{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001050","ANALYSIS_ID":"AN001865","VERSION":"1","CREATED_ON":"02-08-2024"},

"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","DOI":"http://dx.doi.org/10.21228/M8T10P"},

"STUDY":{"STUDY_TITLE":"P4HA1 knockdown in the breast cell line MDA231 Gln metabolism (part II)","STUDY_TYPE":"isotope tracer","STUDY_SUMMARY":"Determine the effect on glutamine metabolism of knocking down P4HA1 in the MDA231 cell line.","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","SUBMIT_DATE":"2018-09-12"},

"SUBJECT":{"SUBJECT_TYPE":"Animal","SUBJECT_SPECIES":"Homo sapiens","TAXONOMY_ID":"9606"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"1_MDA231_12C14NGln_shCTL_rep1-cells-polar_GCMS_A",
"Factors":{"protocol.id":"12C14NGln_shCTL"},
"Additional sample data":{"lineage_1":"1_MDA231_12C14NGln_shCTL_rep1","cell_type":"MDA231","plate_with_media_weight":"19.66","plate_with_media_weight%units":"g","protocol.id":"12C14NGln_shCTL","replicate":"1","species":"Homo sapiens","species_type":"Animal","taxonomy_id":"9606","lineage_2":"1_MDA231_12C14NGln_shCTL_rep1-cells","cell_type":"MDA231","protocol.id":"cell_quench_collection","lineage_3":"1_MDA231_12C14NGln_shCTL_rep1-cells-polar_GCMS_A","protocol.id":"['polar_extraction', 'GCMS_file_storage1']","replicate":"1","replicate%type":"analytical","sample_split_ratio":"0.11609437047418822","type":"polar","weight":"0.19879999999999987","weight%units":"g","lineage_4":"1_MDA231_12C14NGln_shCTL_rep1-cells-protein","dry_weight":"0.0008000000000000229","dry_weight%units":"g","protein_weight":"0.588","protein_weight%units":"mg","protocol.id":"protein_extraction","type":"protein"}
},
{
"Subject ID":"-",
"Sample ID":"5_MDA231_12C14NGln_shP4HA1_rep1-cells-polar_GCMS_A",
"Factors":{"protocol.id":"12C14NGln_shP4HA1"},
"Additional sample data":{"lineage_1":"5_MDA231_12C14NGln_shP4HA1_rep1","cell_type":"MDA231","plate_with_media_weight":"19.25","plate_with_media_weight%units":"g","protocol.id":"12C14NGln_shP4HA1","replicate":"1","species":"Homo sapiens","species_type":"Animal","taxonomy_id":"9606","lineage_2":"5_MDA231_12C14NGln_shP4HA1_rep1-cells","cell_type":"MDA231","protocol.id":"cell_quench_collection","lineage_3":"5_MDA231_12C14NGln_shP4HA1_rep1-cells-polar_GCMS_A","protocol.id":"['polar_extraction', 'GCMS_file_storage5']","replicate":"1","replicate%type":"analytical","sample_split_ratio":"0.11302462816884443","type":"polar","weight":"0.18769999999999998","weight%units":"g","lineage_4":"5_MDA231_12C14NGln_shP4HA1_rep1-cells-protein","dry_weight":"0.0008000000000000229","dry_weight%units":"g","protein_weight":"0.6232000000000001","protein_weight%units":"mg","protocol.id":"protein_extraction","type":"protein"}
},
{
"Subject ID":"-",
"Sample ID":"2_MDA231_13C15NGln_shCTL_rep1-cells-polar_GCMS_A",
"Factors":{"protocol.id":"13C15NGln_shCTL"},
