#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