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.

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Study IDST002375
Study TitleMetabolomics analysis of WT or GOT1 knockout CD8+ T cells cultured in serine-replete or serine-free media
Study SummaryWT 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 NameXu
First NameWei
Address1650 Orleans Street, Baltimore, MD 21287, USA.
Emailwxu29@jhmi.edu
Phone443-220-9936
Submit Date2022-11-30
Raw Data AvailableYes
Raw Data File Type(s)wiff
Analysis Type DetailLC-MS
Release Date2023-11-28
Release Version1
Wei Xu Wei Xu
https://dx.doi.org/10.21228/M8612V
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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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
SA237363sample 6GOT1 KO_Serine-free
SA237364sample 4GOT1 KO_Serine-free
SA237365sample 5GOT1 KO_Serine-free
SA237366sample 11GOT1 KO_Serine-replete
SA237367sample 10GOT1 KO_Serine-replete
SA237368sample 12GOT1 KO_Serine-replete
SA237369sample 1WT_Serine-free
SA237370sample 3WT_Serine-free
SA237371sample 2WT_Serine-free
SA237372sample 7WT_Serine-replete
SA237373sample 8WT_Serine-replete
SA237374sample 9WT_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
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