_13CGlc_shCTL_rep1-cells-protein","dry_weight":"0.00039999999999995595","dry_weight%units":"g","protein_weight":"0.2752","protein_weight%units":"mg","protocol.id":"protein_extraction","type":"protein"}
},
{
"Subject ID":"-",
"Sample ID":"3_MDA231_13CGlc_shCTL_rep2-cells-polar_GCMS_A",
"Factors":{"protocol.id":"13CGlc_shCTL"},
"Additional sample data":{"lineage_1":"3_MDA231_13CGlc_shCTL_rep2","cell_type":"MDA231","plate_with_media_weight":"19.2521","plate_with_media_weight%units":"g","protocol.id":"13CGlc_shCTL","replicate":"2","lineage_2":"3_MDA231_13CGlc_shCTL_rep2-cells","cell_type":"MDA231","protocol.id":"cell_quench_collection","lineage_3":"3_MDA231_13CGlc_shCTL_rep2-cells-polar_GCMS_A","protocol.id":"['polar_extraction', 'GCMS_file_storage3']","replicate":"1","replicate%type":"analytical","sample_split_ratio":"0.1137763563136698","type":"polar","weight":"0.19209999999999994","weight%units":"g","lineage_4":"3_MDA231_13CGlc_shCTL_rep2-cells-protein","dry_weight":"0.000500000000000167","dry_weight%units":"g","protein_weight":"0.35200000000000004","protein_weight%units":"mg","protocol.id":"protein_extraction","type":"protein"}
},
{
"Subject ID":"-",
"Sample ID":"4_MDA231_12CGlc_shP4HA1_rep1-cells-polar_GCMS_A",
"Factors":{"protocol.id":"12CGlc_shP4HA1"},
"Additional sample data":{"lineage_1":"4_MDA231_12CGlc_shP4HA1_rep1","cell_type":"MDA231","plate_with_media_weight":"19.3624","plate_with_media_weight%units":"g","protocol.id":"12CGlc_shP4HA1","replicate":"1","lineage_2":"4_MDA231_12CGlc_shP4HA1_rep1-cells","cell_type":"MDA231","protocol.id":"cell_quench_collection","lineage_3":"4_MDA231_12CGlc_shP4HA1_rep1-cells-polar_GCMS_A","protocol.id":"['polar_extraction', 'GCMS_file_storage4']","replicate":"1","replicate%type":"analytical","sample_split_ratio":"0.11863777089783266","type":"polar","weight":"0.19159999999999977","weight%units":"g","lineage_4":"4_MDA231_12CGlc_shP4HA1_rep1-cells-protein","dry_weight":"0.000700000000000145","dry_weight%units":"g","protein_weight":"0.5268","protein_weight%units":"mg","protocol.id":"protein_extraction","type":"protein"}
},
{
"Subject ID":"-",
"Sample ID":"5_MDA231_13CGlc_shP4HA1_rep1-cells-polar_GCMS_A",
"Factors":{"protocol.id":"13CGlc_shP4HA1"},
"Additional sample data":{"lineage_1":"5_MDA231_13CGlc_shP4HA1_rep1","cell_type":"MDA231","plate_with_media_weight":"19.0997","plate_with_media_weight%units":"g","protocol.id":"13CGlc_shP4HA1","replicate":"1","lineage_2":"5_MDA231_13CGlc_shP4HA1_rep1-cells","cell_type":"MDA231","protocol.id":"cell_quench_collection","lineage_3":"5_MDA231_13CGlc_shP4HA1_rep1-cells-polar_GCMS_A","protocol.id":"['polar_extraction', 'GCMS_file_storage5']","replicate":"1","replicate%type":"analytical","sample_split_ratio":"0.11954887218045103","type":"polar","weight":"0.19079999999999986","weight%units":"g","lineage_4":"5_MDA231_13CGlc_shP4HA1_rep1-cells-protein","dry_weight":"0.0006999999999999229","dry_weight%units":"g","protein_weight":"0.48300000000000004","protein_weight%units":"mg","protocol.id":"protein_extraction","type":"protein"}
},
{
"Subject ID":"-",
"Sample ID":"6_MDA231_13CGlc_shP4HA1_rep2-cells-polar_GCMS_A",
"Factors":{"protocol.id":"13CGlc_shP4HA1"},
