Summary of Study ST002346

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 PR001506. The data can be accessed directly via it's Project DOI: 10.21228/M81D8C 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	ST002346
Study Title	Lipidomics study of the cells defective in peroxisome division
Study Summary	Proliferation of peroxisomes is accompanied by the growth and division of pre-existing peroxisomes. Pex11β induces the elongation of peroxisome membrane and then dynamin-like GTPase, DLP1, elicits the peroxisomal division. Nucleoside diphosphate kinase 3 (NME3) generates GTP for the DLP1 activity. Deficiencies of either of the factors induce abnormal morphology of peroxisomes. In this study, we assessed the phospholipid compositions in cells lacking each of the different division factors. In the fibroblasts from the patients deficient in DLP1, NME3, or Pex11β, docosahexaenoic acid (DHA, C22:6)-containing phospholipids were found to be decreased. Conversely, the levels of several fatty acids such as arachidonic acid (AA, C20:4) and oleic acid (C18:1) were elevated. Mouse embryonic fibroblasts from Drp1- and Pex11β-knockout mice also showed a decrease in the levels of phospholipids containing DHA and AA.
Institute	Kyushu university
Last Name	Abe
First Name	Yuichi
Address	3-1-1 Maidashi, Fukuoka 812-8582, Japan.
Email	y-abe@bio.sojo-u.ac.jp
Phone	+81926426341
Submit Date	2022-10-26
Raw Data Available	Yes
Raw Data File Type(s)	mzML
Analysis Type Detail	LC-MS
Release Date	2022-11-28
Release Version	1

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Sample Preparation:

Sampleprep ID:	SP002441
Sampleprep Summary:	Cells were detached by incubation with trypsin and suspended in PBS. Protein concentration was determined by the bicinchonic acid method (Thermo Fisher Scientific, Rockford, IL). Total lipids were extracted from 50 μg of cellular protein by the Bligh and Dyer method. Cells were dissolved in methanol/chloroform/water at 2:1:0.8 v/v/v and then 50 pmol of 1,2-adidodecanoyl-sn-glycero-3-phosphocholine (Avanti Polar Lipids, Alabaster, AL) and 1,2-didodecanoyl-sn-glycero-3-phosphoethanolamine (Avanti Polar Lipids) were added as internal standards. After incubation for 5 min at room temperature, 1 ml each of water and chloroform were added and the samples were then centrifuged at 2,000 rpm for 5 min in Himac CF-16RX (Hitachi Koki, Tokyo, Japan) to collect the lower organic phase. To re-extract the lipids from the water phase, 1 ml chloroform was added. The combined organic phase was evaporated under a nitrogen stream and the extracted lipids were dissolved in methanol.

Sampleprep ID:

SP002441

Sampleprep Summary:

Cells were detached by incubation with trypsin and suspended in PBS. Protein concentration was determined by the bicinchonic acid method (Thermo Fisher Scientific, Rockford, IL). Total lipids were extracted from 50 μg of cellular protein by the Bligh and Dyer method. Cells were dissolved in methanol/chloroform/water at 2:1:0.8 v/v/v and then 50 pmol of 1,2-adidodecanoyl-sn-glycero-3-phosphocholine (Avanti Polar Lipids, Alabaster, AL) and 1,2-didodecanoyl-sn-glycero-3-phosphoethanolamine (Avanti Polar Lipids) were added as internal standards. After incubation for 5 min at room temperature, 1 ml each of water and chloroform were added and the samples were then centrifuged at 2,000 rpm for 5 min in Himac CF-16RX (Hitachi Koki, Tokyo, Japan) to collect the lower organic phase. To re-extract the lipids from the water phase, 1 ml chloroform was added. The combined organic phase was evaporated under a nitrogen stream and the extracted lipids were dissolved in methanol.