Summary of Study ST003318

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 PR002065. The data can be accessed directly via it's Project DOI: 10.21228/M8PR7B 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 IDST003318
Study TitleKinetic changes in the phospholipid composition of fibroblasts induced by cytotoxic stress
Study SummaryTime-dependent analysis (0, 0.17, 1, 6, 24, 48 h) of thephosphatidylcholine, phosphatidylethanolamine, phosphatidylinositol, phosphatidylserine and phosphatidylglycerol fatty acid composition of NIH-3T3 mouse fibroblasts treated with cytotoxic stressors (staurosporine, cycloheximide, etoposide, thapsigargin, valinomycin, myrtucommulone) or depleted from serum. Please note that parts of the data were previously uploaded to project PR001114 [doi: 10.21228/M8Q39V] and reanalyzed for the current project (PI).
Institute
University of Innsbruck
DepartmentMichael Popp Institute
Last NameKoeberle
First NameAndreas
AddressMitterweg 24, Innsbruck, Tyrol, 6020, Austria
Emailandreas.koeberle@uibk.ac.at
Phone+43 512 507 57903
Submit Date2024-07-05
Raw Data AvailableYes
Raw Data File Type(s)wiff
Analysis Type DetailLC-MS
Release Date2025-01-06
Release Version1
Andreas Koeberle Andreas Koeberle
https://dx.doi.org/10.21228/M8PR7B
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR002065
Project DOI:doi: 10.21228/M8PR7B
Project Title:Changes in phospholipid fatty acid composition under cytotoxic stress facilitate peroxidation
Project Summary:Programs leading to cell death, such as apoptosis, necroptosis, and ferroptosis, involve an oxidative component linked to lipid metabolism that influences membrane homeostasis. Emerging evidence suggests inter-program cross-talk, emphasizing the need for overarching regulatory mechanisms. We show that under specific cytotoxic stress conditions, exogenous or released polyunsaturated fatty acids (PUFAs) are channeled into overall depleting phospholipids that become vulnerable to peroxidation in the presence of associated redox stress. In fibroblasts, this reprogramming results from reduced growth factor receptor tyrosine kinase (RTK) and phosphatidylinositol-3-kinase (PI3K)/Akt signaling, which reduces de novo fatty acid biosynthesis by mechanisms that differ depending on the specific cytotoxic stressors. We conclude that alterations in PUFA metabolism during cytotoxic stress render cells prone to oxidative modifications in phospholipids.
Institute:University of Innsbruck
Department:Michael Popp Institute
Last Name:Koeberle
First Name:Andreas
Address:Mitterweg 24, Innsbruck, Tyrol, 6020, Austria
Email:andreas.koeberle@uibk.ac.at
Phone:+43 512 507 57903
Funding Source:Austrian Science Fund (FWF) (P 36299). German Research Council (GRK 1715 and KO 4589/4-1), the Phospholipid Research Center Heidelberg (AKO-2015-037/1-1, AKO-2019-070/2-1, AKO-2O22-100/2-2), the University of Jena (DRM/2013-05 and 2.7-05).
Contributors:André Gollowitzer, Helmut Pein, Konstantin Loeser, Maria Thuermer, and Andreas Koeberle

Subject:

Subject ID:SU003439
Subject Type:Cultured cells
Subject Species:Mus musculus
Taxonomy ID:10090
Species Group:Mammals

Factors:

