Summary of Study ST002375
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 PR001528. The data can be accessed directly via it's Project DOI: 10.21228/M8612V 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 | ST002375 |
| Study Title | Metabolomics analysis of WT or GOT1 knockout CD8+ T cells cultured in serine-replete or serine-free media |
| Study Summary | WT or GOT1 knockout CD8+ T cells were activated with plate-bound anti-CD3 or soluble anti-CD28, in serine-replete or serine-free media for 24 hours. Intracellular metabolome were assessed by MS. |
| Institute | Johns Hopkins University |
| Last Name | Xu |
| First Name | Wei |
| Address | 1650 Orleans Street, Baltimore, MD 21287, USA. |
| wxu29@jhmi.edu | |
| Phone | 443-220-9936 |
| Submit Date | 2022-11-30 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | wiff |
| Analysis Type Detail | LC-MS |
| Release Date | 2023-11-28 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001528 |
| Project DOI: | doi: 10.21228/M8612V |
| Project Title: | Metabolomics analysis of WT or GOT1 knockout CD8+ T cells cultured in serine-replete or serine-free media |
| Project Summary: | WT or GOT1 knockout CD8+ T cells were activated with plate-bound anti-CD3 or soluble anti-CD28, in serine-replete or serine-free media for 24 hours. Intracellular metabolome were assessed by MS. |
| Institute: | Johns Hopkins University |
| Last Name: | Xu |
| First Name: | Wei |
| Address: | 1650 Orleans Street, Baltimore, MD 21287, USA. |
| Email: | wxu29@jhmi.edu |
| Phone: | 443-220-9936 |
Subject:
| Subject ID: | SU002464 |
| Subject Type: | Cultured cells |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Species Group: | Mammals |
Factors:
Subject type: Cultured cells; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Treatment |
|---|---|---|
| SA237363 | sample 6 | GOT1 KO_Serine-free |
| SA237364 | sample 4 | GOT1 KO_Serine-free |
| SA237365 | sample 5 | GOT1 KO_Serine-free |
| SA237366 | sample 11 | GOT1 KO_Serine-replete |
| SA237367 | sample 10 | GOT1 KO_Serine-replete |
| SA237368 | sample 12 | GOT1 KO_Serine-replete |
| SA237369 | sample 1 | WT_Serine-free |
| SA237370 | sample 3 | WT_Serine-free |
| SA237371 | sample 2 | WT_Serine-free |
| SA237372 | sample 7 | WT_Serine-replete |
| SA237373 | sample 8 | WT_Serine-replete |
| SA237374 | sample 9 | WT_Serine-replete |
| Showing results 1 to 12 of 12 |
Collection:
| Collection ID: | CO002457 |
| Collection Summary: | Cell pellets were spun down and washed twice with pre-warmed PBS. Metabolites were immediately extracted or stored at -80℃ until further extraction. |
| Sample Type: | Cultured cells |
Treatment:
| Treatment ID: | TR002476 |
| Treatment Summary: | CD8+ T cells were isolated from spleens and lymph nodes of WT or T cell conditional GOT1 knockout mice. Cells were then activated with plate-bound anti-CD3 and soluble anti-CD28 for 24 hours in normal media (serine-replete) or serine-free media. |
Sample Preparation:
| Sampleprep ID: | SP002470 |
| Sampleprep Summary: | Cell pellets were spun down and washed twice with pre-warmed PBS. Metabolites were immediately extracted by adding methanol:water (80:20, v/v) extraction solution, sonicated and stored at -80 °C for at least 2 hours to precipitate the proteins. Supernatant after centrifugation at 14,000xg for 10 minutes was dried under nitrogen gas. Metabolites were then reconstituted using ACN:water (50:50, v/v) overnight at 4 °C. Soluble metabolites after centrifugation at 14,000xg for 10 minutes were subjected to targeted metabolite analysis by liquid-chromatography tandem mass spectrometry (LC-MS/MS). |
Chromatography:
| Chromatography ID: | CH002868 |
| Instrument Name: | Shimadzu Prominence UFLC |
| Column Name: | Waters XBridge BEH Amide XP HILIC (150 x 2.1mm,2.5um) |
| Chromatography Type: | HILIC |
Analysis:
| Analysis ID: | AN003870 |
| Analysis Type: | MS |
| Chromatography ID: | CH002868 |
| Num Factors: | 4 |
| Num Metabolites: | 147 |
| Units: | AUC |
