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 |
| 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 |
| Species Group: | Mammals |
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 |
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. |
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 |
Analysis:
| Analysis ID: | AN002645 |
| Analysis Type: | MS |
| Chromatography ID: | CH001954 |
| Num Factors: | 2 |
| Num Metabolites: | 138 |
| Units: | peak area |
| Analysis ID: | AN002646 |
| Analysis Type: | MS |
| Chromatography ID: | CH001954 |
| Num Factors: | 2 |
| Num Metabolites: | 175 |
| Units: | peak area |
