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 |
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). |
Combined analysis:
| Analysis ID | AN003870 |
|---|---|
| Analysis type | MS |
| Chromatography type | HILIC |
| Chromatography system | Shimadzu Prominence UFLC |
| Column | Waters XBridge BEH Amide XP HILIC (150 x 2.1mm,2.5um) |
| MS Type | ESI |
| MS instrument type | Triple quadrupole |
| MS instrument name | ABI Sciex 5500 QTrap |
| Ion Mode | UNSPECIFIED |
| Units | AUC |
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 |
MS:
| MS ID: | MS003611 |
| Analysis ID: | AN003870 |
| Instrument Name: | ABI Sciex 5500 QTrap |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | The optimized MS parameters were: ESI voltage was +5,000 V in positive ion mode and -4,500 V in negative ion mode; dwell time was 3 ms per SRM transition and the total cycle time was 1.57 seconds. Peak integration for each targeted metabolite in SRM transition was processed with MultiQuant software (v2.1, AB Sciex). The preprocessed data with integrated peak areas were exported from MultiQuant and re-imported into Metaboanalyst software for further data analysis (statistical analysis, principal component analysis, generating heatmap, enrichment analysis, etc.). |
| Ion Mode: | UNSPECIFIED |
