#METABOLOMICS WORKBENCH MaMa_20240312_023321 DATATRACK_ID:4718 STUDY_ID:ST003154 ANALYSIS_ID:AN005175 PROJECT_ID:PR001960 VERSION 1 CREATED_ON April 2, 2024, 8:33 am #PROJECT PR:PROJECT_TITLE Nucleotide metabolism of tumor interstitial fluid in one murine model of PR:PROJECT_TITLE pancreatic cancer PR:PROJECT_TYPE Nucleotide metabolism in murine pancreatic tumors PR:PROJECT_SUMMARY The experiment focus on the nucleotide metabolism of tumor interstitial fluid in PR:PROJECT_SUMMARY one murine model of pancreatic cancer. Briefly, KPC FC1245 cells were PR:PROJECT_SUMMARY genetically engineered using doxycycline inducible CRISPR/Cas9 system platform PR:PROJECT_SUMMARY to target specifically cytidine deaminase (sgCda). sgCda and the control sgNT PR:PROJECT_SUMMARY were then orthotopically injected in the head of the pancreas of 8-10 weeks old PR:PROJECT_SUMMARY C57BL/6J female mice. When the tumor weight reached approximately 0.2-0.4g, mice PR:PROJECT_SUMMARY were sacrificed and tumor interstitial fluid was collected as reported in the PR:PROJECT_SUMMARY Collection section of this study. Standard curves for glutamine, cytidine, PR:PROJECT_SUMMARY uridine, glucose, UTP and UDP were prepared and extracted along with the PR:PROJECT_SUMMARY interstitial fluid samples. The concentrations of glutamine, cytidine, uridine, PR:PROJECT_SUMMARY UDP and UTP were measured by LC-MS, and glucose was measured by GC-MS. A PR:PROJECT_SUMMARY decrease in uridine content, and accordingly in UDP and UTP, and a concomitant PR:PROJECT_SUMMARY accumulation of cytidine was observed in sgCda tumors. On the other hand, no PR:PROJECT_SUMMARY differences were observed in glucose and glutamine abundance. PR:INSTITUTE VIB Center for Cancer Biology PR:LAST_NAME Mazzone PR:FIRST_NAME Massimiliano PR:ADDRESS Herestraat 49, box 912, Leuven, Flemish Brabant, 3000, Belgium PR:EMAIL massimiliano.mazzone@kuleuven.be PR:PHONE +32-16-37.32.13 #STUDY ST:STUDY_TITLE Nucleotide metabolism of tumor interstitial fluid in one murine model of ST:STUDY_TITLE pancreatic cancer ST:STUDY_SUMMARY The experiment focus on the nucleotide metabolism of tumor interstitial fluid in ST:STUDY_SUMMARY one murine model of pancreatic cancer. Briefly, KPC FC1245 cells were ST:STUDY_SUMMARY genetically engineered using doxycycline inducible CRISPR/Cas9 system platform ST:STUDY_SUMMARY to target specifically cytidine deaminase (sgCda). sgCda and the control sgNT ST:STUDY_SUMMARY were then orthotopically injected in the head of the pancreas of 8-10 weeks old ST:STUDY_SUMMARY C57BL/6J female mice. When the tumor weight reached approximately 0.2-0.4g, mice ST:STUDY_SUMMARY were sacrificed and tumor interstitial fluid was collected as reported in the ST:STUDY_SUMMARY Collection section of this study. Standard curves for glutamine, cytidine, ST:STUDY_SUMMARY uridine, glucose, UTP and UDP were prepared and extracted along with the ST:STUDY_SUMMARY interstitial fluid samples. The concentrations of glutamine, cytidine, uridine, ST:STUDY_SUMMARY UDP and UTP were measured by LC-MS, and glucose was measured by GC-MS. A ST:STUDY_SUMMARY decrease in uridine content, and accordingly in UDP and UTP, and a concomitant ST:STUDY_SUMMARY accumulation of cytidine was observed in sgCda tumors. On the other hand, no ST:STUDY_SUMMARY differences were observed in glucose and glutamine abundance. ST:INSTITUTE VIB-KU Leuven Center for Cancer Biology ST:LAST_NAME Mazzone ST:FIRST_NAME Massimiliano ST:ADDRESS Herestraat 49, box 912, Leuven, Flemish Brabant, 3000, Belgium ST:EMAIL massimiliano.mazzone@kuleuven.be ST:PHONE +32-16-37.32.13 #SUBJECT SU:SUBJECT_TYPE Mammal SU:SUBJECT_SPECIES Mus musculus SU:TAXONOMY_ID 10090 SU:GENOTYPE_STRAIN C57BL/6J #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Raw file names and additional sample data SUBJECT_SAMPLE_FACTORS 1 TIF1 Sample source:Pancreatic tumor interstitial fluid | Genotype:sgNT 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_SAMPLE_FACTORS 2 TIF2 Sample source:Pancreatic tumor