#METABOLOMICS WORKBENCH MaMa_20240312_023321 DATATRACK_ID:4718 STUDY_ID:ST003154 ANALYSIS_ID:AN005174 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_TYPE           	Reversed phase
CH:INSTRUMENT_NAME               	Thermo Dionex Ultimate 3000
CH:COLUMN_NAME                   	Waters ACQUITY UPLC HSS T3 (100 x 2.1mm,1.8um)
CH:SOLVENT_A                     	100% water; 10 mM tributyl-amine; 15 mM acetic acid
CH:SOLVENT_B                     	100% methanol
CH:FLOW_GRADIENT                 	The gradient started with 5% of solvent B and 95% solvent A and remained at 5% B
CH:FLOW_GRADIENT                 	until 2 min post injection. A linear gradient to 37% B was carried out until 7
CH:FLOW_GRADIENT                 	min and increased to 41% until 14 min. Between 14 and 26 minutes the gradient
CH:FLOW_GRADIENT                 	increased to 95% of B and remained at 95% B for 4 minutes. At 30 min the
CH:FLOW_GRADIENT                 	gradient returned to 5% B. The chromatography was stopped at 40 min.
CH:FLOW_RATE                     	0.25 mL/min
CH:COLUMN_TEMPERATURE            	40
#ANALYSIS
AN:ANALYSIS_TYPE                 	MS
#MS
MS:INSTRUMENT_NAME               	Thermo Q Exactive Orbitrap
MS:INSTRUMENT_TYPE               	Orbitrap
MS:MS_TYPE                       	ESI
MS:ION_MODE                      	NEGATIVE
MS:MS_COMMENTS                   	The MS was operated in negative full scan mode (m/z range: 70–900 and 400-500)
MS:MS_COMMENTS                   	using a spray voltage of 4.0 kV, capillary temperature of 350 °C, sheath gas at
MS:MS_COMMENTS                   	50.0, auxiliary gas at 10.0. The AGC target was set at 3.0E6 using a resolution
MS:MS_COMMENTS                   	if 140000, with a maximum IT fill time of 512 ms. Data was collected and
MS:MS_COMMENTS                   	analyzed using the Xcalibur software (Thermo Scientific) considering a 5 ppm
MS:MS_COMMENTS                   	error. The chromatographic peaks for UDP, UTP, cytidine, uridine and glutamine
MS:MS_COMMENTS                   	were normalized to the internal standard glutaric acid. Tumor interstitial fluid
MS:MS_COMMENTS                   	samples were interpolated to the standard curve and normalized for tumor
MS:MS_COMMENTS                   	interstitial fluid volume in order to quantify metabolite concentration.
#MS_METABOLITE_DATA
MS_METABOLITE_DATA:UNITS	Ion Counts (AUC) 
MS_METABOLITE_DATA_START
Samples	TIF1	TIF2	TIF3	TIF4	TIF5	TIF6	TIF7	TIF8	TIF9	TIF10	TIF11	TIF12	TIF13	STD2_a	STD3_a	STD4_a	STD5_a	STD6_a	STD7_a	STD8_a	STD9_a	STD10_a	STD11_a	STD12_a	STD13_a	STD14_a	STD15_a	TIF14	TIF15	TIF16	TIF17	TIF18	TIF19	TIF20	TIF21	STD3_b	STD4_b	STD5_b	STD6_b	STD7_b	STD8_b	STD9_b	STD10_b	STD11_b	STD12_b	STD13_b	STD14_b
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	Sample source:Calibration Curve | Genotype:N/A	Sample source:Calibration Curve | Genotype:N/A	Sample source:Calibration Curve | Genotype:N/A	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: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	Sample source:Calibration Curve | Genotype:N/A
