{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST003154","ANALYSIS_ID":"AN005175","VERSION":"1","CREATED_ON":"April 2, 2024, 8:33 am"},

"PROJECT":{"PROJECT_TITLE":"Nucleotide metabolism of tumor interstitial fluid in one murine model of pancreatic cancer","PROJECT_TYPE":"Nucleotide metabolism in murine pancreatic tumors","PROJECT_SUMMARY":"The experiment focus on the nucleotide metabolism of tumor interstitial fluid in one murine model of pancreatic cancer. Briefly, KPC FC1245 cells were genetically engineered using doxycycline inducible CRISPR/Cas9 system platform to target specifically cytidine deaminase (sgCda). sgCda and the control sgNT were then orthotopically injected in the head of the pancreas of 8-10 weeks old C57BL/6J female mice. When the tumor weight reached approximately 0.2-0.4g, mice were sacrificed and tumor interstitial fluid was collected as reported in the Collection section of this study. Standard curves for glutamine, cytidine, uridine, glucose, UTP and UDP were prepared and extracted along with the interstitial fluid samples. The concentrations of glutamine, cytidine, uridine, UDP and UTP were measured by LC-MS, and glucose was measured by GC-MS. A decrease in uridine content, and accordingly in UDP and UTP, and a concomitant accumulation of cytidine was observed in sgCda tumors. On the other hand, no differences were observed in glucose and glutamine abundance.","INSTITUTE":"VIB Center for Cancer Biology","LAST_NAME":"Mazzone","FIRST_NAME":"Massimiliano","ADDRESS":"Herestraat 49, box 912, Leuven, Flemish Brabant, 3000, Belgium","EMAIL":"massimiliano.mazzone@kuleuven.be","PHONE":"+32-16-37.32.13"},

"STUDY":{"STUDY_TITLE":"Nucleotide metabolism of tumor interstitial fluid in one murine model of pancreatic cancer","STUDY_SUMMARY":"The experiment focus on the nucleotide metabolism of tumor interstitial fluid in one murine model of pancreatic cancer. Briefly, KPC FC1245 cells were genetically engineered using doxycycline inducible CRISPR/Cas9 system platform to target specifically cytidine deaminase (sgCda). sgCda and the control sgNT were then orthotopically injected in the head of the pancreas of 8-10 weeks old C57BL/6J female mice. When the tumor weight reached approximately 0.2-0.4g, mice were sacrificed and tumor interstitial fluid was collected as reported in the Collection section of this study. Standard curves for glutamine, cytidine, uridine, glucose, UTP and UDP were prepared and extracted along with the interstitial fluid samples. The concentrations of glutamine, cytidine, uridine, UDP and UTP were measured by LC-MS, and glucose was measured by GC-MS. A decrease in uridine content, and accordingly in UDP and UTP, and a concomitant accumulation of cytidine was observed in sgCda tumors. On the other hand, no differences were observed in glucose and glutamine abundance.","INSTITUTE":"VIB-KU Leuven Center for Cancer Biology","LAST_NAME":"Mazzone","FIRST_NAME":"Massimiliano","ADDRESS":"Herestraat 49, box 912, Leuven, Flemish Brabant, 3000, Belgium","EMAIL":"massimiliano.mazzone@kuleuven.be","PHONE":"+32-16-37.32.13"},

"SUBJECT":{"SUBJECT_TYPE":"Mammal","SUBJECT_SPECIES":"Mus musculus","TAXONOMY_ID":"10090","GENOTYPE_STRAIN":"C57BL/6J"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"1",
"Sample ID":"TIF1",
"Factors":{"Sample source":"Pancreatic tumor interstitial fluid","Genotype":"sgNT"},
"Additional sample data":{"Cell Line":"KPC FC1245","Batch":"a","Standard Dilution Factor":"N/A","Extracted Volume (µL)":"0.625","RAW_FILE_NAME(Raw file name)":"TIF1.mzML"}
},
{
"Subject ID":"2",
"Sample ID":"TIF2",