interstitial fluid | Genotype:sgNT 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_SAMPLE_FACTORS 3 TIF3 Sample source:Pancreatic tumor interstitial fluid | Genotype:sgNT 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_SAMPLE_FACTORS 4 TIF4 Sample source:Pancreatic tumor interstitial fluid | Genotype:sgNT 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_SAMPLE_FACTORS 5 TIF5 Sample source:Pancreatic tumor interstitial fluid | Genotype:sgCda 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_SAMPLE_FACTORS 6 TIF6 Sample source:Pancreatic tumor interstitial fluid | Genotype:sgCda 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_SAMPLE_FACTORS 7 TIF7 Sample source:Pancreatic tumor interstitial fluid | Genotype:sgCda 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_SAMPLE_FACTORS 8 TIF8 Sample source:Pancreatic tumor interstitial fluid | Genotype:sgNT 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_SAMPLE_FACTORS 9 TIF9 Sample source:Pancreatic tumor interstitial fluid | Genotype:sgNT 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_SAMPLE_FACTORS 10 TIF10 Sample source:Pancreatic tumor interstitial fluid | Genotype:sgNT 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_SAMPLE_FACTORS 11 TIF11 Sample source:Pancreatic tumor interstitial fluid | Genotype:sgCda 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_SAMPLE_FACTORS 12 TIF12 Sample source:Pancreatic tumor interstitial fluid | Genotype:sgCda 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_SAMPLE_FACTORS 13 TIF13 Sample source:Pancreatic tumor interstitial fluid | Genotype:sgCda 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_SAMPLE_FACTORS 14 TIF14 Sample source:Pancreatic tumor interstitial fluid | Genotype:sgNT 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_SAMPLE_FACTORS 15 TIF15 Sample source:Pancreatic tumor interstitial fluid | Genotype:sgNT 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_SAMPLE_FACTORS 16 TIF16 Sample source:Pancreatic tumor interstitial fluid | Genotype:sgNT 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_SAMPLE_FACTORS 17 TIF17 Sample source:Pancreatic tumor interstitial fluid | Genotype:sgNT 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_SAMPLE_FACTORS 18 TIF18 Sample source:Pancreatic tumor interstitial fluid | Genotype:sgCda 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_SAMPLE_FACTORS 19 TIF19 Sample source:Pancreatic tumor interstitial fluid | Genotype:sgCda 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_SAMPLE_FACTORS 20 TIF20 Sample source:Pancreatic tumor interstitial fluid | Genotype:sgCda 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_SAMPLE_FACTORS 21 TIF21 Sample source:Pancreatic tumor interstitial fluid | Genotype:sgCda 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_SAMPLE_FACTORS N/A STD2_a Sample source:Calibration Curve | Genotype:N/A 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_SAMPLE_FACTORS N/A STD3_a Sample source:Calibration Curve | Genotype:N/A 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_SAMPLE_FACTORS N/A STD4_a Sample source:Calibration Curve | Genotype:N/A 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_SAMPLE_FACTORS N/A STD5_a Sample source:Calibration Curve | Genotype:N/A 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_SAMPLE_FACTORS N/A STD6_a Sample source:Calibration Curve | Genotype:N/A 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_SAMPLE_FACTORS N/A STD7_a Sample source:Calibration Curve | Genotype:N/A 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_SAMPLE_FACTORS N/A STD8_a Sample source:Calibration Curve | Genotype:N/A 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_SAMPLE_FACTORS N/A STD9_a Sample source:Calibration Curve | Genotype:N/A 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_SAMPLE_FACTORS N/A STD10_a Sample source:Calibration Curve | Genotype:N/A 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_SAMPLE_FACTORS N/A STD11_a Sample source:Calibration