Subject type: Cultured cells; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id local_sample_id Sample source time treatment
SA359550HP_140214_AP4und5_48h_10min_#10 - 5cultured cells 0.17h CHX
SA359551HP_140211_AP4_10m_1h_#45 - 5cultured cells 0.17h CHX
SA359552HP_140211_AP4_10m_1h_#32 - 5cultured cells 0.17h CHX
SA359553HP_140214_AP4und5_48h_10min_#23 - 5cultured cells 0.17h CHX
SA359554HP_140214_AP4and5_48h_10min_#97 - 5cultured cells 0.17h CHX
SA359555HP_140311_AP6_10min_#58 - 5cultured cells 0.17h CHX
SA359556HP_140211_AP4_10m_1h_#58 - 5cultured cells 0.17h CHX
SA359557HP_140311_AP6_10min_#6 - 5cultured cells 0.17h CHX
SA359558HP_140211_AP4_10m_1h_#19 - 5cultured cells 0.17h CHX
SA359559HP_140214_AP4and5_48h_10min_#84 - 5cultured cells 0.17h CHX
SA359560HP_140311_AP6_10min_#19 - 5cultured cells 0.17h CHX
SA359561HP_140311_AP6_10min_#45 - 5cultured cells 0.17h CHX
SA359562HP_140214_AP4and5_48h_10min_#71 - 5cultured cells 0.17h CHX
SA359563HP_140311_AP6_10min_#32 - 5cultured cells 0.17h CHX
SA359564HP_140211_AP4_10m_1h_#6 - 5cultured cells 0.17h CHX
SA359565HP_140311_AP6_10min_#7 - 6cultured cells 0.17h ETO
SA359566HP_140211_AP4_10m_1h_#59 - 6cultured cells 0.17h ETO
SA359567HP_140311_AP6_10min_#20 - 6cultured cells 0.17h ETO
SA359568HP_140311_AP6_10min_#46 - 6cultured cells 0.17h ETO
SA359569HP_140214_AP4und5_48h_10min_#24 - 6cultured cells 0.17h ETO
SA359570HP_140211_AP4_10m_1h_#46 - 6cultured cells 0.17h ETO
SA359571HP_140214_AP4und5_48h_10min_#11 - 6cultured cells 0.17h ETO
SA359572HP_140311_AP6_10min_#59 - 6cultured cells 0.17h ETO
SA359573HP_140311_AP6_10min_#33 - 6cultured cells 0.17h ETO
SA359574HP_140214_AP4and5_48h_10min_#98 - 6cultured cells 0.17h ETO
SA359575HP_140211_AP4_10m_1h_#7 - 6cultured cells 0.17h ETO
SA359576HP_140214_AP4and5_48h_10min_#72 - 6cultured cells 0.17h ETO
SA359577HP_140211_AP4_10m_1h_#20 - 6cultured cells 0.17h ETO
SA359578HP_140214_AP4and5_48h_10min_#85 - 6cultured cells 0.17h ETO
SA359579HP_140211_AP4_10m_1h_#33 - 6cultured cells 0.17h ETO
SA359580HP_140214_AP4und5_48h_10min_#2 - 10cultured cells 0.17h MC
SA359581HP_140311_AP6_10min_#63 - 10cultured cells 0.17h MC
SA359582HP_140214_AP4und5_48h_10min_#15 - 10cultured cells 0.17h MC
SA359583HP_140311_AP6_10min_#37 - 10cultured cells 0.17h MC
SA359584HP_140214_AP4and5_48h_10min_#76 - 10cultured cells 0.17h MC
SA359585HP_140311_AP6_10min_#24 - 10cultured cells 0.17h MC
SA359586HP_140211_AP4_10m_1h_#11 - 10cultured cells 0.17h MC
SA359587HP_140311_AP6_10min_#50 - 10cultured cells 0.17h MC
SA359588HP_140211_AP4_10m_1h_#63 - 10cultured cells 0.17h MC
SA359589HP_140311_AP6_10min_#11 - 10cultured cells 0.17h MC
SA359590HP_140211_AP4_10m_1h_#37 - 10cultured cells 0.17h MC
SA359591HP_140214_AP4and5_48h_10min_#89 - 10cultured cells 0.17h MC
SA359592HP_140211_AP4_10m_1h_#50 - 10cultured cells 0.17h MC
SA359593HP_140214_AP4und5_48h_10min_#28 - 10cultured cells 0.17h MC
SA359594HP_140211_AP4_10m_1h_#24 - 10cultured cells 0.17h MC
SA359610HP_140214_AP4and5_48h_10min_#88 - 9cultured cells 0.17h Serum
SA359611HP_140211_AP4_10m_1h_#62 - 9cultured cells 0.17h Serum
SA359612HP_140214_AP4und5_48h_10min_#1 - 9cultured cells 0.17h Serum
SA359613HP_140211_AP4_10m_1h_#36 - 9cultured cells 0.17h Serum
SA359614HP_140214_AP4und5_48h_10min_#14 - 9cultured cells 0.17h Serum