"Factors":{"Sample source":"Pancreatic tumor interstitial fluid","Genotype":"sgNT"},
"Additional sample data":{"Cell Line":"KPC FC1245","Batch":"a","Standard Dilution Factor":"N/A","Extracted Volume (µL)":"1.2","RAW_FILE_NAME(Raw file name)":"TIF2.mzML"}
},
{
"Subject ID":"3",
"Sample ID":"TIF3",
"Factors":{"Sample source":"Pancreatic tumor interstitial fluid","Genotype":"sgNT"},
"Additional sample data":{"Cell Line":"KPC FC1245","Batch":"a","Standard Dilution Factor":"N/A","Extracted Volume (µL)":"2.5","RAW_FILE_NAME(Raw file name)":"TIF3.mzML"}
},
{
"Subject ID":"4",
"Sample ID":"TIF4",
"Factors":{"Sample source":"Pancreatic tumor interstitial fluid","Genotype":"sgNT"},
"Additional sample data":{"Cell Line":"KPC FC1245","Batch":"a","Standard Dilution Factor":"N/A","Extracted Volume (µL)":"1.5","RAW_FILE_NAME(Raw file name)":"TIF4.mzML"}
},
{
"Subject ID":"5",
"Sample ID":"TIF5",
"Factors":{"Sample source":"Pancreatic tumor interstitial fluid","Genotype":"sgCda"},
"Additional sample data":{"Cell Line":"KPC FC1245","Batch":"a","Standard Dilution Factor":"N/A","Extracted Volume (µL)":"3.7","RAW_FILE_NAME(Raw file name)":"TIF5.mzML"}
},
{
"Subject ID":"6",
"Sample ID":"TIF6",
"Factors":{"Sample source":"Pancreatic tumor interstitial fluid","Genotype":"sgCda"},
"Additional sample data":{"Cell Line":"KPC FC1245","Batch":"a","Standard Dilution Factor":"N/A","Extracted Volume (µL)":"1.6","RAW_FILE_NAME(Raw file name)":"TIF6.mzML"}
},
{
"Subject ID":"7",
"Sample ID":"TIF7",
"Factors":{"Sample source":"Pancreatic tumor interstitial fluid","Genotype":"sgCda"},
"Additional sample data":{"Cell Line":"KPC FC1245","Batch":"a","Standard Dilution Factor":"N/A","Extracted Volume (µL)":"2.2","RAW_FILE_NAME(Raw file name)":"TIF7.mzML"}
},
{
"Subject ID":"8",
"Sample ID":"TIF8",
"Factors":{"Sample source":"Pancreatic tumor interstitial fluid","Genotype":"sgNT"},
"Additional sample data":{"Cell Line":"KPC FC1245","Batch":"a","Standard Dilution Factor":"N/A","Extracted Volume (µL)":"2.5","RAW_FILE_NAME(Raw file name)":"TIF8.mzML"}
},
{
"Subject ID":"9",
"Sample ID":"TIF9",
"Factors":{"Sample source":"Pancreatic tumor interstitial fluid","Genotype":"sgNT"},
"Additional sample data":{"Cell Line":"KPC FC1245","Batch":"a","Standard Dilution Factor":"N/A","Extracted Volume (µL)":"2.7","RAW_FILE_NAME(Raw file name)":"TIF9.mzML"}
},
{
"Subject ID":"10",
"Sample ID":"TIF10",
"Factors":{"Sample source":"Pancreatic tumor interstitial fluid","Genotype":"sgNT"},
"Additional sample data":{"Cell Line":"KPC FC1245","Batch":"a","Standard Dilution Factor":"N/A","Extracted Volume (µL)":"1.6","RAW_FILE_NAME(Raw file name)":"TIF10.mzML"}
},
{
"Subject ID":"11",
"Sample ID":"TIF11",
"Factors":{"Sample source":"Pancreatic tumor interstitial fluid","Genotype":"sgCda"},
"Additional sample data":{"Cell Line":"KPC FC1245","Batch":"a","Standard Dilution Factor":"N/A","Extracted Volume (µL)":"2.1","RAW_FILE_NAME(Raw file name)":"TIF11.mzML"}
},
{
"Subject ID":"12",
"Sample ID":"TIF12",
"Factors":{"Sample source":"Pancreatic tumor interstitial fluid","Genotype":"sgCda"},
"Additional sample data":{"Cell Line":"KPC FC1245","Batch":"a","Standard Dilution Factor":"N/A","Extracted Volume (µL)":"0.95","RAW_FILE_NAME(Raw file name)":"TIF12.mzML"}
},
{
"Subject ID":"13",
"Sample ID":"TIF13",
"Factors":{"Sample source":"Pancreatic tumor interstitial fluid","Genotype":"sgCda"},
"Additional sample data":{"Cell Line":"KPC FC1245","Batch":"a","Standard Dilution Factor":"N/A","Extracted Volume (µL)":"1.4","RAW_FILE_NAME(Raw file name)":"TIF13.mzML"}
},
{
"Subject ID":"14",
"Sample ID":"TIF14",