"Additional sample data":{"lineage_1":"2_MDA231_13C15NGln_shCTL_rep1","cell_type":"MDA231","plate_with_media_weight":"19.66","plate_with_media_weight%units":"g","protocol.id":"13C15NGln_shCTL","replicate":"1","species":"Homo sapiens","species_type":"Animal","taxonomy_id":"9606","lineage_2":"2_MDA231_13C15NGln_shCTL_rep1-cells","cell_type":"MDA231","protocol.id":"cell_quench_collection","lineage_3":"2_MDA231_13C15NGln_shCTL_rep1-cells-polar_GCMS_A","protocol.id":"['polar_extraction', 'GCMS_file_storage2']","replicate":"1","replicate%type":"analytical","sample_split_ratio":"0.1135852185242211","type":"polar","weight":"0.19179999999999975","weight%units":"g","lineage_4":"2_MDA231_13C15NGln_shCTL_rep1-cells-protein","dry_weight":"0.0008000000000000229","dry_weight%units":"g","protein_weight":"0.5884","protein_weight%units":"mg","protocol.id":"protein_extraction","type":"protein"}
},
{
"Subject ID":"-",
"Sample ID":"3_MDA231_13C15NGln_shCTL_rep2-cells-polar_GCMS_A",
"Factors":{"protocol.id":"13C15NGln_shCTL"},
"Additional sample data":{"lineage_1":"3_MDA231_13C15NGln_shCTL_rep2","cell_type":"MDA231","plate_with_media_weight":"19.65","plate_with_media_weight%units":"g","protocol.id":"13C15NGln_shCTL","replicate":"2","species":"Homo sapiens","species_type":"Animal","taxonomy_id":"9606","lineage_2":"3_MDA231_13C15NGln_shCTL_rep2-cells","cell_type":"MDA231","protocol.id":"cell_quench_collection","lineage_3":"3_MDA231_13C15NGln_shCTL_rep2-cells-polar_GCMS_A","protocol.id":"['polar_extraction', 'GCMS_file_storage3']","replicate":"1","replicate%type":"analytical","sample_split_ratio":"0.1135516196690749","type":"polar","weight":"0.19490000000000007","weight%units":"g","lineage_4":"3_MDA231_13C15NGln_shCTL_rep2-cells-protein","dry_weight":"0.0006999999999999229","dry_weight%units":"g","protein_weight":"0.5808","protein_weight%units":"mg","protocol.id":"protein_extraction","type":"protein"}
},
{
"Subject ID":"-",
"Sample ID":"4_MDA231_13C15NGln_shCTL_rep3-cells-polar_GCMS_A",
"Factors":{"protocol.id":"13C15NGln_shCTL"},
"Additional sample data":{"lineage_1":"4_MDA231_13C15NGln_shCTL_rep3","cell_type":"MDA231","plate_with_media_weight":"19.17","plate_with_media_weight%units":"g","protocol.id":"13C15NGln_shCTL","replicate":"3","species":"Homo sapiens","species_type":"Animal","taxonomy_id":"9606","lineage_2":"4_MDA231_13C15NGln_shCTL_rep3-cells","cell_type":"MDA231","protocol.id":"cell_quench_collection","lineage_3":"4_MDA231_13C15NGln_shCTL_rep3-cells-polar_GCMS_A","protocol.id":"['polar_extraction', 'GCMS_file_storage4']","replicate":"1","replicate%type":"analytical","sample_split_ratio":"0.11416716064018967","type":"polar","weight":"0.1926000000000001","weight%units":"g","lineage_4":"4_MDA231_13C15NGln_shCTL_rep3-cells-protein","dry_weight":"0.0007000000000000339","dry_weight%units":"g","protein_weight":"0.5344000000000001","protein_weight%units":"mg","protocol.id":"protein_extraction","type":"protein"}
},
{
"Subject ID":"-",