Glutamine	2.33E+08	1.87E+08	2.30E+08	2.35E+08	3.07E+08	2.04E+08	2.05E+08	2.44E+08	2.46E+08	2.05E+08	1.62E+08	1.45E+08	2.61E+08	5.55E+09	3.75E+09	2.69E+09	1.78E+09	1.31E+09	7.82E+08	4.43E+08	2.39E+08	1.34E+08	6.77E+07	3.09E+07	1.71E+07	9.44E+06	4.10E+06	2.43E+08	3.53E+08	2.57E+08	2.79E+08	3.92E+08	3.98E+08	5.33E+08	3.75E+08	4.31E+09	2.78E+09	1.74E+09	9.46E+08	6.01E+08	2.64E+08	1.52E+08	7.70E+07	3.74E+07	2.10E+07	1.14E+07	9.14E+06
Cytidine	4.64E+06	1.19E+07	1.54E+07	1.99E+07	3.02E+07	3.09E+07	3.74E+07	1.86E+07	1.39E+07	1.19E+07	3.18E+07	1.65E+07	1.47E+07	2.08E+09	1.27E+09	7.91E+08	4.74E+08	3.29E+08	1.82E+08	9.62E+07	5.28E+07	2.85E+07	1.43E+07	6.76E+06	3.39E+06	1.92E+06	7.18E+05	1.60E+07	2.88E+07	NF	NF	3.16E+07	6.18E+07	NF	5.48E+07	1.25E+09	7.50E+08	4.35E+08	2.17E+08	1.37E+08	6.24E+07	3.56E+07	1.80E+07	8.30E+06	4.57E+06	2.50E+06	1.28E+06
Uridine	3.42E+07	8.63E+07	1.67E+08	1.49E+08	1.49E+08	9.07E+07	1.02E+08	1.65E+08	1.94E+08	1.31E+08	9.42E+07	6.52E+07	3.03E+07	3.14E+09	1.84E+09	1.16E+09	6.75E+08	4.20E+08	2.53E+08	1.42E+08	7.85E+07	4.39E+07	2.22E+07	1.03E+07	5.57E+06	5.11E+06	1.60E+06	7.91E+07	2.25E+08	1.18E+08	3.72E+08	8.31E+07	2.02E+08	8.83E+07	9.67E+07	1.98E+09	1.17E+09	7.00E+08	3.56E+08	2.28E+08	1.09E+08	6.45E+07	3.21E+07	1.72E+07	9.44E+06	4.83E+06	4.17E+06
UDP	1.96E+07	7.02E+06	8.11E+06	6.31E+06	2.13E+06	9.69E+05	1.13E+06	2.91E+06	5.76E+05	1.12E+07	7.60E+05	3.01E+06	3.09E+06	1.25E+09	6.90E+08	4.06E+08	2.14E+08	1.35E+08	7.05E+07	3.54E+07	1.80E+07	9.70E+06	4.69E+06	2.11E+06	1.16E+06	6.20E+05	2.82E+05	5.74E+06	1.65E+07	3.15E+07	2.39E+07	1.59E+07	4.07E+06	4.85E+07	1.62E+07	7.65E+08	4.22E+08	2.27E+08	1.03E+08	6.13E+07	2.64E+07	1.40E+07	6.93E+06	3.16E+06	1.70E+06	8.88E+05	4.62E+05
UTP	3.87E+07	8.19E+06	1.15E+07	5.04E+07	3.67E+07	3.89E+06	6.93E+06	1.73E+07	1.05E+07	2.97E+07	6.12E+06	6.30E+06	3.22E+06	1.75E+10	8.51E+09	4.25E+09	2.11E+09	1.28E+09	5.97E+08	2.76E+08	1.32E+08	6.67E+07	3.14E+07	1.32E+07	7.03E+06	4.13E+06	1.80E+06	6.31E+06	7.01E+07	2.83E+08	1.39E+08	3.90E+07	3.12E+07	4.40E+07	2.57E+07	9.40E+09	4.60E+09	2.26E+09	9.60E+08	5.37E+08	2.01E+08	1.01E+08	4.59E+07	1.96E+07	1.03E+07	5.45E+06	2.77E+06
Glutaric acid	2008300601	1776471769	1504458007	2022038202	1208963216	2270293170	2434264594	1493767261	1562850883	1800915252	2011792474	2396237926	1921384143	3257151486	2804017108	2838225589	2623898694	2626401518	2739918930	2733538598	2696150242	2745559275	2776588898	2611333883	2829182183	2847671041	2633397791	2378311068	1403818827	1570637691	1266070050	1923040584	1725725157	1353297926	1821853148	3941856945	3659372120	3421758016	2928243548	3231484837	2772479138	2925260875	2876798539	2898752066	3001309602	3024284066	3126101316
MS_METABOLITE_DATA_END
#METABOLITES
METABOLITES_START
metabolite_name	Pubchem Id	Kegg Id	RT (min)	m/z window
Glutamine	5961	C00064	1.46	145.06075-145.06260
Cytidine	6175	C00475	2.12	242.07648-242.07916
Uridine	6029	C00299	2.96	243.06049-243.06309
UDP	6031	C00015	15.69	402.99253-402.99693
UTP	6133	C00075	19.89	482.95884-482.96372
Glutaric acid	743	C00489	14.42	131.03432-131.03564
METABOLITES_END
#END