{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST001909","ANALYSIS_ID":"AN003106","VERSION":"1","CREATED_ON":"August 18, 2021, 9:46 am"},

"PROJECT":{"PROJECT_TITLE":"ATF3 regulation of serine metabolism","PROJECT_TYPE":"Isotope Tracing, GC-MS","PROJECT_SUMMARY":"ATF3 is a common stress sensor, and its expression can be induced by serine deprivation. The goal of this project is to determine whether ATF3 regulates serine biosynthesis. ATF3-wildtype and –knockout cells are cultured in complete or serine-free medium supplemented with 13C-6-glucose for 24 h for stable isotope tracing. The results show that ATF3 appears to promote serine biosynthesis.","INSTITUTE":"Augusta University","DEPARTMENT":"Georgia Cancer Center","LAST_NAME":"Yan","FIRST_NAME":"Chunhong","ADDRESS":"1410 Laney Walker Blvd, Augusta, GA, 30912, USA","EMAIL":"cyan@augusta.edu","PHONE":"7067210099","FUNDING_SOURCE":"NIH/NCI R01CA240933, R01CA190429, R01CA236890"},

"STUDY":{"STUDY_TITLE":"ATF3 regulation of serine metabolism","STUDY_SUMMARY":"ATF3 is a common stress sensor, and its expression can be induced by serine deprivation. The goal of this project is to determine whether ATF3 regulates serine biosynthesis. ATF3-wildtype and –knockout cells are cultured in complete or serine-free medium supplemented with 13C-6-glucose for 24 h for stable isotope tracing. The results show that ATF3 appears to promote serine biosynthesis.","INSTITUTE":"Augusta University","LAST_NAME":"Yan","FIRST_NAME":"Chunhong","ADDRESS":"1410 Laney Walker Blvd, Augusta, GA, 30912, USA","EMAIL":"cyan@augusta.edu","STUDY_TYPE":"stable isotope tracing","PHONE":"7067210099"},

"SUBJECT":{"SUBJECT_TYPE":"Cultured cells","SUBJECT_SPECIES":"Homo sapiens","TAXONOMY_ID":"9606","GENOTYPE_STRAIN":"ATF3(+/+) vs ATF3(-/-)","CELL_STRAIN_DETAILS":"HCT116 cells engineered to knockout ATF3 expression via rAAV-mediated homologous recombination"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"Ding_A-1_001",
"Factors":{"Genotype_Media supplement":"WT-complete"},
"Additional sample data":{"RAW_FILE_NAME":"210517_Ding_A-1_001_TBS.D"}
},
{
"Subject ID":"-",
"Sample ID":"Ding_A-2_002",
"Factors":{"Genotype_Media supplement":"WT-complete"},
"Additional sample data":{"RAW_FILE_NAME":"210517_Ding_A-2_002_TBS.D"}
},
{
"Subject ID":"-",
"Sample ID":"Ding_A-3_003",
"Factors":{"Genotype_Media supplement":"WT-complete"},
"Additional sample data":{"RAW_FILE_NAME":"210517_Ding_A-3_003_TBS.D"}
},
{
"Subject ID":"-",
"Sample ID":"Ding_A-4_004",
"Factors":{"Genotype_Media supplement":"WT-complete"},
"Additional sample data":{"RAW_FILE_NAME":"210517_Ding_A-4_004_TBS.D"}
},
{
"Subject ID":"-",
"Sample ID":"Ding_A-5_005",
"Factors":{"Genotype_Media supplement":"WT-complete"},
