Summary of Study ST001677

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 PR001078. The data can be accessed directly via it's Project DOI: 10.21228/M8C111 This work is supported by NIH grant, U2C- DK119886.

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Study IDST001677
Study TitleQuantitative targeted measurements of sphingolipids in Th17 cells before and after the triple knockdown of SPTLC1,2,3 genes (SPT, de novo pathway: sphingolipid metabolism) (part-III)
Study TypeMS: Targeted analysis
Study SummaryPart 3/5: It includes quantitative targeted measurements of sphingolipids (ceramides and glycosphingolipids)in Th17 cells before(scrambled / control)and after the triple knockdown of SPTLC1,2,3 genes (SPT de novo pathway: sphingolipid metabolism).
Institute
University of Turku
DepartmentSystems Medicine, Turku Bioscience
LaboratoryMetabolomics
Last NameSen
First NamePartho
AddressTykistökatu 6B, BioCity, 5th Floor, Turku, Southwest, 20521, Finland
Emailpartho.sen@utu.fi
Phone0469608145
Submit Date2021-01-31
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2021-11-02
Release Version1
Partho Sen Partho Sen
https://dx.doi.org/10.21228/M8C111
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Sample Preparation:

Sampleprep ID:SP001760
Sampleprep Summary:The frozen cell preps were defrosted on ice. The samples were extracted using a modified Folch method[1]. 1. Sen, P. et al. Persistent Alterations in Plasma Lipid Profiles Before Introduction of Gluten in the Diet Associated With Progression to Celiac Disease. Clin Transl Gastroenterol 10, 1-10, doi:10.14309/ctg.0000000000000044 (2019). Briefly, 120 µL of cold (4 °C) extraction solvent (CHCl3: MeOH, (2:1 v/v) was added to the samples. The extraction solvent containing the following internal standards: C17 Lactosyl(beta) ceramide (D18:1/17:0, 20 ppb), C17 Glucosyl(beta) ceramide (D18:1/17:0, 20 ppb), C17 ceramide (D18:1/17:0, 20 ppb), C16 ceramide-d7 (d18:1-d7/16:0, 16,57 ppb), C18 ceramide-d7 (d18:1-d7/18:0, 8.75 ppb), C24 ceramide-d7 (d18:1-d7/24:0, 20 ppb), and C24:1 ceramide-d7 (d18:1-d7/24:1(15Z), 9,96 ppb). The samples were the vortexed briefly and left on ice for 30 minutes. The samples were then centrifuged (9400g, 5 min, 4 °C) and then 60 µL of the bottom layer was transfer to a clean mass spectrometry vial (2 mL). The samples were then stored at –80 °C.
Processing Storage Conditions:-80℃
Extract Storage:-80℃
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