"Factors":{"Sample source":"Pancreatic tumor interstitial fluid","Genotype":"sgNT"},
"Additional sample data":{"Cell Line":"KPC FC1245","Batch":"b","Standard Dilution Factor":"N/A","Extracted Volume (µL)":"1.45","RAW_FILE_NAME(Raw file name)":"TIF14.mzML"}
},
{
"Subject ID":"15",
"Sample ID":"TIF15",
"Factors":{"Sample source":"Pancreatic tumor interstitial fluid","Genotype":"sgNT"},
"Additional sample data":{"Cell Line":"KPC FC1245","Batch":"b","Standard Dilution Factor":"N/A","Extracted Volume (µL)":"5.9","RAW_FILE_NAME(Raw file name)":"TIF15.mzML"}
},
{
"Subject ID":"16",
"Sample ID":"TIF16",
"Factors":{"Sample source":"Pancreatic tumor interstitial fluid","Genotype":"sgNT"},
"Additional sample data":{"Cell Line":"KPC FC1245","Batch":"b","Standard Dilution Factor":"N/A","Extracted Volume (µL)":"4.2","RAW_FILE_NAME(Raw file name)":"TIF16.mzML"}
},
{
"Subject ID":"17",
"Sample ID":"TIF17",
"Factors":{"Sample source":"Pancreatic tumor interstitial fluid","Genotype":"sgNT"},
"Additional sample data":{"Cell Line":"KPC FC1245","Batch":"b","Standard Dilution Factor":"N/A","Extracted Volume (µL)":"6.9","RAW_FILE_NAME(Raw file name)":"TIF17.mzML"}
},
{
"Subject ID":"18",
"Sample ID":"TIF18",
"Factors":{"Sample source":"Pancreatic tumor interstitial fluid","Genotype":"sgCda"},
"Additional sample data":{"Cell Line":"KPC FC1245","Batch":"b","Standard Dilution Factor":"N/A","Extracted Volume (µL)":"3.55","RAW_FILE_NAME(Raw file name)":"TIF18.mzML"}
},
{
"Subject ID":"19",
"Sample ID":"TIF19",
"Factors":{"Sample source":"Pancreatic tumor interstitial fluid","Genotype":"sgCda"},
"Additional sample data":{"Cell Line":"KPC FC1245","Batch":"b","Standard Dilution Factor":"N/A","Extracted Volume (µL)":"3.75","RAW_FILE_NAME(Raw file name)":"TIF19.mzML"}
},
{
"Subject ID":"20",
"Sample ID":"TIF20",
"Factors":{"Sample source":"Pancreatic tumor interstitial fluid","Genotype":"sgCda"},
"Additional sample data":{"Cell Line":"KPC FC1245","Batch":"b","Standard Dilution Factor":"N/A","Extracted Volume (µL)":"4.7","RAW_FILE_NAME(Raw file name)":"TIF20.mzML"}
},
{
"Subject ID":"21",
"Sample ID":"TIF21",
"Factors":{"Sample source":"Pancreatic tumor interstitial fluid","Genotype":"sgCda"},
"Additional sample data":{"Cell Line":"KPC FC1245","Batch":"b","Standard Dilution Factor":"N/A","Extracted Volume (µL)":"4.85","RAW_FILE_NAME(Raw file name)":"TIF21.mzML"}
},
{
"Subject ID":"N/A",
"Sample ID":"STD2_a",
"Factors":{"Sample source":"Calibration Curve","Genotype":"N/A"},
"Additional sample data":{"Cell Line":"N/A","Batch":"a","Standard Dilution Factor":"1/2","Extracted Volume (µL)":"10","RAW_FILE_NAME(Raw file name)":"STD2_a.mzML"}
},
{
"Subject ID":"N/A",
"Sample ID":"STD3_a",
"Factors":{"Sample source":"Calibration Curve","Genotype":"N/A"},
"Additional sample data":{"Cell Line":"N/A","Batch":"a","Standard Dilution Factor":"1/4","Extracted Volume (µL)":"10","RAW_FILE_NAME(Raw file name)":"STD3_a.mzML"}
},
{
"Subject ID":"N/A",
"Sample ID":"STD4_a",
"Factors":{"Sample source":"Calibration Curve","Genotype":"N/A"},
"Additional sample data":{"Cell Line":"N/A","Batch":"a","Standard Dilution Factor":"1/8","Extracted Volume (µL)":"10","RAW_FILE_NAME(Raw file name)":"STD4_a.mzML"}
},
{
"Subject ID":"N/A",
"Sample ID":"STD5_a",
"Factors":{"Sample source":"Calibration Curve","Genotype":"N/A"},
"Additional sample data":{"Cell Line":"N/A","Batch":"a","Standard Dilution Factor":"1/16","Extracted Volume (µL)":"10","RAW_FILE_NAME(Raw file name)":"STD5_a.mzML"}
},
{
"Subject ID":"N/A",
"Sample ID":"STD6_a",
"Factors":{"Sample source":"Calibration Curve","Genotype":"N/A"},