"Sample ID":"6_MDA231_13C15NGln_shP4HA1_rep1-cells-polar_GCMS_A",
"Factors":{"protocol.id":"13C15NGln_shP4HA1"},
"Additional sample data":{"lineage_1":"6_MDA231_13C15NGln_shP4HA1_rep1","cell_type":"MDA231","plate_with_media_weight":"19.13","plate_with_media_weight%units":"g","protocol.id":"13C15NGln_shP4HA1","replicate":"1","species":"Homo sapiens","species_type":"Animal","taxonomy_id":"9606","lineage_2":"6_MDA231_13C15NGln_shP4HA1_rep1-cells","cell_type":"MDA231","protocol.id":"cell_quench_collection","lineage_3":"6_MDA231_13C15NGln_shP4HA1_rep1-cells-polar_GCMS_A","protocol.id":"['polar_extraction', 'GCMS_file_storage6']","replicate":"1","replicate%type":"analytical","sample_split_ratio":"0.11430485354119722","type":"polar","weight":"0.18769999999999998","weight%units":"g","lineage_4":"6_MDA231_13C15NGln_shP4HA1_rep1-cells-protein","dry_weight":"0.0009000000000000119","dry_weight%units":"g","protein_weight":"0.5952000000000001","protein_weight%units":"mg","protocol.id":"protein_extraction","type":"protein"}
},
{
"Subject ID":"-",
"Sample ID":"7_MDA231_13C15NGln_shP4HA1_rep2-cells-polar_GCMS_A",
"Factors":{"protocol.id":"13C15NGln_shP4HA1"},
"Additional sample data":{"lineage_1":"7_MDA231_13C15NGln_shP4HA1_rep2","cell_type":"MDA231","plate_with_media_weight":"19.66","plate_with_media_weight%units":"g","protocol.id":"13C15NGln_shP4HA1","replicate":"2","species":"Homo sapiens","species_type":"Animal","taxonomy_id":"9606","lineage_2":"7_MDA231_13C15NGln_shP4HA1_rep2-cells","cell_type":"MDA231","protocol.id":"cell_quench_collection","lineage_3":"7_MDA231_13C15NGln_shP4HA1_rep2-cells-polar_GCMS_A","protocol.id":"['polar_extraction', 'GCMS_file_storage7']","replicate":"1","replicate%type":"analytical","sample_split_ratio":"0.11465347714677317","type":"polar","weight":"0.19240000000000013","weight%units":"g","lineage_4":"7_MDA231_13C15NGln_shP4HA1_rep2-cells-protein","dry_weight":"0.0010999999999999899","dry_weight%units":"g","protein_weight":"0.5852","protein_weight%units":"mg","protocol.id":"protein_extraction","type":"protein"}
},
{
"Subject ID":"-",
"Sample ID":"8_MDA231_13C15NGln_shP4HA1_rep3-cells-polar_GCMS_A",
"Factors":{"protocol.id":"13C15NGln_shP4HA1"},
"Additional sample data":{"lineage_1":"8_MDA231_13C15NGln_shP4HA1_rep3","cell_type":"MDA231","plate_with_media_weight":"19.3","plate_with_media_weight%units":"g","protocol.id":"13C15NGln_shP4HA1","replicate":"3","species":"Homo sapiens","species_type":"Animal","taxonomy_id":"9606","lineage_2":"8_MDA231_13C15NGln_shP4HA1_rep3-cells","cell_type":"MDA231","protocol.id":"cell_quench_collection","lineage_3":"8_MDA231_13C15NGln_shP4HA1_rep3-cells-polar_GCMS_A","protocol.id":"['polar_extraction', 'GCMS_file_storage8']","replicate":"1","replicate%type":"analytical","sample_split_ratio":"0.11736305656553601","type":"polar","weight":"0.19689999999999985","weight%units":"g","lineage_4":"8_MDA231_13C15NGln_shP4HA1_rep3-cells-protein","dry_weight":"0.0008999999999999009","dry_weight%units":"g","protein_weight":"0.6532","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 