Curve | Genotype:N/A 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_SAMPLE_FACTORS N/A STD12_a Sample source:Calibration Curve | Genotype:N/A 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_SAMPLE_FACTORS N/A STD13_a Sample source:Calibration Curve | Genotype:N/A 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_SAMPLE_FACTORS N/A STD14_a Sample source:Calibration Curve | Genotype:N/A 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_SAMPLE_FACTORS N/A STD15_a Sample source:Calibration Curve | Genotype:N/A 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_SAMPLE_FACTORS N/A STD3_b Sample source:Calibration Curve | Genotype:N/A 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_SAMPLE_FACTORS N/A STD4_b Sample source:Calibration Curve | Genotype:N/A 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_SAMPLE_FACTORS N/A STD5_b Sample source:Calibration Curve | Genotype:N/A 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_SAMPLE_FACTORS N/A STD6_b Sample source:Calibration Curve | Genotype:N/A 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_SAMPLE_FACTORS N/A STD7_b Sample source:Calibration Curve | Genotype:N/A 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_SAMPLE_FACTORS N/A STD8_b Sample source:Calibration Curve | Genotype:N/A 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_SAMPLE_FACTORS N/A STD9_b Sample source:Calibration Curve | Genotype:N/A 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_SAMPLE_FACTORS N/A STD10_b Sample source:Calibration Curve | Genotype:N/A 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_SAMPLE_FACTORS N/A STD11_b Sample source:Calibration Curve | Genotype:N/A 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_SAMPLE_FACTORS N/A STD12_b Sample source:Calibration Curve | Genotype:N/A 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_SAMPLE_FACTORS N/A STD13_b Sample source:Calibration Curve | Genotype:N/A 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_SAMPLE_FACTORS N/A STD14_b Sample source:Calibration Curve | Genotype:N/A 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_SAMPLE_FACTORS 1 TIF1_GC Sample source:Pancreatic tumor interstitial fluid | Genotype:sgNT 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_SAMPLE_FACTORS 2 TIF2_GC Sample source:Pancreatic tumor interstitial fluid | Genotype:sgNT 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_SAMPLE_FACTORS 3 TIF3_GC Sample source:Pancreatic tumor interstitial fluid | Genotype:sgNT 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_SAMPLE_FACTORS 4 TIF4_GC Sample source:Pancreatic tumor interstitial fluid | Genotype:sgNT 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_SAMPLE_FACTORS 5 TIF5_GC Sample source:Pancreatic tumor interstitial fluid | Genotype:sgCda 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_SAMPLE_FACTORS 6 TIF6_GC Sample source:Pancreatic tumor interstitial fluid | Genotype:sgCda 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_SAMPLE_FACTORS 7 TIF7_GC Sample source:Pancreatic tumor interstitial fluid | Genotype:sgCda 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_SAMPLE_FACTORS 8 TIF8_GC Sample source:Pancreatic tumor interstitial fluid | Genotype:sgNT 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_SAMPLE_FACTORS 9 TIF9_GC Sample source:Pancreatic tumor interstitial fluid | Genotype:sgNT 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_SAMPLE_FACTORS 10 TIF10_GC Sample source:Pancreatic tumor interstitial fluid | Genotype:sgNT 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_SAMPLE_FACTORS 11 TIF11_GC Sample source:Pancreatic tumor interstitial fluid | Genotype:sgCda 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_SAMPLE_FACTORS 12 TIF12_GC Sample source:Pancreatic tumor interstitial fluid | Genotype:sgCda 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_SAMPLE_FACTORS 13 TIF13_GC Sample source:Pancreatic tumor interstitial fluid | Genotype:sgCda 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_SAMPLE_FACTORS