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.

Perform statistical analysis  |  Show all samples  |  Show named metabolites  |  Download named metabolite data  
Download mwTab file (text)   |  Download mwTab file(JSON)   |  Download data files (Contains raw data)
Study IDST002346
Study TitleLipidomics study of the cells defective in peroxisome division
Study SummaryProliferation 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 NameAbe
First NameYuichi
Address3-1-1 Maidashi, Fukuoka 812-8582, Japan.
Emaily-abe@bio.sojo-u.ac.jp
Phone+81926426341
Submit Date2022-10-26
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2022-11-28
Release Version1
Yuichi Abe Yuichi Abe
https://dx.doi.org/10.21228/M81D8C
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001506
Project DOI:doi: 10.21228/M81D8C
Project Title:Lipidomics study of peroxisomal dysmorphogenesis
Project Summary:Lipidomic study of the cells defective in peroxisomal dysmorphogenesis.
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:+81-92-642-6341

Subject:

Subject ID:SU002435
Subject Type:Cultured cells
Subject Species:Homo sapiens
Taxonomy ID:9606/10090
Species Group:Mammals

Factors:

Subject type: Cultured cells; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Genotype
SA235396FContA-3-PCControl1
SA235397FContA-2-PCControl1
SA235398FContA-4-PCControl1
SA235399FContA-5-PCControl1
SA235400FContA-6-PCControl1
SA235401FContA-1-PEControl1
SA235402FContA-1-PCControl1
SA235403FContA-5-PEControl1
SA235404FContA-3-PEControl1
SA235405FContA-2-PEControl1
SA235406FContA-6-PEControl1
SA235407FContA-4-PEControl1
SA235408FContB-5-PEControl2
SA235409FContB-3-PEControl2
SA235410FContB-6-PEControl2
SA235411FContB-1-PEControl2
SA235412FContB-2-PCControl2
SA235413FContB-3-PCControl2
SA235414FContB-4-PEControl2
SA235415FContB-6-PCControl2
SA235416FContB-5-PCControl2
SA235417FContB-4-PCControl2
SA235418FContB-2-PEControl2
SA235419FContB-1-PCControl2
SA235420FContC-4-PEControl3
SA235421FContC-5-PEControl3
SA235422FContC-6-PEControl3
SA235423FContC-2-PEControl3
SA235424FContC-2-PCControl3
SA235425FContC-3-PCControl3
SA235426FContC-3-PEControl3
SA235427FContC-6-PCControl3
SA235428FContC-5-PCControl3
SA235429FContC-4-PCControl3
SA235430FContC-1-PEControl3
SA235431FContC-1-PCControl3
SA235432FContD-2-PEControl4
SA235433FContD-3-PEControl4
SA235434FContD-4-PEControl4
SA235435FContD-5-PEControl4
SA235436FContD-1-PEControl4
SA235437FContD-2-PCControl4
SA235438FContD-6-PCControl4
SA235439FContD-5-PCControl4
SA235440FContD-4-PCControl4
SA235441FContD-3-PCControl4
SA235442FContD-6-PEControl4
SA235443FContD-1-PCControl4
SA235444FDLP1-1-PEDLP1mut
SA235445FDLP1-3-PEDLP1mut
SA235446FDLP1-4-PEDLP1mut
SA235447FDLP1-5-PEDLP1mut
SA235448FDLP1-1-PCDLP1mut
SA235449FDLP1-2-PCDLP1mut
SA235450FDLP1-6-PCDLP1mut
SA235451FDLP1-5-PCDLP1mut
SA235452FDLP1-4-PCDLP1mut
SA235453FDLP1-3-PCDLP1mut
SA235454FDLP1-6-PEDLP1mut
SA235455FDLP1-2-PEDLP1mut
SA235488FNME3-3-PEdNME3
SA235489FNME3-1-PCdNME3
SA235490FNME3-4-PEdNME3
SA235491FNME3-3-PCdNME3
SA235492FNME3-5-PEdNME3
SA235493FNME3-6-PEdNME3
SA235494FNME3-1-PEdNME3
SA235495FNME3-2-PEdNME3
SA235496FNME3-4-PCdNME3
SA235497FNME3-2-PCdNME3
SA235498FNME3-5-PCdNME3
SA235499FNME3-6-PCdNME3
SA235500FP11b-5-PCdPEX11b
SA235501FP11b-6-PCdPEX11b
SA235502FP11b-1-PEdPEX11b
SA235503FP11b-3-PCdPEX11b
SA235504FP11b-1-PCdPEX11b
SA235505FP11b-4-PCdPEX11b
SA235506FP11b-6-PEdPEX11b
SA235507FP11b-2-PCdPEX11b
SA235508FP11b-3-PEdPEX11b
SA235509FP11b-4-PEdPEX11b
SA235510FP11b-5-PEdPEX11b
SA235511FP11b-2-PEdPEX11b
SA235456MDRP1-3-PCDrp1-KO
SA235457MDRP1-4-PCDrp1-KO
SA235458MDRP1-5-PCDrp1-KO
SA235459MDRP1-1-PEDrp1-KO
SA235460MDRP1-2-PCDrp1-KO
SA235461MDRP1-2-PEDrp1-KO
SA235462MDRP1-4-PEDrp1-KO
SA235463MDRP1-1-PCDrp1-KO
SA235464MDRP1-5-PEDrp1-KO
SA235465MDRP1-3-PEDrp1-KO
SA235466MP11b-2-PCPex11b-KO
SA235467MP11b-1-PCPex11b-KO
SA235468MP11b-3-PCPex11b-KO
SA235469MP11b-5-PEPex11b-KO
SA235470MP11b-2-PEPex11b-KO
SA235471MP11b-1-PEPex11b-KO
Showing page 1 of 2     Results:    1  2  Next     Showing results 1 to 100 of 116