glutamine and infected with empty vector. Cells grown in unlabeled glutamine and infected with shP4HA1 lentivirus. Cells grown in labeled glutamine and infected with empty vector. Cells grown in labeled glutamine and infected with shP4HA1 lentivirus.","TREATMENT_PROTOCOL_ID":"12C14NGln_shCTL 12C14NGln_shP4HA1 13C15NGln_shCTL 13C15NGln_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","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)","CHROMATOGRAPHY_TYPE":"GC"},

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

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

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

"Data":[{"Metabolite":"a-glycerol-3P_#1-13C0_15N0","1_MDA231_12C14NGln_shCTL_rep1-cells-polar_GCMS_A":"2.2310","5_MDA231_12C14NGln_shP4HA1_rep1-cells-polar_GCMS_A":"4.3511","2_MDA231_13C15NGln_shCTL_rep1-cells-polar_GCMS_A":"5.2225","3_MDA231_13C15NGln_shCTL_rep2-cells-polar_GCMS_A":"70.5788","4_MDA231_13C15NGln_shCTL_rep3-cells-polar_GCMS_A":"3.0110","6_MDA231_13C15NGln_shP4HA1_rep1-cells-polar_GCMS_A":"10.3189","7_MDA231_13C15NGln_shP4HA1_rep2-cells-polar_GCMS_A":"2.3633","8_MDA231_13C15NGln_shP4HA1_rep3-cells-polar_GCMS_A":"6.1527"},{"Metabolite":"a-glycerol-3P_#1-13C1_15N0","1_MDA231_12C14NGln_shCTL_rep1-cells-polar_GCMS_A":"1.1106","5_MDA231_12C14NGln_shP4HA1_rep1-cells-polar_GCMS_A":"","2_MDA231_13C15NGln_shCTL_rep1-cells-polar_GCMS_A":"2.8842","3_MDA231_13C15NGln_shCTL_rep2-cells-polar_GCMS_A":"","4_MDA231_13C15NGln_shCTL_rep3-cells-polar_GCMS_A":"0.6669","6_MDA231_13C15NGln_shP4HA1_rep1-cells-polar_GCMS_A":"","7_MDA231_13C15NGln_shP4HA1_rep2-cells-polar_GCMS_A":"4.6578","8_MDA231_13C15NGln_shP4HA1_rep3-cells-polar_GCMS_A":""},{"Metabolite":"a-glycerol-3P_#1-13C2_15N0","1_MDA231_12C14NGln_shCTL_rep1-cells-polar_GCMS_A":"3.3711","5_MDA231_12C14NGln_shP4HA1_rep1-cells-polar_GCMS_A":"","2_MDA231_13C15NGln_shCTL_rep1-cells-polar_GCMS_A":"","3_MDA231_13C15NGln_shCTL_rep2-cells-polar_GCMS_A":"","4_MDA231_13C15NGln_shCTL_rep3-cells-polar_GCMS_A":"0.5767","6_MDA231_13C15NGln_shP4HA1_rep1-cells-polar_GCMS_A":"","7_MDA231_13C15NGln_shP4HA1_rep2-cells-polar_GCMS_A":"","8_MDA231_13C15NGln_shP4HA1_rep3-cells-polar_GCMS_A":"0.8528"},{"Metabolite":"a-glycerol-3P_#1-13C3_15N0","1_MDA231_12C14NGln_shCTL_rep1-cells-polar_GCMS_A":"","5_MDA231_12C14NGln_shP4HA1_rep1-cells-polar_GCMS_A":"","2_MDA231_13C15NGln_shCTL_rep1-cells-polar_GCMS_A":"","3_MDA231_13C15NGln_shCTL_rep2-cells-polar_GCMS_A":"","4_MDA231_13C15NGln_shCTL_rep3-cells-polar_GCMS_A":"0.2297","6_MDA231_13C15NGln_shP4HA1_rep1-cells-polar_GCMS_A":"1.6848","7_MDA231_13C15NGln_shP4HA1_rep2-cells-polar_GCMS_A":"","8_MDA231_13C15NGln_shP4HA1_rep3-cells-polar_GCMS_A":"0.3528"},{"Metabolite":"a-glycerol-3P_#1-ALL","1_MDA231_12C14NGln_shCTL_rep1-cells-polar_