N/A STD2_c Sample source:Calibration Curve | Genotype:N/A 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_SAMPLE_FACTORS N/A STD3_c Sample source:Calibration Curve | Genotype:N/A 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_SAMPLE_FACTORS N/A STD4_c Sample source:Calibration Curve | Genotype:N/A 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_SAMPLE_FACTORS N/A STD5_c Sample source:Calibration Curve | Genotype:N/A 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_SAMPLE_FACTORS N/A STD6_c Sample source:Calibration Curve | Genotype:N/A 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_SAMPLE_FACTORS N/A STD7_c Sample source:Calibration Curve | Genotype:N/A 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_SAMPLE_FACTORS N/A STD8_c Sample source:Calibration Curve | Genotype:N/A 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_SAMPLE_FACTORS N/A STD9_c Sample source:Calibration Curve | Genotype:N/A 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_SAMPLE_FACTORS N/A STD10_c Sample source:Calibration Curve | Genotype:N/A 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_SAMPLE_FACTORS N/A STD11_c Sample source:Calibration Curve | Genotype:N/A 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_SAMPLE_FACTORS N/A STD12_c Sample source:Calibration Curve | Genotype:N/A 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 CO:COLLECTION_SUMMARY 8-10 weeks old C57BL/6J female mice were euthanized with 75 µl of a 60 mg ml-1 CO:COLLECTION_SUMMARY Dolethal solution (pentobarbital sodium, Vetoquinol). Subsequently, sgNT and CO:COLLECTION_SUMMARY sgCda primary tumors were collected by surgical resection, washed with blood CO:COLLECTION_SUMMARY bank saline and dried from liquid excess. Tissues were then placed in a CO:COLLECTION_SUMMARY home-made filtered centrifugation tube supplemented with a 20 µm nylon mesh CO:COLLECTION_SUMMARY filter (Repligen) and centrifuged at 400 x g at 4 °C for 10 minutes. Between CO:COLLECTION_SUMMARY 1-14 µl of tumor interstitial fluid were collected and stored on dry ice. CO:COLLECTION_SUMMARY Interstitial fluid volume was used to determine the metabolites concentration CO:COLLECTION_SUMMARY measured by mass spectrometry. CO:SAMPLE_TYPE Interstitial fluid #TREATMENT TR:TREATMENT_SUMMARY KPC FC1245 cells were genetically engineered using doxycycline inducible TR:TREATMENT_SUMMARY CRISPR/Cas9 system platform to target specifically cytidine deaminase (sgCda). TR:TREATMENT_SUMMARY sgCda and the control sgNT were then orthotopically injected in the head of the TR:TREATMENT_SUMMARY pancreas of 8-10 weeks old C57BL/6J female mice. When the tumor weight reached TR:TREATMENT_SUMMARY approximately 0.2-0.4g, mice were sacrificed and tumor interstitial fluid was TR:TREATMENT_SUMMARY collected #SAMPLEPREP SP:SAMPLEPREP_SUMMARY Standard curves for Glucose (Sigma-Aldrich, G7021), UDP (Sigma-Aldrich, 94330), SP:SAMPLEPREP_SUMMARY UTP (Jena Bioscience, NU-1024S), cytidine (Sigma-Aldrich, C4654), uridine SP:SAMPLEPREP_SUMMARY (Sigma-Aldrich, U3003) and glutamine (Gibco, 25030-34) were used to calculate SP:SAMPLEPREP_SUMMARY the concentration of these metabolites in the samples. The standard curve was SP:SAMPLEPREP_SUMMARY prepared with a dilution series starting from 5 mM Glucose and Glutamine, 1 mM SP:SAMPLEPREP_SUMMARY Cytidine, Uridine, UDP and UTP. Specific dilutions are indicated in the Study SP:SAMPLEPREP_SUMMARY Design table. Metabolites and calibration curves were extracted simultaneously SP:SAMPLEPREP_SUMMARY by addition of 800 μl of MS-grade methanol-water buffer (MeOH:H2O, 5:3, v/v) SP:SAMPLEPREP_SUMMARY containing the internal standards glutaric acid (5 μg ml-1, Sigma-Aldrich, SP:SAMPLEPREP_SUMMARY G3407) and 13C6-Glucose (30 μg ml-1, Cambridge Isotope Laboratories, Inc., SP:SAMPLEPREP_SUMMARY CLM-1396), followed by 500 μl of chloroform. Samples were then vortexed and SP:SAMPLEPREP_SUMMARY centrifuged (4 °C for 10 min each). The polar (upper) phases were