Summary of Study ST001611

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 PR001036. The data can be accessed directly via it's Project DOI: 10.21228/M8SD7T This work is supported by NIH grant, U2C- DK119886.

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

Study ID	ST001611
Study Title	Mouse model of sarcoma (STS) to characterize tumor vulnerabilities and identify novel targets for anti-cancer treatment
Study Summary	For metabolomics study, tumor-bearing mice were starved for 6 hours before sarcoma and skeletal muscles were harvested.
Institute	North Carolina State University
Last Name	Liu
First Name	Xiaojing
Address	Polk Hall, RM 128
Email	xliu68@ncsu.edu
Phone	9195154387
Submit Date	2020-11-10
Raw Data Available	Yes
Raw Data File Type(s)	raw(Thermo)
Analysis Type Detail	LC-MS
Release Date	2021-05-11
Release Version	1

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Project:

Project ID:	PR001036
Project DOI:	doi: 10.21228/M8SD7T
Project Title:	Mouse model of sarcoma (STS) to characterize tumor vulnerabilities and identify novel targets for anti-cancer treatment
Project Summary:	Here, we use a genetically engineered mouse model of soft tissue sarcoma (STS) along with metabolomics together with tracing technology to characterize tumor vulnerabilities and identify novel targets for anti-cancer treatment. We identified multiple metabolic pathways which are altered in sarcoma and may also serve as potential targets. As a proof of concept, in this study, we used metabolomics together with in vivo tracing approach and identified proline metabolism as a potential target for anti-tumor treatment.
Institute:	North Carolina State University
Last Name:	Liu
First Name:	Xiaojing
Address:	Polk Hall, RM 128
Email:	xliu68@ncsu.edu
Phone:	9195154387

Subject:

Subject ID:	SU001688
Subject Type:	Mammal
Subject Species:	Mus musculus
Taxonomy ID:	10090

Factors:

Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id	local_sample_id	Treatment
SA136766	Sample8-NoISD	Sarcoma
SA136767	Sample9-NoISD	Sarcoma
SA136768	Sample10-NoISD	Sarcoma
SA136769	Sample7-NoISD	Sarcoma
SA136770	Sample6-NoISD	Sarcoma
SA136771	Sample2-NoISD	Skeletal muscle
SA136772	Sample3-NoISD	Skeletal muscle
SA136773	Sample4-NoISD	Skeletal muscle
SA136774	Sample5-NoISD	Skeletal muscle
SA136775	Sample1-NoISD	Skeletal muscle

Showing results 1 to 10 of 10

Showing results 1 to 10 of 10

Collection:

Collection ID:	CO001681
Collection Summary:	5 skeletal muscle and 5 sarcoma samples. Tissue polar metabolites were extracted into 80% methanol/water.
Sample Type:	Blood;Sarcoma;Skeletal muscle

Treatment:

Treatment ID:	TR001701
Treatment Summary:	The mouse model of soft-tissue sarcoma was generated on a mixed background (129/SvJae and C57BL/6) using a combination of alleles that were previously described: Pax7CreER-T2 20, p53FL/FL 21, LSL-NrasG12D 22 and ROSA26mTmG Primary mouse soft tissue sarcomas were generated in the mouse hind limb as previously described 19 by intramuscular (IM) injection of (Z)-4-hydroxytamoxifen (4-OHT). 4-OHT was dissolved in 100% DMSO at a concentration of 10 mg/ml and 50 ul of the solution was injected into the gastrocnemius muscle.

Treatment ID:

TR001701

Treatment Summary:

The mouse model of soft-tissue sarcoma was generated on a mixed background (129/SvJae and C57BL/6) using a combination of alleles that were previously described: Pax7CreER-T2 20, p53FL/FL 21, LSL-NrasG12D 22 and ROSA26mTmG Primary mouse soft tissue sarcomas were generated in the mouse hind limb as previously described 19 by intramuscular (IM) injection of (Z)-4-hydroxytamoxifen (4-OHT). 4-OHT was dissolved in 100% DMSO at a concentration of 10 mg/ml and 50 ul of the solution was injected into the gastrocnemius muscle.