"Additional sample data":{"Cell Line":"N/A","Batch":"a","Standard Dilution Factor":"1/32","Extracted Volume (µL)":"10","RAW_FILE_NAME(Raw file name)":"STD6_a.mzML"}
},
{
"Subject ID":"N/A",
"Sample ID":"STD7_a",
"Factors":{"Sample source":"Calibration Curve","Genotype":"N/A"},
"Additional sample data":{"Cell Line":"N/A","Batch":"a","Standard Dilution Factor":"1/64","Extracted Volume (µL)":"10","RAW_FILE_NAME(Raw file name)":"STD7_a.mzML"}
},
{
"Subject ID":"N/A",
"Sample ID":"STD8_a",
"Factors":{"Sample source":"Calibration Curve","Genotype":"N/A"},
"Additional sample data":{"Cell Line":"N/A","Batch":"a","Standard Dilution Factor":"1/128","Extracted Volume (µL)":"10","RAW_FILE_NAME(Raw file name)":"STD8_a.mzML"}
},
{
"Subject ID":"N/A",
"Sample ID":"STD9_a",
"Factors":{"Sample source":"Calibration Curve","Genotype":"N/A"},
"Additional sample data":{"Cell Line":"N/A","Batch":"a","Standard Dilution Factor":"1/256","Extracted Volume (µL)":"10","RAW_FILE_NAME(Raw file name)":"STD9_a.mzML"}
},
{
"Subject ID":"N/A",
"Sample ID":"STD10_a",
"Factors":{"Sample source":"Calibration Curve","Genotype":"N/A"},
"Additional sample data":{"Cell Line":"N/A","Batch":"a","Standard Dilution Factor":"1/512","Extracted Volume (µL)":"10","RAW_FILE_NAME(Raw file name)":"STD10_a.mzML"}
},
{
"Subject ID":"N/A",
"Sample ID":"STD11_a",
"Factors":{"Sample source":"Calibration Curve","Genotype":"N/A"},
"Additional sample data":{"Cell Line":"N/A","Batch":"a","Standard Dilution Factor":"1/1024","Extracted Volume (µL)":"10","RAW_FILE_NAME(Raw file name)":"STD11_a.mzML"}
},
{
"Subject ID":"N/A",
"Sample ID":"STD12_a",
"Factors":{"Sample source":"Calibration Curve","Genotype":"N/A"},
"Additional sample data":{"Cell Line":"N/A","Batch":"a","Standard Dilution Factor":"1/2048","Extracted Volume (µL)":"10","RAW_FILE_NAME(Raw file name)":"STD12_a.mzML"}
},
{
"Subject ID":"N/A",
"Sample ID":"STD13_a",
"Factors":{"Sample source":"Calibration Curve","Genotype":"N/A"},
"Additional sample data":{"Cell Line":"N/A","Batch":"a","Standard Dilution Factor":"1/4096","Extracted Volume (µL)":"10","RAW_FILE_NAME(Raw file name)":"STD13_a.mzML"}
},
{
"Subject ID":"N/A",
"Sample ID":"STD14_a",
"Factors":{"Sample source":"Calibration Curve","Genotype":"N/A"},
"Additional sample data":{"Cell Line":"N/A","Batch":"a","Standard Dilution Factor":"1/8192","Extracted Volume (µL)":"10","RAW_FILE_NAME(Raw file name)":"STD14_a.mzML"}
},
{
"Subject ID":"N/A",
"Sample ID":"STD15_a",
"Factors":{"Sample source":"Calibration Curve","Genotype":"N/A"},
"Additional sample data":{"Cell Line":"N/A","Batch":"a","Standard Dilution Factor":"1/16384","Extracted Volume (µL)":"10","RAW_FILE_NAME(Raw file name)":"STD15_a.mzML"}
},
{
"Subject ID":"N/A",
"Sample ID":"STD3_b",
"Factors":{"Sample source":"Calibration Curve","Genotype":"N/A"},
"Additional sample data":{"Cell Line":"N/A","Batch":"b","Standard Dilution Factor":"1/4","Extracted Volume (µL)":"10","RAW_FILE_NAME(Raw file name)":"STD3_b.mzML"}
},
{
"Subject ID":"N/A",
"Sample ID":"STD4_b",
"Factors":{"Sample source":"Calibration Curve","Genotype":"N/A"},
"Additional sample data":{"Cell Line":"N/A","Batch":"b","Standard Dilution Factor":"1/8","Extracted Volume (µL)":"10","RAW_FILE_NAME(Raw file name)":"STD4_b.mzML"}
},
{
"Subject ID":"N/A",
"Sample ID":"STD5_b",
"Factors":{"Sample source":"Calibration Curve","Genotype":"N/A"},
"Additional sample data":{"Cell Line":"N/A","Batch":"b","Standard Dilution Factor":"1/16","Extracted Volume (µL)":"10","RAW_FILE_NAME(Raw file name)":"STD5_b.mzML"}
},
{
"Subject ID":"N/A",
"Sample ID":"STD6_b",
"Factors":{"Sample source":"Calibration Curve","Genotype":"N/A"},