SA359615HP_140311_AP6_10min_#36 - 9cultured cells 0.17h Serum
SA359616HP_140214_AP4und5_48h_10min_#27 - 9cultured cells 0.17h Serum
SA359617HP_140211_AP4_10m_1h_#49 - 9cultured cells 0.17h Serum
SA359618HP_140311_AP6_10min_#62 - 9cultured cells 0.17h Serum
SA359619HP_140311_AP6_10min_#10 - 9cultured cells 0.17h Serum
SA359620HP_140211_AP4_10m_1h_#23 - 9cultured cells 0.17h Serum
SA359621HP_140311_AP6_10min_#23 - 9cultured cells 0.17h Serum
SA359622HP_140214_AP4and5_48h_10min_#75 - 9cultured cells 0.17h Serum
SA359623HP_140211_AP4_10m_1h_#10 - 9cultured cells 0.17h Serum
SA359624HP_140311_AP6_10min_#49 - 9cultured cells 0.17h Serum
SA359595HP_140214_AP4und5_48h_10min_#22 - 4cultured cells 0.17h STS
SA359596HP_140311_AP6_10min_#18 - 4cultured cells 0.17h STS
SA359597HP_140214_AP4and5_48h_10min_#83 - 4cultured cells 0.17h STS
SA359598HP_140311_AP6_10min_#5 - 4cultured cells 0.17h STS
SA359599HP_140211_AP4_10m_1h_#5 - 4cultured cells 0.17h STS
SA359600HP_140214_AP4and5_48h_10min_#96 - 4cultured cells 0.17h STS
SA359601HP_140311_AP6_10min_#31 - 4cultured cells 0.17h STS
SA359602HP_140214_AP4und5_48h_10min_#9 - 4cultured cells 0.17h STS
SA359603HP_140214_AP4and5_48h_10min_#70 - 4cultured cells 0.17h STS
SA359604HP_140211_AP4_10m_1h_#31 - 4cultured cells 0.17h STS
SA359605HP_140311_AP6_10min_#44 - 4cultured cells 0.17h STS
SA359606HP_140211_AP4_10m_1h_#18 - 4cultured cells 0.17h STS
SA359607HP_140211_AP4_10m_1h_#44 - 4cultured cells 0.17h STS
SA359608HP_140311_AP6_10min_#57 - 4cultured cells 0.17h STS
SA359609HP_140211_AP4_10m_1h_#57 - 4cultured cells 0.17h STS
SA359625HP_140211_AP4_10m_1h_#8 - 7cultured cells 0.17h TPG
SA359626HP_140311_AP6_10min_#47 - 7cultured cells 0.17h TPG
SA359627HP_140311_AP6_10min_#60 - 7cultured cells 0.17h TPG
SA359628HP_140214_AP4and5_48h_10min_#73 - 7cultured cells 0.17h TPG
SA359629HP_140211_AP4_10m_1h_#47 - 7cultured cells 0.17h TPG
SA359630HP_140211_AP4_10m_1h_#34 - 7cultured cells 0.17h TPG
SA359631HP_140214_AP4und5_48h_10min_#25 - 7cultured cells 0.17h TPG
SA359632HP_140211_AP4_10m_1h_#21 - 7cultured cells 0.17h TPG
SA359633HP_140214_AP4and5_48h_10min_#86 - 7cultured cells 0.17h TPG
SA359634HP_140214_AP4und5_48h_10min_#12 - 7cultured cells 0.17h TPG
SA359635HP_140311_AP6_10min_#34 - 7cultured cells 0.17h TPG
SA359636HP_140311_AP6_10min_#21 - 7cultured cells 0.17h TPG
SA359637HP_140211_AP4_10m_1h_#60 - 7cultured cells 0.17h TPG
SA359638HP_140311_AP6_10min_#8 - 7cultured cells 0.17h TPG
SA359639HP_140214_AP4and5_48h_10min_#99 - 7cultured cells 0.17h TPG
SA359640HP_140311_AP6_10min_#35 - 8cultured cells 0.17h VAL
SA359641HP_140214_AP4and5_48h_10min_#100 - 8cultured cells 0.17h VAL
SA359642HP_140211_AP4_10m_1h_#35 - 8cultured cells 0.17h VAL
SA359643HP_140214_AP4and5_48h_10min_#87 - 8cultured cells 0.17h VAL
SA359644HP_140311_AP6_10min_#48 - 8cultured cells 0.17h VAL
SA359645HP_140214_AP4und5_48h_10min_#13 - 8cultured cells 0.17h VAL
SA359646HP_140211_AP4_10m_1h_#9 - 8cultured cells 0.17h VAL
SA359647HP_140211_AP4_10m_1h_#48 - 8cultured cells 0.17h VAL
SA359648HP_140214_AP4und5_48h_10min_#26 - 8cultured cells 0.17h VAL
SA359649HP_140311_AP6_10min_#22 - 8cultured cells 0.17h VAL
Showing page 1 of 7     Results:    1  2  3  4  5  Next  Last     Showing results 1 to 100 of 684