Collection:

Collection ID:CO002428
Collection Summary:Fibroblasts and MEFs were cultured under 5% CO2 at 37°C in Dulbecco's modified medium (DMEM; Invitrogen, Carlsbad, CA) supplemented with 10% fetal bovine serum. For the extraction of phospholipids, fibroblasts were seeded in 6-well plate and cultured overnight, followed by replacement of fresh culture medium. Cells were harvested at 48 hours after the medium change as described below.
Sample Type:Cultured fibroblasts

Treatment:

Treatment ID:TR002447
Treatment Summary:No treatment

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.

Combined analysis:

Analysis ID AN003830 AN003831
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Waters Acquity Waters Acquity
Column Waters Aquity BEH C18 (150 x 1.0mm,1.7um) Waters Aquity BEH C18 (150 x 1.0mm,1.7um)
MS Type ESI ESI
MS instrument type Triple quadrupole Triple quadrupole
MS instrument name ABI Sciex 4000 QTrap ABI Sciex 4000 QTrap
Ion Mode POSITIVE POSITIVE
Units The ratio to total amount of each phospholipid species The ratio to total amount of each phospholipid species

Chromatography:

Chromatography ID:CH002835
Chromatography Summary:PE and pPE detection method
Instrument Name:Waters Acquity
Column Name:Waters Aquity BEH C18 (150 x 1.0mm,1.7um)
Chromatography Type:Reversed phase
  
Chromatography ID:CH002836
Chromatography Summary:PC and aPC detection method
Instrument Name:Waters Acquity
Column Name:Waters Aquity BEH C18 (150 x 1.0mm,1.7um)
Chromatography Type:Reversed phase

MS:

MS ID:MS003572
Analysis ID:AN003830
Instrument Name:ABI Sciex 4000 QTrap
Instrument Type:Triple quadrupole
MS Type:ESI
MS Comments:MS were detected by neutral loss, precoursour ion scan, and MRM. Peaks were detected by quantification wizard on Ananlyst software (version 1.42).
Ion Mode:POSITIVE
  
MS ID:MS003573
Analysis ID:AN003831
Instrument Name:ABI Sciex 4000 QTrap
Instrument Type:Triple quadrupole
MS Type:ESI
MS Comments:MS were detected by neutral loss, precoursour ion scan, and MRM. Peaks were detected by quantification wizard on Ananlyst software (version 1.42).
Ion Mode:POSITIVE
  logo