"Additional sample data":{"Cell Line":"N/A","Batch":"b","Standard Dilution Factor":"1/32","Extracted Volume (µL)":"10","RAW_FILE_NAME(Raw file name)":"STD6_b.mzML"}
},
{
"Subject ID":"N/A",
"Sample ID":"STD7_b",
"Factors":{"Sample source":"Calibration Curve","Genotype":"N/A"},
"Additional sample data":{"Cell Line":"N/A","Batch":"b","Standard Dilution Factor":"1/64","Extracted Volume (µL)":"10","RAW_FILE_NAME(Raw file name)":"STD7_b.mzML"}
},
{
"Subject ID":"N/A",
"Sample ID":"STD8_b",
"Factors":{"Sample source":"Calibration Curve","Genotype":"N/A"},
"Additional sample data":{"Cell Line":"N/A","Batch":"b","Standard Dilution Factor":"1/128","Extracted Volume (µL)":"10","RAW_FILE_NAME(Raw file name)":"STD8_b.mzML"}
},
{
"Subject ID":"N/A",
"Sample ID":"STD9_b",
"Factors":{"Sample source":"Calibration Curve","Genotype":"N/A"},
"Additional sample data":{"Cell Line":"N/A","Batch":"b","Standard Dilution Factor":"1/256","Extracted Volume (µL)":"10","RAW_FILE_NAME(Raw file name)":"STD9_b.mzML"}
},
{
"Subject ID":"N/A",
"Sample ID":"STD10_b",
"Factors":{"Sample source":"Calibration Curve","Genotype":"N/A"},
"Additional sample data":{"Cell Line":"N/A","Batch":"b","Standard Dilution Factor":"1/512","Extracted Volume (µL)":"10","RAW_FILE_NAME(Raw file name)":"STD10_b.mzML"}
},
{
"Subject ID":"N/A",
"Sample ID":"STD11_b",
"Factors":{"Sample source":"Calibration Curve","Genotype":"N/A"},
"Additional sample data":{"Cell Line":"N/A","Batch":"b","Standard Dilution Factor":"1/1024","Extracted Volume (µL)":"10","RAW_FILE_NAME(Raw file name)":"STD11_b.mzML"}
},
{
"Subject ID":"N/A",
"Sample ID":"STD12_b",
"Factors":{"Sample source":"Calibration Curve","Genotype":"N/A"},
"Additional sample data":{"Cell Line":"N/A","Batch":"b","Standard Dilution Factor":"1/2048","Extracted Volume (µL)":"10","RAW_FILE_NAME(Raw file name)":"STD12_b.mzML"}
},
{
"Subject ID":"N/A",
"Sample ID":"STD13_b",
"Factors":{"Sample source":"Calibration Curve","Genotype":"N/A"},
"Additional sample data":{"Cell Line":"N/A","Batch":"b","Standard Dilution Factor":"1/4096","Extracted Volume (µL)":"10","RAW_FILE_NAME(Raw file name)":"STD13_b.mzML"}
},
{
"Subject ID":"N/A",
"Sample ID":"STD14_b",
"Factors":{"Sample source":"Calibration Curve","Genotype":"N/A"},
"Additional sample data":{"Cell Line":"N/A","Batch":"b","Standard Dilution Factor":"1/8192","Extracted Volume (µL)":"10","RAW_FILE_NAME(Raw file name)":"STD14_b.mzML"}
},
{
"Subject ID":"1",
"Sample ID":"TIF1_GC",
"Factors":{"Sample source":"Pancreatic tumor interstitial fluid","Genotype":"sgNT"},
"Additional sample data":{"Cell Line":"KPC FC1245","Batch":"c","Standard Dilution Factor":"N/A","Extracted Volume (µL)":"0.625","RAW_FILE_NAME(Raw file name)":"TIF1_GC.mzML"}
},
{
"Subject ID":"2",
"Sample ID":"TIF2_GC",
"Factors":{"Sample source":"Pancreatic tumor interstitial fluid","Genotype":"sgNT"},
"Additional sample data":{"Cell Line":"KPC FC1245","Batch":"c","Standard Dilution Factor":"N/A","Extracted Volume (µL)":"1.2","RAW_FILE_NAME(Raw file name)":"TIF2_GC.mzML"}
},
{
"Subject ID":"3",
"Sample ID":"TIF3_GC",
"Factors":{"Sample source":"Pancreatic tumor interstitial fluid","Genotype":"sgNT"},
"Additional sample data":{"Cell Line":"KPC FC1245","Batch":"c","Standard Dilution Factor":"N/A","Extracted Volume (µL)":"2.5","RAW_FILE_NAME(Raw file name)":"TIF3_GC.mzML"}
},
{
"Subject ID":"4",
"Sample ID":"TIF4_GC",
"Factors":{"Sample source":"Pancreatic tumor interstitial fluid","Genotype":"sgNT"},
"Additional sample data":{"Cell Line":"KPC FC1245","Batch":"c","Standard Dilution Factor":"N/A","Extracted Volume (µL)":"1.5","RAW_FILE_NAME(Raw file name)":"TIF4_GC.mzML"}
