Summary of Study ST002373
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 PR001526. The data can be accessed directly via it's Project DOI: 10.21228/M8FH84 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 | ST002373 |
| Study Title | Extracellular metabolome of activated CD8+ T cells |
| Study Summary | WT OT-I CD8+ T cells were activated with plate-bound anti-CD3 and soluble anti-CD28. Blank media or media post 10hr, 30hr or 48hr cell culture were collected for mass spectrometry analysis. |
| 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 | 2022-11-29 |
| 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: | PR001526 |
| Project DOI: | doi: 10.21228/M8FH84 |
| Project Title: | Extracellular metabolome of activated CD8+ T cells |
| Project Summary: | WT OT-I CD8+ T cells were activated with plate-bound anti-CD3 and soluble anti-CD28. Blank media or media post 10hr, 30hr or 48hr cell culture were collected for mass spectrometry analysis. |
| 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: | SU002462 |
| Subject Type: | Cultured cells |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Genotype Strain: | C57BL/6J |
| Age Or Age Range: | 6-8 weeks |
| Gender: | Male and female |
Factors:
Subject type: Cultured cells; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Treatment |
|---|---|---|
| SA237339 | 10hr_M_01 | 10hr blank media |
| SA237340 | 10hr_M_03 | 10hr blank media |
| SA237341 | 10hr_M_02 | 10hr blank media |
| SA237342 | 30hr_M_03 | 30hr blank media |
| SA237343 | 30hr_M_02 | 30hr blank media |
| SA237344 | 30hr_M_01 | 30hr blank media |
| SA237345 | 48hr_M_02 | 48hr blank media |
| SA237346 | 48hr_M_01 | 48hr blank media |
| SA237347 | 48hr_M_03 | 48hr blank media |
| SA237348 | 10hr_WT_02 | media post 10hr cell activation |
| SA237349 | 10hr_WT_03 | media post 10hr cell activation |
| SA237350 | 10hr_WT_01 | media post 10hr cell activation |
| SA237351 | 30hr_WT_01 | media post 30hr cell activation |
| SA237352 | 30hr_WT_03 | media post 30hr cell activation |
| SA237353 | 30hr_WT_02 | media post 30hr cell activation |
| SA237354 | 48hr_WT_03 | media post 48hr cell activation |
| SA237355 | 48hr_WT_02 | media post 48hr cell activation |
| SA237356 | 48hr_WT_01 | media post 48hr cell activation |
| Showing results 1 to 18 of 18 |
Collection:
| Collection ID: | CO002455 |
| Collection Summary: | Blank media or media post cell culture were collected and centrifuged at 1200rpm for 5min. Supernatant were flash frozen in liquid nitrogen until further analysis. |
| Sample Type: | Cultured cells |
Treatment:
| Treatment ID: | TR002474 |
| Treatment Summary: | CD8+ T cells were isolated from spleens and lymph nodes from WT mice. Cells were activated with plate-bound anti-CD3 and soluble anti-CD28. Blank media post 10, 30, 48 hours in the incubator or media post 10, 30, 48 hr activated CD8+ T cell culture were collected for MS analysis. |
Sample Preparation:
| Sampleprep ID: | SP002468 |
| Sampleprep Summary: | For measurement of extracellular metabolome, 625 µL of media was added to 375 µL acetonitrile ACN. Samples were stored at -20 °C for at least two hours followed by centrifugation at 14,000xg to precipitate any proteins. 250 µL of the supernatant was mixed with 250 µL of water and added to a 3 kDa molecular weight cut-off filter spin column (Microcon YM-3 Centrifugal Filter, Millipore). Samples were centrifuged at 14,000xg at 4 °C for 30 min. The flow-through was saved for LC-MS/MS analysis. |
Combined analysis:
| Analysis ID | AN003868 |
|---|---|
| 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 | QTRAP |
| MS instrument name | ABI Sciex 5500 QTrap |
| Ion Mode | UNSPECIFIED |
| Units | AUC |
Chromatography:
| Chromatography ID: | CH002866 |
| 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: | MS003609 |
| Analysis ID: | AN003868 |
| Instrument Name: | ABI Sciex 5500 QTrap |
| Instrument Type: | QTRAP |
| 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 |