"Additional sample data":{"RAW_FILE_NAME":"210517_Ding_A-5_005_TBS.D"}
},
{
"Subject ID":"-",
"Sample ID":"Ding_A-6_006",
"Factors":{"Genotype_Media supplement":"WT-complete"},
"Additional sample data":{"RAW_FILE_NAME":"210517_Ding_A-6_006_TBS.D"}
},
{
"Subject ID":"-",
"Sample ID":"Ding_B-1_007",
"Factors":{"Genotype_Media supplement":"WT-serine(-)"},
"Additional sample data":{"RAW_FILE_NAME":"210517_Ding_B-1_007_TBS.D"}
},
{
"Subject ID":"-",
"Sample ID":"Ding_B-2_008",
"Factors":{"Genotype_Media supplement":"WT-serine(-)"},
"Additional sample data":{"RAW_FILE_NAME":"210517_Ding_B-2_008_TBS.D"}
},
{
"Subject ID":"-",
"Sample ID":"Ding_B-3_009",
"Factors":{"Genotype_Media supplement":"WT-serine(-)"},
"Additional sample data":{"RAW_FILE_NAME":"210517_Ding_B-3_009_TBS.D"}
},
{
"Subject ID":"-",
"Sample ID":"Ding_B-4_010",
"Factors":{"Genotype_Media supplement":"WT-serine(-)"},
"Additional sample data":{"RAW_FILE_NAME":"210517_Ding_B-4_010_TBS.D"}
},
{
"Subject ID":"-",
"Sample ID":"Ding_B-5_011",
"Factors":{"Genotype_Media supplement":"WT-serine(-)"},
"Additional sample data":{"RAW_FILE_NAME":"210517_Ding_B-5_011_TBS.D"}
},
{
"Subject ID":"-",
"Sample ID":"Ding_B-6_012",
"Factors":{"Genotype_Media supplement":"WT-serine(-)"},
"Additional sample data":{"RAW_FILE_NAME":"210517_Ding_B-6_012_TBS.D"}
},
{
"Subject ID":"-",
"Sample ID":"Ding_C-1_013",
"Factors":{"Genotype_Media supplement":"KO-complete"},
"Additional sample data":{"RAW_FILE_NAME":"210517_Ding_C-1_013_TBS.D"}
},
{
"Subject ID":"-",
"Sample ID":"Ding_C-2_014",
"Factors":{"Genotype_Media supplement":"KO-complete"},
"Additional sample data":{"RAW_FILE_NAME":"210517_Ding_C-2_014_TBS.D"}
},
{
"Subject ID":"-",
"Sample ID":"Ding_C-3_015",
"Factors":{"Genotype_Media supplement":"KO-complete"},
"Additional sample data":{"RAW_FILE_NAME":"210517_Ding_C-3_015_TBS.D"}
},
{
"Subject ID":"-",
"Sample ID":"Ding_C-4_016",
"Factors":{"Genotype_Media supplement":"KO-complete"},
"Additional sample data":{"RAW_FILE_NAME":"210517_Ding_C-4_016_TBS.D"}
},
{
"Subject ID":"-",
"Sample ID":"Ding_C-5_017",
"Factors":{"Genotype_Media supplement":"KO-complete"},
"Additional sample data":{"RAW_FILE_NAME":"210517_Ding_C-5_017_TBS.D"}
},
{
"Subject ID":"-",
"Sample ID":"Ding_C-6_018",
"Factors":{"Genotype_Media supplement":"KO-complete"},
"Additional sample data":{"RAW_FILE_NAME":"210517_Ding_C-6_018_TBS.D"}
},
{
"Subject ID":"-",
"Sample ID":"Ding_D-1_019",
"Factors":{"Genotype_Media supplement":"KO-serine(-)"},
"Additional sample data":{"RAW_FILE_NAME":"210517_Ding_D-1_019_TBS.D"}
},
{
"Subject ID":"-",
"Sample ID":"Ding_D-2_020",
"Factors":{"Genotype_Media supplement":"KO-serine(-)"},
"Additional sample data":{"RAW_FILE_NAME":"210517_Ding_D-2_020_TBS.D"}
},
{
"Subject ID":"-",
"Sample ID":"Ding_D-3_021",
"Factors":{"Genotype_Media supplement":"KO-serine(-)"},
"Additional sample data":{"RAW_FILE_NAME":"210517_Ding_D-3_021_TBS.D"}
},
{
"Subject ID":"-",
"Sample ID":"Ding_D-4_022",
"Factors":{"Genotype_Media supplement":"KO-serine(-)"},
"Additional sample data":{"RAW_FILE_NAME":"210517_Ding_D-4_022_TBS.D"}
},
{
"Subject ID":"-",
"Sample ID":"Ding_D-5_023",
"Factors":{"Genotype_Media supplement":"KO-serine(-)"},
"Additional sample data":{"RAW_FILE_NAME":"210517_Ding_D-5_023_TBS.D"}
},
{
"Subject ID":"-",
"Sample ID":"Ding_D-6_024",
"Factors":{"Genotype_Media supplement":"KO-serine(-)"},
"Additional sample data":{"RAW_FILE_NAME":"210517_Ding_D-6_024_TBS.D"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Cells were counted, washed with cold PBS and then flash-frozen in liquid nitrogen","SAMPLE_TYPE":"Cultured cells"},

"TREATMENT":{"TREATMENT_SUMMARY":"HCT116 cells (~50% confluence) were washed with PBS, and cultured in HEPES buffered Krebs-Ringer solution supplemented with 25 mM [U-13C]-D-glucose, 10% dialysed FBS, 2×MEM amino acids, 2× Vitamin Solution and 4 mM L-glutamine, with or without 0.4 mM serine and glycine, for 24 h. Cells were washed with PBS and metabolites extracted using 1 mL of acetonitrile:isopropanol:water (3:3:2, v/v/v) mixture."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"The extraction solvent was degassed and pre-chilled at −20°C. Samples were homogenized using Geno/Grinder 2010 (SPEX SamplePrep) at 1500 rpm for 30s, then shaken at 4°C for 5 min and centrifuged for 2 minutes at 14,000 rcf. 450 μL supernatant was transferred to a new tube and dried down using Centrivap cold trap concentrator (Labconco). 10 μL of methoxyamine hydrochloride in pyridine (40 mg/mL) was added to dried sample and shaken at 30°C for 1.5 hours for methoximation. 90 μL of N-tert-Butyldimethylsilyl-N-methyltrifluoroacetamide (MTBSTFA, Sigma-Aldrich) was used for tertbutylsilylation. C8–C30 fatty acid methyl esters (FAMEs) were added to MTBSTFA as internal standards for retention time correction. Samples were shaken at 37°C for 30 min for TMS or shaken at 80°C for 30 min for TBS and then ready for injection."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"Gas chromatography-Quadrupole-time of flight mass spectrometry (GC-Q-TOF MS) was used for Stable Isotope enrichment. Rtx-5Sil MS column (30m length, 0.25 mm i.d, 0.25 μM 95% dimethyl 5% diphenyl polysiloxane film) with an additional 10 m guard column was installed on Agilent 7890 GC (Agilent Technologies). 