"Additional sample data":{"lineage_1":"6_MDA231_13CGlc_shP4HA1_rep2","cell_type":"MDA231","plate_with_media_weight":"19.595","plate_with_media_weight%units":"g","protocol.id":"13CGlc_shP4HA1","replicate":"2","lineage_2":"6_MDA231_13CGlc_shP4HA1_rep2-cells","cell_type":"MDA231","protocol.id":"cell_quench_collection","lineage_3":"6_MDA231_13CGlc_shP4HA1_rep2-cells-polar_GCMS_A","protocol.id":"['polar_extraction', 'GCMS_file_storage6']","replicate":"1","replicate%type":"analytical","sample_split_ratio":"0.11783557253790207","type":"polar","weight":"0.19119999999999981","weight%units":"g","lineage_4":"6_MDA231_13CGlc_shP4HA1_rep2-cells-protein","dry_weight":"0.0005999999999999339","dry_weight%units":"g","protein_weight":"0.45480000000000004","protein_weight%units":"mg","protocol.id":"protein_extraction","type":"protein"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Collection and quench of cells in culture","COLLECTION_PROTOCOL_ID":"cell_quench_collection","COLLECTION_PROTOCOL_FILENAME":"3A_Cells_Quench_Cell_Fan_20170412.pdf","SAMPLE_TYPE":"cultured cells"},

"TREATMENT":{"TREATMENT_SUMMARY":"Cells grown in unlabeled glucose and infected with empty vector. Cells grown in unlabeled glucose and infected with shP4HA1 lentivirus. Cells grown in labeled glucose and infected with empty vector. Cells grown in labeled glucose and infected with shP4HA1 lentivirus.","TREATMENT_PROTOCOL_ID":"12CGlc_shCTL 12CGlc_shP4HA1 13CGlc_shCTL 13CGlc_shP4HA1"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Polar extraction from cells. Protein extraction and quantification.","SAMPLEPREP_PROTOCOL_ID":"polar_extraction protein_extraction","SAMPLEPREP_PROTOCOL_FILENAME":"4B_Extract_Polar_Lipid_Prot_Fan_070417.pdf;4D_17Jun4_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",
[],

"EXTENDED_METABOLITE_DATA":{

"Data":[{"Metabolite":"Ala-13C0","1_MDA231_12CGlc_shCTL_rep1-cells-polar_GCMS_A":"506256.238477944","2_MDA231_13CGlc_shCTL_rep1-cells-polar_GCMS_A":"229964.073849618","3_MDA231_13CGlc_shCTL_rep2-cells-polar_GCMS_A":"249489.439276942","4_MDA231_12CGlc_shP4HA1_rep1-cells-polar_GCMS_A":"911911.352500099","5_MDA231_13CGlc_shP4HA1_rep1-cells-polar_GCMS_A":"338638.862742118","6_MDA231_13CGlc_shP4HA1_rep2-cells-polar_GCMS_A":"378222.230159121"},{"Metabolite":"Ala-13C1","1_MDA231_12CGlc_shCTL_rep1-cells-polar_GCMS_A":"144562.147070982","2_MDA231_13CGlc_shCTL_rep1-cells-polar_GCMS_A":"82815.7728955919","3_MDA231_13CGlc_shCTL_rep2-cells-polar_GCMS_A":"731.540067467209","4_MDA231_12CGlc_shP4HA1_rep1-cells-polar_GCMS_A":"220647.17289539","5_MDA231_13CGlc_shP4HA1_rep1-cells-polar_GCMS_A":"88341.3509370836","6_MDA231_13CGlc_shP4HA1_rep2-cells-polar_GCMS_A":"108559.53056973"},{"Metabolite":"Ala-13C2","1_MDA231_12CGlc_shCTL_rep1-cells-polar_GCMS_A":"49187.2285303682","2_MDA231_13CGlc_shCTL_rep1-cells-polar_GCMS_A":"226327.999000629","3_MDA231_13CGlc_shCTL_rep2-cells-polar_GCMS_A":"231567.691922174","4_MDA231_12CGlc_shP4HA1_rep1-cells-polar_GCMS_A":"88169.3921545687","5_MDA231_13CGlc_shP4HA1_rep1-cells-polar_GCMS_A":"250380.273623857","6_MDA231_13CGlc_shP4HA1_rep2-cells-polar_GCMS_A":"237994.247508388"},{"Metabolite":"Ala-13C3","1_MDA231_12CGlc_shCTL_rep1-cells-polar_GCMS_A":"29775.4216637624","2_MDA231_13CGlc_shCTL_rep1-cells-polar_GCMS_A":"128311.130315961","3_MDA231_13CGlc_shCTL_rep2-cells-polar_GCMS_A":"158092.005390602","4_MDA231_12CGlc_shP4HA1_rep1-cells-polar_GCMS_A":"35468.3622575522","5_MDA231_13CGlc_shP4HA1_rep1-cells-polar_GCMS_A":"247372.439054826","6_MDA231_13CGlc_shP4HA1_rep2-cells-polar_GCMS_A":"270082.399736745"},{"Metabolite":"Ala-ALL","1_MDA231_12CGlc_shCTL_rep1-cells-polar_GCMS_A":"1921560.01145741","2_MDA231_13CGlc_shCTL_rep1-cells-polar_GCMS_A":"910702.032956958","3_MDA231_13CGlc_shCTL_rep2-cells-polar_GCMS_A":"1021540.77561014","4_MDA231_12CGlc_shP4HA1_rep1-cells-polar_GCMS_A":"2986793.54637897","5_MDA231_13CGlc_shP4HA1_rep1-cells-polar_GCMS_A":"1282036.44889102","6_MDA231_13CGlc_shP4HA1_rep2-cells-polar_GCMS_A":"1365623.2412963"},{"Metabolite":"Arg-13C0","1_MDA231_12CGlc_shCTL_rep1-cells-polar_GCMS_A":"91674.1119080221","2_MDA231_13CGlc_shCTL_rep1-cells-polar_GCMS_A":"55141.763204899","3_MDA231_13CGlc_shCTL_rep2-cells-polar_GCMS_A":"58697.8323507317","4_MDA231_12CGlc_shP4HA1_rep1-cells-polar_GCMS_A":"195448.029111307","5_MDA231_13CGlc_shP4HA1_rep1-cells-polar_GCMS_A":"100129.320382883","6_MDA231_13CGlc_shP4HA1_rep2-cells-polar_GCMS_A":"147249.034420649"},{"Metabolite":"Arg-13C1","1_MDA231_12CGlc_shCTL_rep1-cells-polar_GCMS_A":"56791.4631593401","2_MDA231_13CGlc_shCTL_rep1-cells-polar_GCMS_A":"39876.3439210716","3_MDA231_13CGlc_shCTL_rep2-cells-polar_GCMS_A":"41304.473270103","4_MDA231_12CGlc_shP4HA1_rep1-cells-polar_GCMS_A":"105513.709294199","5_MDA231_13CGlc_shP4HA1_rep1-cells-polar_GCMS_A":"40446.8230859974","6_MDA231_13CGlc_shP4HA1_rep2-cells-polar_GCMS_A":"59320.8296802882"},{"Metabolite":"Arg-13C2","1_MDA231_12CGlc_shCTL_rep1-cells-polar_GCMS_A":"19696.868051077","2_MDA231_13CGlc_shCTL_rep1-cells-polar_GCMS_A":"13810.0386978497","3_MDA231_13CGlc_shCTL_rep2-cells-polar_GCMS_A":"17556.1414749448","4_MDA231_12CGlc_shP4HA1_rep1-cells-polar_GCMS_A":"42608.0371627586","5_MDA231_13CGlc_shP4HA1_rep1-cells-polar_GCMS_A":"21142.8618182165","6_MDA231_13CGlc_shP4HA1_rep2-cells-polar_GCMS_A":"37154.2959448681"},{"Metabolite":"Arg-13C3","1_MDA231_12CGlc_shCTL_rep1-cells-polar_GCMS_A":"11902.8998332849","2_MDA231_13CGlc_shCTL_rep1-cells-polar_GCMS_A":"11474.9766243521","3_MDA231_13CGlc_shCTL_rep2-cells-polar_GCMS_A":"7693.25440082897","4_MDA231_12CGlc_shP4HA1_rep1-cells-polar_GCMS_A":"13414.8565658469","5_MDA231_13CGlc_shP4HA1_rep1-cells-polar_GCMS_A":"7687.866893769","6_MDA231_13CGlc_shP4HA1_rep2-cells-polar_GCMS_A":"4893.6956267556"},{"Metabolite":"Arg-13C4","1_MDA231_12CGlc_shCTL_rep1-cells-polar_GCMS_A":"6818.50094601351","2_MDA231_13CGlc_shCTL_rep1-cells-polar_GCMS_A":"1068.0307730571","3_MDA231_13CGlc_shCTL_rep2-cells-polar_GCMS_A":"747.431759177354","4_MDA231_12CGlc_shP4HA1_rep1-cells-polar_GCMS_A":"4100.62151747004","5_MDA231_13CGlc_shP4HA1_rep1-cells-polar_GCMS_A":"946.442864717776","6_MDA231_13CGlc_shP4HA1_rep2-cells-polar_GCMS_A":"3918.35707975093"},{"Metabolite":"Arg-13C5","1_MDA231_12CGlc_shCTL_rep1-cells-polar_GCMS_A":"907.272757247752","2_MDA231_13CGlc_shCTL_rep1-cells-polar_GCMS_A":"359.846754252547","3_MDA231_13CGlc_shCTL_rep2-cells-polar_GCMS_A":"662.268064302592","4_MDA231_12CGlc_shP4HA1_rep1-cells-polar_GCMS_A":"2451.12698297877","5_MDA231_13CGlc_shP4HA1_rep1-cells-polar_GCMS_A":"2225.29786733379","6_MDA231_13CGlc_shP4HA1_rep2-cells-polar_GCMS_A":"4438.8286374608"},{"Metabolite":"Arg-13C6","1_MDA231_12CGlc_shCTL_rep1-cells-polar_GCMS_A":"2177.0790533307","2_MDA231_13CGlc_shCTL_rep1-cells-polar_GCMS_A":"984.435807118166","3_MDA231_13CGlc_shCTL_rep2-cells-polar_GCMS_A":"1570.90068429392","4_MD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}

}