},
{
"Subject ID":"5",
"Sample ID":"TIF5_GC",
"Factors":{"Sample source":"Pancreatic tumor interstitial fluid","Genotype":"sgCda"},
"Additional sample data":{"Cell Line":"KPC FC1245","Batch":"c","Standard Dilution Factor":"N/A","Extracted Volume (µL)":"3.7","RAW_FILE_NAME(Raw file name)":"TIF5_GC.mzML"}
},
{
"Subject ID":"6",
"Sample ID":"TIF6_GC",
"Factors":{"Sample source":"Pancreatic tumor interstitial fluid","Genotype":"sgCda"},
"Additional sample data":{"Cell Line":"KPC FC1245","Batch":"c","Standard Dilution Factor":"N/A","Extracted Volume (µL)":"1.6","RAW_FILE_NAME(Raw file name)":"TIF6_GC.mzML"}
},
{
"Subject ID":"7",
"Sample ID":"TIF7_GC",
"Factors":{"Sample source":"Pancreatic tumor interstitial fluid","Genotype":"sgCda"},
"Additional sample data":{"Cell Line":"KPC FC1245","Batch":"c","Standard Dilution Factor":"N/A","Extracted Volume (µL)":"2.2","RAW_FILE_NAME(Raw file name)":"TIF7_GC.mzML"}
},
{
"Subject ID":"8",
"Sample ID":"TIF8_GC",
"Factors":{"Sample source":"Pancreatic tumor interstitial fluid","Genotype":"sgNT"},
"Additional sample data":{"Cell Line":"KPC FC1245","Batch":"c","Standard Dilution Factor":"N/A","Extracted Volume (µL)":"2.5","RAW_FILE_NAME(Raw file name)":"TIF8_GC.mzML"}
},
{
"Subject ID":"9",
"Sample ID":"TIF9_GC",
"Factors":{"Sample source":"Pancreatic tumor interstitial fluid","Genotype":"sgNT"},
"Additional sample data":{"Cell Line":"KPC FC1245","Batch":"c","Standard Dilution Factor":"N/A","Extracted Volume (µL)":"2.7","RAW_FILE_NAME(Raw file name)":"TIF9_GC.mzML"}
},
{
"Subject ID":"10",
"Sample ID":"TIF10_GC",
"Factors":{"Sample source":"Pancreatic tumor interstitial fluid","Genotype":"sgNT"},
"Additional sample data":{"Cell Line":"KPC FC1245","Batch":"c","Standard Dilution Factor":"N/A","Extracted Volume (µL)":"1.6","RAW_FILE_NAME(Raw file name)":"TIF10_GC.mzML"}
},
{
"Subject ID":"11",
"Sample ID":"TIF11_GC",
"Factors":{"Sample source":"Pancreatic tumor interstitial fluid","Genotype":"sgCda"},
"Additional sample data":{"Cell Line":"KPC FC1245","Batch":"c","Standard Dilution Factor":"N/A","Extracted Volume (µL)":"2.1","RAW_FILE_NAME(Raw file name)":"TIF11_GC.mzML"}
},
{
"Subject ID":"12",
"Sample ID":"TIF12_GC",
"Factors":{"Sample source":"Pancreatic tumor interstitial fluid","Genotype":"sgCda"},
"Additional sample data":{"Cell Line":"KPC FC1245","Batch":"c","Standard Dilution Factor":"N/A","Extracted Volume (µL)":"0.95","RAW_FILE_NAME(Raw file name)":"TIF12_GC.mzML"}
},
{
"Subject ID":"13",
"Sample ID":"TIF13_GC",
"Factors":{"Sample source":"Pancreatic tumor interstitial fluid","Genotype":"sgCda"},
"Additional sample data":{"Cell Line":"KPC FC1245","Batch":"c","Standard Dilution Factor":"N/A","Extracted Volume (µL)":"1.4","RAW_FILE_NAME(Raw file name)":"TIF13_GC.mzML"}
},
{
"Subject ID":"N/A",
"Sample ID":"STD2_c",
"Factors":{"Sample source":"Calibration Curve","Genotype":"N/A"},
"Additional sample data":{"Cell Line":"N/A","Batch":"c","Standard Dilution Factor":"1/2","Extracted Volume (µL)":"10","RAW_FILE_NAME(Raw file name)":"STD2_c.mzML"}
},
{
"Subject ID":"N/A",
"Sample ID":"STD3_c",
"Factors":{"Sample source":"Calibration Curve","Genotype":"N/A"},
"Additional sample data":{"Cell Line":"N/A","Batch":"c","Standard Dilution Factor":"1/4","Extracted Volume (µL)":"10","RAW_FILE_NAME(Raw file name)":"STD3_c.mzML"}
},
{
"Subject ID":"N/A",
"Sample ID":"STD4_c",
"Factors":{"Sample source":"Calibration Curve","Genotype":"N/A"},
"Additional sample data":{"Cell Line":"N/A","Batch":"c","Standard Dilution Factor":"1/8","Extracted Volume (µL)":"10","RAW_FILE_NAME(Raw file name)":"STD4_c.mzML"}