Collection:

Collection ID:CO003432
Collection Summary:Cultured cells were washed, trypsinized, counted and flash-frozen in liquid N2 and stored at -80°C.
Sample Type:Fibroblasts
Collection Method:Trypsinization of cultured cells
Storage Conditions:-80℃

Treatment:

Treatment ID:TR003448
Treatment Summary:Mouse NIH-3T3 fibroblasts were cultivated in DMEM high glucose medium containing heat-inactivated fetal calf serum (FCS, 10%). After cultivation for 24 h, cells were treated with vehicle, STS (0.3 µM), CHX (20 µg/ml), ETO (10 µM), TPG (2 µM), VAL (10 µM), MC (10 µM) at 37°C and 5% CO2. Serum depletion of NIH-3T3 fibroblasts was achieved by cultivation of cells in serum-free DMEM.
Treatment Vehicle:DMSO
Cell Media:DMEM + 10% FCS
Cell Envir Cond:37°C, 5% CO2

Sample Preparation:

Sampleprep ID:SP003446
Sampleprep Summary:Phospholipids were extracted from cell pellets by successive addition of PBS pH 7.4, methanol, chloroform, and saline to a final ratio of 14:34:35:17. Evaporation of the organic layer yielded a lipid film that was dissolved in methanol, diluted, and subjected to UPLC-MS/MS.
Extract Storage:-20℃

Combined analysis:

Analysis ID AN005432
Analysis type MS
Chromatography type Reversed phase
Chromatography system Waters Acquity H-Class
Column Waters ACQUITY UPLC BEH C8 (100 x 2.1mm,1.7um)
MS Type ESI
MS instrument type Triple quadrupole
MS instrument name ABI Sciex 5500 QTrap
Ion Mode NEGATIVE
Units relative units

Chromatography:

Chromatography ID:CH004121
Chromatography Summary:Chromatographic separation of phospholipids was carried out on an Acquity BEH C8 column (1.7 μm, 2.1×100 mm, Waters, Milford, MA) using an Acquity Ultraperformance LC system (Waters).
Instrument Name:Waters Acquity H-Class
Column Name:Waters ACQUITY UPLC BEH C8 (100 x 2.1mm,1.7um)
Column Temperature:45
Flow Gradient:The gradient was ramped from 70 to 80% B over 5 min and further increased to 100% B within 2 min, followed by isocratic elution for another 2 min.
Flow Rate:0.75 ml/min
Solvent A:90% Water/10% Acetonitrile; 10 mM ammonium acetate
Solvent B:5% Water/95% Acetonitrile; 10 mM ammonium acetate
Chromatography Type:Reversed phase

MS:

MS ID:MS005158
Analysis ID:AN005432
Instrument Name:ABI Sciex 5500 QTrap
Instrument Type:Triple quadrupole
MS Type:ESI
MS Comments:Targeted MRM with pre-optimized settings and subsequent automated integration of selected signals using Analyst 1.6 (Sciex).
Ion Mode:NEGATIVE
  logo