Sample Preparation:

Sampleprep ID:	SP001694
Sampleprep Summary:	The tumor sample was first homogenized in liquid nitrogen and then 5 to 10 mg was weighed in a new Eppendorf tube. Ice cold extraction solvent (250 ul 80% MeOH/water) was added to the tissue sample, and a pellet mixer was used to further break down the tissue chunk and form an even suspension, followed by the addition of 250 ul to rinse the pellet mixer. After incubation on ice for an additional 10 min, the tissue extract was centrifuged with a speed of 20,000 g at 4 °C for 10 min. The dry pellets were reconstituted into 30 ul (per 3 mg tissue) sample solvent (water:methanol: acetonitrile, 2:1:1, v/v), and 3 ul was injected to LC-HRMS. 5 ul mouse plasma was mixed with 5 ul water, and 40 ul ice cold methanol was added. After vortex for 1 min, the mixture was centrifuged with a speed of 20,000 g at 4 °C for 10 min, and 3 l was injected to LC-HRMS.

Sampleprep ID:

SP001694

Sampleprep Summary:

The tumor sample was first homogenized in liquid nitrogen and then 5 to 10 mg was weighed in a new Eppendorf tube. Ice cold extraction solvent (250 ul 80% MeOH/water) was added to the tissue sample, and a pellet mixer was used to further break down the tissue chunk and form an even suspension, followed by the addition of 250 ul to rinse the pellet mixer. After incubation on ice for an additional 10 min, the tissue extract was centrifuged with a speed of 20,000 g at 4 °C for 10 min. The dry pellets were reconstituted into 30 ul (per 3 mg tissue) sample solvent (water:methanol: acetonitrile, 2:1:1, v/v), and 3 ul was injected to LC-HRMS. 5 ul mouse plasma was mixed with 5 ul water, and 40 ul ice cold methanol was added. After vortex for 1 min, the mixture was centrifuged with a speed of 20,000 g at 4 °C for 10 min, and 3 l was injected to LC-HRMS.

Combined analysis:

Analysis ID	AN002645	AN002646
Analysis type	MS	MS
Chromatography type	HILIC	HILIC
Chromatography system	Thermo Dionex Ultimate 3000	Thermo Dionex Ultimate 3000
Column	Waters Xbridge amide (100 x 2.1mm,3.5um)	Waters Xbridge amide (100 x 2.1mm,3.5um)
MS Type	ESI	ESI
MS instrument type	Orbitrap	Orbitrap
MS instrument name	Thermo Exactive Plus Orbitrap	Thermo Exactive Plus Orbitrap
Ion Mode	POSITIVE	NEGATIVE
Units	peak area	peak area

Chromatography:

Chromatography ID:	CH001954
Chromatography Summary:	HILIC method is for general metabolomics analysis.
Instrument Name:	Thermo Dionex Ultimate 3000
Column Name:	Waters Xbridge amide (100 x 2.1mm,3.5um)
Chromatography Type:	HILIC

MS:

MS ID:	MS002457
Analysis ID:	AN002645
Instrument Name:	Thermo Exactive Plus Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	It was operated in the full-scan mode with the resolution set at 70 000 (at m/z 200).LC-MS data were analyzed using Sieve 2.0 (Thermo Scientific), and the integrated area under metabolite peak was used to compare the relative abundance of each metabolite in different samples in the same batch.
Ion Mode:	POSITIVE

MS ID:	MS002458
Analysis ID:	AN002646
Instrument Name:	Thermo Exactive Plus Orbitrap
Instrument Type:	Orbitrap
MS Type:	ESI
MS Comments:	It was operated in the full-scan mode with the resolution set at 70 000 (at m/z 200).LC-MS data were analyzed using Sieve 2.0 (Thermo Scientific), and the integrated area under metabolite peak was used to compare the relative abundance of each metabolite in different samples in the same batch.
Ion Mode:	NEGATIVE