},
{
"Subject ID":"N/A",
"Sample ID":"STD5_c",
"Factors":{"Sample source":"Calibration Curve","Genotype":"N/A"},
"Additional sample data":{"Cell Line":"N/A","Batch":"c","Standard Dilution Factor":"1/16","Extracted Volume (µL)":"10","RAW_FILE_NAME(Raw file name)":"STD5_c.mzML"}
},
{
"Subject ID":"N/A",
"Sample ID":"STD6_c",
"Factors":{"Sample source":"Calibration Curve","Genotype":"N/A"},
"Additional sample data":{"Cell Line":"N/A","Batch":"c","Standard Dilution Factor":"1/32","Extracted Volume (µL)":"10","RAW_FILE_NAME(Raw file name)":"STD6_c.mzML"}
},
{
"Subject ID":"N/A",
"Sample ID":"STD7_c",
"Factors":{"Sample source":"Calibration Curve","Genotype":"N/A"},
"Additional sample data":{"Cell Line":"N/A","Batch":"c","Standard Dilution Factor":"1/64","Extracted Volume (µL)":"10","RAW_FILE_NAME(Raw file name)":"STD7_c.mzML"}
},
{
"Subject ID":"N/A",
"Sample ID":"STD8_c",
"Factors":{"Sample source":"Calibration Curve","Genotype":"N/A"},
"Additional sample data":{"Cell Line":"N/A","Batch":"c","Standard Dilution Factor":"1/128","Extracted Volume (µL)":"10","RAW_FILE_NAME(Raw file name)":"STD8_c.mzML"}
},
{
"Subject ID":"N/A",
"Sample ID":"STD9_c",
"Factors":{"Sample source":"Calibration Curve","Genotype":"N/A"},
"Additional sample data":{"Cell Line":"N/A","Batch":"c","Standard Dilution Factor":"1/256","Extracted Volume (µL)":"10","RAW_FILE_NAME(Raw file name)":"STD9_c.mzML"}
},
{
"Subject ID":"N/A",
"Sample ID":"STD10_c",
"Factors":{"Sample source":"Calibration Curve","Genotype":"N/A"},
"Additional sample data":{"Cell Line":"N/A","Batch":"c","Standard Dilution Factor":"1/512","Extracted Volume (µL)":"10","RAW_FILE_NAME(Raw file name)":"STD10_c.mzML"}
},
{
"Subject ID":"N/A",
"Sample ID":"STD11_c",
"Factors":{"Sample source":"Calibration Curve","Genotype":"N/A"},
"Additional sample data":{"Cell Line":"N/A","Batch":"c","Standard Dilution Factor":"1/1024","Extracted Volume (µL)":"10","RAW_FILE_NAME(Raw file name)":"STD11_c.mzML"}
},
{
"Subject ID":"N/A",
"Sample ID":"STD12_c",
"Factors":{"Sample source":"Calibration Curve","Genotype":"N/A"},
"Additional sample data":{"Cell Line":"N/A","Batch":"c","Standard Dilution Factor":"1/2048","Extracted Volume (µL)":"10","RAW_FILE_NAME(Raw file name)":"STD12_c.mzML"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"8-10 weeks old C57BL/6J female mice were euthanized with 75 µl of a 60 mg ml-1 Dolethal solution (pentobarbital sodium, Vetoquinol). Subsequently, sgNT and sgCda primary tumors were collected by surgical resection, washed with blood bank saline and dried from liquid excess. Tissues were then placed in a home-made filtered centrifugation tube supplemented with a 20 µm nylon mesh filter (Repligen) and centrifuged at 400 x g at 4 °C for 10 minutes. Between 1-14 µl of tumor interstitial fluid were collected and stored on dry ice. Interstitial fluid volume was used to determine the metabolites concentration measured by mass spectrometry.","SAMPLE_TYPE":"Interstitial fluid"},

"TREATMENT":{"TREATMENT_SUMMARY":"KPC FC1245 cells were genetically engineered using doxycycline inducible CRISPR/Cas9 system platform to target specifically cytidine deaminase (sgCda). sgCda and the control sgNT were then orthotopically injected in the head of the pancreas of 8-10 weeks old C57BL/6J female mice. When the tumor weight reached approximately 0.2-0.4g, mice were sacrificed and tumor interstitial fluid was collected"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Standard curves for Glucose (Sigma-Aldrich, G7021), UDP (Sigma-Aldrich, 94330), UTP (Jena Bioscience, NU-1024S), cytidine (Sigma-Aldrich, C4654), uridine (Sigma-Aldrich, U3003) and glutamine (Gibco, 25030-34) were used to calculate the concentration of these metabolites in the samples. The standard curve was prepared with a dilution series starting from 5 mM Glucose and Glutamine, 1 mM Cytidine, Uridine, UDP and UTP. Specific dilutions are indicated in the Study Design table. Metabolites and calibration curves were extracted simultaneously by addition of 800 μl of MS-grade methanol-water buffer (MeOH:H2O, 5:3, v/v) containing the internal standards glutaric acid (5 μg ml-1, Sigma-Aldrich, G3407) and 13C6-Glucose (30 μg ml-1, Cambridge Isotope Laboratories, Inc., CLM-1396), followed by 500 μl of chloroform. Samples were then vortexed and centrifuged (4 °C for 10 min each). The polar (upper) phases were collected, divided into two equal parts for gas chromatography (GC) and liquid chromatography (LC) mass spectrometry analysis, and dried using a vacuum concentrator. The dried metabolite extracts were stored at -80 °C until analysis."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"Inlet Temperature: 270; Helium flow rate: 0.88 mL/min; The GC oven was kept at 100°C and for 1 min, increased with a gradient of 2.5°C min-1 to 105°C for 2 min, then ramped with a gradient of 15°C min-1 to 260°, and after that ramped with a gradient of 20°C min-1 up to 300°C for 5 min.","CHROMATOGRAPHY_TYPE":"GC","INSTRUMENT_NAME":"Agilent 8860","COLUMN_NAME":"Agilent J&W DB-35ms (30 m x 0.25 mm, 0.25 µm)","SOLVENT_A":"N/A","SOLVENT_B":"N/A","FLOW_GRADIENT":"N/A","FLOW_RATE":"N/A","COLUMN_TEMPERATURE":"100-300"},

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

"MS":{"INSTRUMENT_NAME":"Agilent 5977C","INSTRUMENT_TYPE":"Single quadrupole","MS_TYPE":"EI","ION_MODE":"POSITIVE","MS_COMMENTS":"5977C quipped with EI inert source. Mass spectrometry was performed at 70 eV and a mass range of 150-650 atomic mass units was measured. The chromatographic peaks were extracted from raw chromatograms with a custom MATLAB Script. The chromatographic peaks for 12C-Glucose were normalized to the internal standard 13C6-glucose. Tumor interstitial fluid samples were interpolated to the standard curve and normalized for tumor interstitial fluid volume to quantify metabolite concentration."},

"MS_METABOLITE_DATA":{
"Units":"Ion Counts (AUC)",

"Data":[{"Metabolite":"Glucose","TIF1_GC":"1.27E+05","TIF2_GC":"3.75E+05","TIF3_GC":"6.71E+05","TIF4_GC":"3.85E+05","TIF5_GC":"1.83E+06","TIF6_GC":"4.76E+05","TIF7_GC":"3.52E+05","TIF8_GC":"8.99E+05","TIF9_GC":"2.50E+05","TIF10_GC":"3.13E+05","TIF11_GC":"4.56E+05","TIF12_GC":"1.50E+05","TIF13_GC":"2.88E+05","STD2_c":"4.64E+05","STD3_c":"2.46E+05","STD4_c":"1.20E+05","STD5_c":"5.89E+04","STD6_c":"2.57E+04","STD7_c":"1.39E+04","STD8_c":"8.19E+03","STD9_c":"4.13E+03","STD10_c":"3.59E+03","STD11_c":"2.45E+03","STD12_c":"9.57E+02"},{"Metabolite":"13C6 Glucose","TIF1_GC":"3.10E+05","TIF2_GC":"5.10E+05","TIF3_GC":"6.36E+05","TIF4_GC":"6.13E+05","TIF5_GC":"6.55E+05","TIF6_GC":"7.46E+05","TIF7_GC":"7.16E+05","TIF8_GC":"6.90E+05","TIF9_GC":"6.64E+05","TIF10_GC":"8.36E+05","TIF11_GC":"7.05E+05","TIF12_GC":"6.77E+05","TIF13_GC":"5.74E+05","STD2_c":"1.38E+05","STD3_c":"1.36E+05","STD4_c":"1.43E+05","STD5_c":"1.34E+05","STD6_c":"1.10E+05","STD7_c":"1.37E+05","STD8_c":"1.20E+05","STD9_c":"1.11E+05","STD10_c":"1.26E+05","STD11_c":"1.27E+05","STD12_c":"1.16E+05"}],

"Metabolites":[{"Metabolite":"Glucose","Pubchem Id":"5793","Kegg Id":"C00031","m/z window":"239.7-240.7","RT":"16.74"},{"Metabolite":"13C6 Glucose","Pubchem Id":"5794","Kegg Id":"C00032","m/z window":"244.7-245.7","RT":"16.74"}]
}

}