Summary of Study ST003154

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR001960. The data can be accessed directly via it's Project DOI: 10.21228/M8CF0S This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

Study ID	ST003154
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
Submit Date	2024-03-12
Raw Data Available	Yes
Raw Data File Type(s)	mzML
Analysis Type Detail	GC/LC-MS
Release Date	2024-04-05
Release Version	1

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Sample Preparation:

Sampleprep ID:	SP003278
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.

Sampleprep ID:

SP003278

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.