GCMS_A":"6.7128","5_MDA231_12C14NGln_shP4HA1_rep1-cells-polar_GCMS_A":"4.3511","2_MDA231_13C15NGln_shCTL_rep1-cells-polar_GCMS_A":"8.1066","3_MDA231_13C15NGln_shCTL_rep2-cells-polar_GCMS_A":"70.5788","4_MDA231_13C15NGln_shCTL_rep3-cells-polar_GCMS_A":"4.4844","6_MDA231_13C15NGln_shP4HA1_rep1-cells-polar_GCMS_A":"12.0038","7_MDA231_13C15NGln_shP4HA1_rep2-cells-polar_GCMS_A":"7.0210","8_MDA231_13C15NGln_shP4HA1_rep3-cells-polar_GCMS_A":"7.3582"},{"Metabolite":"a-glycerol-3P_#2-13C0_15N0","1_MDA231_12C14NGln_shCTL_rep1-cells-polar_GCMS_A":"0.4955","5_MDA231_12C14NGln_shP4HA1_rep1-cells-polar_GCMS_A":"0.1847","2_MDA231_13C15NGln_shCTL_rep1-cells-polar_GCMS_A":"0.1902","3_MDA231_13C15NGln_shCTL_rep2-cells-polar_GCMS_A":"0.0752","4_MDA231_13C15NGln_shCTL_rep3-cells-polar_GCMS_A":"0.5198","6_MDA231_13C15NGln_shP4HA1_rep1-cells-polar_GCMS_A":"","7_MDA231_13C15NGln_shP4HA1_rep2-cells-polar_GCMS_A":"17.7667","8_MDA231_13C15NGln_shP4HA1_rep3-cells-polar_GCMS_A":"0.0652"},{"Metabolite":"a-glycerol-3P_#2-13C1_15N0","1_MDA231_12C14NGln_shCTL_rep1-cells-polar_GCMS_A":"","5_MDA231_12C14NGln_shP4HA1_rep1-cells-polar_GCMS_A":"","2_MDA231_13C15NGln_shCTL_rep1-cells-polar_GCMS_A":"0.0251","3_MDA231_13C15NGln_shCTL_rep2-cells-polar_GCMS_A":"0.0504","4_MDA231_13C15NGln_shCTL_rep3-cells-polar_GCMS_A":"","6_MDA231_13C15NGln_shP4HA1_rep1-cells-polar_GCMS_A":"","7_MDA231_13C15NGln_shP4HA1_rep2-cells-polar_GCMS_A":"","8_MDA231_13C15NGln_shP4HA1_rep3-cells-polar_GCMS_A":"0.0957"},{"Metabolite":"a-glycerol-3P_#2-13C2_15N0","1_MDA231_12C14NGln_shCTL_rep1-cells-polar_GCMS_A":"","5_MDA231_12C14NGln_shP4HA1_rep1-cells-polar_GCMS_A":"0.1175","2_MDA231_13C15NGln_shCTL_rep1-cells-polar_GCMS_A":"0.0260","3_MDA231_13C15NGln_shCTL_rep2-cells-polar_GCMS_A":"0.1200","4_MDA231_13C15NGln_shCTL_rep3-cells-polar_GCMS_A":"","6_MDA231_13C15NGln_shP4HA1_rep1-cells-polar_GCMS_A":"","7_MDA231_13C15NGln_shP4HA1_rep2-cells-polar_GCMS_A":"","8_MDA231_13C15NGln_shP4HA1_rep3-cells-polar_GCMS_A":""},{"Metabolite":"a-glycerol-3P_#2-13C3_15N0","1_MDA231_12C14NGln_shCTL_rep1-cells-polar_GCMS_A":"","5_MDA231_12C14NGln_shP4HA1_rep1-cells-polar_GCMS_A":"0.0173","2_MDA231_13C15NGln_shCTL_rep1-cells-polar_GCMS_A":"","3_MDA231_13C15NGln_shCTL_rep2-cells-polar_GCMS_A":"","4_MDA231_13C15NGln_shCTL_rep3-cells-polar_GCMS_A":"","6_MDA231_13C15NGln_shP4HA1_rep1-cells-polar_GCMS_A":"","7_MDA231_13C15NGln_shP4HA1_rep2-cells-polar_GCMS_A":"0.1887","8_MDA231_13C15NGln_shP4HA1_rep3-cells-polar_GCMS_A":"0.0477"},{"Metabolite":"a-glycerol-3P_#2-ALL","1_MDA231_12C14NGln_shCTL_rep1-cells-polar_GCMS_A":"0.4955","5_MDA231_12C14NGln_shP4HA1_rep1-cells-polar_GCMS_A":"0.3195","2_MDA231_13C15NGln_shCTL_rep1-cells-polar_GCMS_A":"0.2413","3_MDA231_13C15NGln_shCTL_rep2-cells-polar_GCMS_A":"0.2457","4_MDA231_13C15NGln_shCTL_rep3-cells-polar_GCMS_A":"0.5198","6_MDA231_13C15NGln_shP4HA1_rep1-cells-polar_G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