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.

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Study IDST001611
Study TitleMouse model of sarcoma (STS) to characterize tumor vulnerabilities and identify novel targets for anti-cancer treatment
Study SummaryFor metabolomics study, tumor-bearing mice were starved for 6 hours before sarcoma and skeletal muscles were harvested.
Institute
North Carolina State University
Last NameLiu
First NameXiaojing
AddressPolk Hall, RM 128
Emailxliu68@ncsu.edu
Phone9195154387
Submit Date2020-11-10
Raw Data AvailableYes
Raw Data File Type(s).raw
Analysis Type DetailLC-MS
Release Date2021-05-11
Release Version1
Xiaojing Liu Xiaojing Liu
https://dx.doi.org/10.21228/M8SD7T
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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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
SA136766Sample8-NoISDSarcoma
SA136767Sample9-NoISDSarcoma
SA136768Sample10-NoISDSarcoma
SA136769Sample7-NoISDSarcoma
SA136770Sample6-NoISDSarcoma
SA136771Sample2-NoISDSkeletal muscle
SA136772Sample3-NoISDSkeletal muscle
SA136773Sample4-NoISDSkeletal muscle
SA136774Sample5-NoISDSkeletal muscle
SA136775Sample1-NoISDSkeletal muscle
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.

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.

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 × 2.1 mm i.d., 3.5 μm) Waters Xbridge amide (100 × 2.1 mm i.d., 3.5 μm)
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 × 2.1 mm i.d., 3.5 μm)
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
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