99.9999% pure Helium gas was used as a mobile phase with a flow rate of 1mL/min. GC temperature was held at 50°C for 1 min, ramped at 20°C/min to 330°C and then held for 5 min. Electron ionization at -70eV was employed on a Agilent 7250 Quadrupole time of flight mass spectrometer (Agilent Technologies) with ion source temperature at 250°C and detector voltage at 1850V. Mass spectra were acquired at an acquisition rate of 5 spectra/s, with a scan range of 85-900 Da.","CHROMATOGRAPHY_TYPE":"GC","INSTRUMENT_NAME":"Agilent 7890A","COLUMN_NAME":"Restek Rtx-5Sil MS (30 x 0.25mm, 0.25um)"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS","LABORATORY_NAME":"West Coast Metabolomics Center"},

"MS":{"INSTRUMENT_NAME":"Agilent 7890A","INSTRUMENT_TYPE":"GC-TOF","MS_TYPE":"EI","ION_MODE":"UNSPECIFIED","MS_COMMENTS":"Agilent MassHunter Quantitative Analysis software B.10.00 (Agilent Technologies) was used for post data processing."},

"MS_METABOLITE_DATA":{
"Units":"enrichment percentage",

"Data":[{"Metabolite":"3-Phosphoglyceric acid","Ding_A-1_001":"138","Ding_A-2_002":"56","Ding_A-3_003":"84","Ding_A-4_004":"155","Ding_A-5_005":"130","Ding_A-6_006":"210","Ding_B-1_007":"63","Ding_B-2_008":"48","Ding_B-3_009":"86","Ding_B-4_010":"69","Ding_B-5_011":"69","Ding_B-6_012":"77","Ding_C-1_013":"59","Ding_C-2_014":"81","Ding_C-3_015":"81","Ding_C-4_016":"95","Ding_C-5_017":"69","Ding_C-6_018":"84","Ding_D-1_019":"81","Ding_D-2_020":"65","Ding_D-3_021":"68","Ding_D-4_022":"","Ding_D-5_023":"108","Ding_D-6_024":"172"},{"Metabolite":"alanine","Ding_A-1_001":"430","Ding_A-2_002":"365","Ding_A-3_003":"433","Ding_A-4_004":"291","Ding_A-5_005":"337","Ding_A-6_006":"260","Ding_B-1_007":"385","Ding_B-2_008":"418","Ding_B-3_009":"438","Ding_B-4_010":"364","Ding_B-5_011":"293","Ding_B-6_012":"279","Ding_C-1_013":"242","Ding_C-2_014":"331","Ding_C-3_015":"236","Ding_C-4_016":"150","Ding_C-5_017":"254","Ding_C-6_018":"204","Ding_D-1_019":"215","Ding_D-2_020":"263","Ding_D-3_021":"303","Ding_D-4_022":"249","Ding_D-5_023":"218","Ding_D-6_024":"283"},{"Metabolite":"asparagine","Ding_A-1_001":"","Ding_A-2_002":"","Ding_A-3_003":"","Ding_A-4_004":"","Ding_A-5_005":"","Ding_A-6_006":"","Ding_B-1_007":"","Ding_B-2_008":"","Ding_B-3_009":"27","Ding_B-4_010":"","Ding_B-5_011":"27","Ding_B-6_012":"18","Ding_C-1_013":"28","Ding_C-2_014":"","Ding_C-3_015":"","Ding_C-4_016":"21","Ding_C-5_017":"","Ding_C-6_018":"","Ding_D-1_019":"28","Ding_D-2_020":"35","Ding_D-3_021":"13","Ding_D-4_022":"","Ding_D-5_023":"","Ding_D-6_024":""},{"Metabolite":"aspartic acid","Ding_A-1_001":"39","Ding_A-2_002":"51","Ding_A-3_003":"41","Ding_A-4_004":"41","Ding_A-5_005":"30","Ding_A-6_006":"37","Ding_B-1_007":"","Ding_B-2_008":"33","Ding_B-3_009":"","Ding_B-4_010":"","Ding_B-5_011":"23","Ding_B-6_012":"24","Ding_C-1_013":"23","Ding_C-2_014":"25","Ding_C-3_015":"22","Ding_C-4_016":"30","Ding_C-5_017":"30","Ding_C-6_018":"43","Ding_D-1_019":"25","Ding_D-2_020":"22","Ding_D-3_021":"20","Ding_D-4_022":"29","Ding_D-5_023":"13","Ding_D-6_024":"20"},{"Metabolite":"cis-Aconitic