collected, SP:SAMPLEPREP_SUMMARY divided into two equal parts for gas chromatography (GC) and liquid SP:SAMPLEPREP_SUMMARY chromatography (LC) mass spectrometry analysis, and dried using a vacuum SP:SAMPLEPREP_SUMMARY concentrator. The dried metabolite extracts were stored at -80 °C until SP:SAMPLEPREP_SUMMARY analysis. #CHROMATOGRAPHY CH:CHROMATOGRAPHY_SUMMARY Inlet Temperature: 270; Helium flow rate: 0.88 mL/min; The GC oven was kept at CH:CHROMATOGRAPHY_SUMMARY 100°C and for 1 min, increased with a gradient of 2.5°C min-1 to 105°C for 2 CH:CHROMATOGRAPHY_SUMMARY min, then ramped with a gradient of 15°C min-1 to 260°, and after that ramped CH:CHROMATOGRAPHY_SUMMARY with a gradient of 20°C min-1 up to 300°C for 5 min. CH:CHROMATOGRAPHY_TYPE GC CH:INSTRUMENT_NAME Agilent 8860 CH:COLUMN_NAME Agilent J&W DB-35ms (30 m x 0.25 mm, 0.25 µm) CH:SOLVENT_A N/A CH:SOLVENT_B N/A CH:FLOW_GRADIENT N/A CH:FLOW_RATE N/A CH:COLUMN_TEMPERATURE 100-300 #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:INSTRUMENT_NAME Agilent 5977C MS:INSTRUMENT_TYPE Single quadrupole MS:MS_TYPE EI MS:ION_MODE POSITIVE MS:MS_COMMENTS 5977C quipped with EI inert source. Mass spectrometry was performed at 70 eV and MS:MS_COMMENTS a mass range of 150-650 atomic mass units was measured. The chromatographic MS:MS_COMMENTS peaks were extracted from raw chromatograms with a custom MATLAB Script. The MS:MS_COMMENTS chromatographic peaks for 12C-Glucose were normalized to the internal standard MS:MS_COMMENTS 13C6-glucose. Tumor interstitial fluid samples were interpolated to the standard MS:MS_COMMENTS curve and normalized for tumor interstitial fluid volume to quantify metabolite MS:MS_COMMENTS concentration. #MS_METABOLITE_DATA MS_METABOLITE_DATA:UNITS Ion Counts (AUC) MS_METABOLITE_DATA_START Samples TIF1_GC TIF2_GC TIF3_GC TIF4_GC TIF5_GC TIF6_GC TIF7_GC TIF8_GC TIF9_GC TIF10_GC TIF11_GC TIF12_GC TIF13_GC STD2_c STD3_c STD4_c STD5_c STD6_c STD7_c STD8_c STD9_c STD10_c STD11_c STD12_c Factors Sample source:Pancreatic tumor interstitial fluid | Genotype:sgNT Sample source:Pancreatic tumor interstitial fluid | Genotype:sgNT Sample source:Pancreatic tumor interstitial fluid | Genotype:sgNT Sample source:Pancreatic tumor interstitial fluid | Genotype:sgNT Sample source:Pancreatic tumor interstitial fluid | Genotype:sgCda Sample source:Pancreatic tumor interstitial fluid | Genotype:sgCda Sample source:Pancreatic tumor interstitial fluid | Genotype:sgCda Sample source:Pancreatic tumor interstitial fluid | Genotype:sgNT Sample source:Pancreatic tumor interstitial fluid | Genotype:sgNT Sample source:Pancreatic tumor interstitial fluid | Genotype:sgNT Sample source:Pancreatic tumor interstitial fluid | Genotype:sgCda Sample source:Pancreatic tumor interstitial fluid | Genotype:sgCda Sample source:Pancreatic tumor interstitial fluid | Genotype:sgCda Sample source:Calibration Curve | Genotype:N/A Sample source:Calibration Curve | Genotype:N/A Sample source:Calibration Curve | Genotype:N/A Sample source:Calibration Curve | Genotype:N/A Sample source:Calibration Curve | Genotype:N/A Sample source:Calibration Curve | Genotype:N/A Sample source:Calibration Curve | Genotype:N/A Sample source:Calibration Curve | Genotype:N/A Sample source:Calibration Curve | Genotype:N/A Sample source:Calibration Curve | Genotype:N/A Sample source:Calibration Curve | Genotype:N/A Glucose 1.27E+05 3.75E+05 6.71E+05 3.85E+05 1.83E+06 4.76E+05 3.52E+05 8.99E+05 2.50E+05 3.13E+05 4.56E+05 1.50E+05 2.88E+05 4.64E+05 2.46E+05 1.20E+05 5.89E+04 2.57E+04 1.39E+04 8.19E+03 4.13E+03 3.59E+03 2.45E+03 9.57E+02 13C6 Glucose 3.10E+05 5.10E+05 6.36E+05 6.13E+05 6.55E+05 7.46E+05 7.16E+05 6.90E+05 6.64E+05 8.36E+05 7.05E+05 6.77E+05 5.74E+05 1.38E+05 1.36E+05 1.43E+05 1.34E+05 1.10E+05 1.37E+05 1.20E+05 1.11E+05 1.26E+05 1.27E+05 1.16E+05 MS_METABOLITE_DATA_END #METABOLITES METABOLITES_START metabolite_name Pubchem Id Kegg Id m/z window RT Glucose 5793 C00031 239.7-240.7 16.74 13C6 Glucose 5794 C00032 244.7-245.7 16.74 METABOLITES_END #END