acid","Ding_A-1_001":"","Ding_A-2_002":"48","Ding_A-3_003":"153","Ding_A-4_004":"198","Ding_A-5_005":"99","Ding_A-6_006":"","Ding_B-1_007":"","Ding_B-2_008":"87","Ding_B-3_009":"117","Ding_B-4_010":"179","Ding_B-5_011":"","Ding_B-6_012":"86","Ding_C-1_013":"37","Ding_C-2_014":"43","Ding_C-3_015":"17","Ding_C-4_016":"27","Ding_C-5_017":"37","Ding_C-6_018":"35","Ding_D-1_019":"31","Ding_D-2_020":"31","Ding_D-3_021":"37","Ding_D-4_022":"35","Ding_D-5_023":"52","Ding_D-6_024":"26"},{"Metabolite":"citric acid","Ding_A-1_001":"209","Ding_A-2_002":"252","Ding_A-3_003":"270","Ding_A-4_004":"269","Ding_A-5_005":"262","Ding_A-6_006":"273","Ding_B-1_007":"172","Ding_B-2_008":"264","Ding_B-3_009":"191","Ding_B-4_010":"188","Ding_B-5_011":"161","Ding_B-6_012":"227","Ding_C-1_013":"185","Ding_C-2_014":"151","Ding_C-3_015":"173","Ding_C-4_016":"132","Ding_C-5_017":"141","Ding_C-6_018":"140","Ding_D-1_019":"113","Ding_D-2_020":"149","Ding_D-3_021":"120","Ding_D-4_022":"107","Ding_D-5_023":"121","Ding_D-6_024":"153"},{"Metabolite":"Fumaric acid","Ding_A-1_001":"13","Ding_A-2_002":"15","Ding_A-3_003":"16","Ding_A-4_004":"15","Ding_A-5_005":"15","Ding_A-6_006":"18","Ding_B-1_007":"10","Ding_B-2_008":"11","Ding_B-3_009":"12","Ding_B-4_010":"11","Ding_B-5_011":"12","Ding_B-6_012":"13","Ding_C-1_013":"10","Ding_C-2_014":"10","Ding_C-3_015":"10","Ding_C-4_016":"11","Ding_C-5_017":"10","Ding_C-6_018":"11","Ding_D-1_019":"8","Ding_D-2_020":"8","Ding_D-3_021":"7","Ding_D-4_022":"8","Ding_D-5_023":"8","Ding_D-6_024":"9"},{"Metabolite":"glutamic acid","Ding_A-1_001":"33","Ding_A-2_002":"28","Ding_A-3_003":"22","Ding_A-4_004":"23","Ding_A-5_005":"30","Ding_A-6_006":"24","Ding_B-1_007":"25","Ding_B-2_008":"14","Ding_B-3_009":"20","Ding_B-4_010":"23","Ding_B-5_011":"18","Ding_B-6_012":"24","Ding_C-1_013":"12","Ding_C-2_014":"15","Ding_C-3_015":"17","Ding_C-4_016":"12","Ding_C-5_017":"15","Ding_C-6_018":"14","Ding_D-1_019":"12","Ding_D-2_020":"14","Ding_D-3_021":"12","Ding_D-4_022":"11","Ding_D-5_023":"11","Ding_D-6_024":"11"},{"Metabolite":"glycine","Ding_A-1_001":"","Ding_A-2_002":"","Ding_A-3_003":"","Ding_A-4_004":"4","Ding_A-5_005":"","Ding_A-6_006":"","Ding_B-1_007":"36","Ding_B-2_008":"35","Ding_B-3_009":"36","Ding_B-4_010":"41","Ding_B-5_011":"36","Ding_B-6_012":"33","Ding_C-1_013":"","Ding_C-2_014":"0","Ding_C-3_015":"1","Ding_C-4_016":"3","Ding_C-5_017":"0","Ding_C-6_018":"","Ding_D-1_019":"44","Ding_D-2_020":"50","Ding_D-3_021":"44","Ding_D-4_022":"49","Ding_D-5_023":"46","Ding_D-6_024":"45"},{"Metabolite":"Isocitric 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}

}