Summary of Study ST001740

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 PR001114. The data can be accessed directly via it's Project DOI: 10.21228/M8Q39V 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 IDST001740
Study TitleTimecourse of NIH-3T3 cells treated with apoptotic inducers
Study TypeTargeted lipidomics
Study SummaryTime-dependent changes of phosphatidylinositol profiles in mouse NIH-3T3 fibroblasts treated with mechanistically diverse apoptotic inducers.
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 Date2021-04-01
Raw Data AvailableYes
Raw Data File Type(s)wiff
Analysis Type DetailLC-MS
Release Date2021-04-20
Release Version1
Andreas Koeberle Andreas Koeberle
https://dx.doi.org/10.21228/M8Q39V
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001114
Project DOI:doi: 10.21228/M8Q39V
Project Title:Regulation of stress signalling by SCD1-derived phosphatidylinositols
Project Type:Targeted lipidomics
Project Summary:Cytotoxic stress activates stress-activated kinases, initiates adaptive mechanisms, including the unfolded protein response (UPR) and autophagy, and induces programmed cell death. Fatty acid unsaturation, controlled by stearoyl-CoA desaturase (SCD)1, prevents cytotoxic stress but the mechanisms are diffuse. We found that 1,2-dioleoyl-sn-glycero-3-phospho-(1’-myo-inositol) [PI(18:1/18:1)] is a SCD1-derived signaling lipid, which inhibits p38 mitogen-activated protein kinase (MAPK) activation, counteracts UPR, autophagy and apoptosis induction, and maintains cell morphology and proliferation. SCD1 expression and the cellular PI(18:1/18:1) proportion decrease during the onset of cell death, thereby activating stress signaling. This counter-regulation applies to mechanistically diverse death-inducing conditions and occurs in tissues of Scd1-defective mice.
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:German Research Council (GRK 1715 and KO 4589/4-1), Phospholipid Research Center Heidelberg (AKO-2019-070/2-1 and AKO-2015-037/1-1), University of Jena (DRM/2013-05 and 2.7-05), Free State of Thuringia (41-5507-2016) and Leibniz ScienceCampus InfectoOptics (SAS-2015-HKI-LWC).
Publications:PI(18:1/18:1) is a SCD1-derived lipokine that limits stress signaling. Thürmer M, Gollowitzer A, Pein H, Neukirch K, Gelmez E, Waltl L, Wielsch N, Winkler R, Löser K, Grander J, Hotze M, Harder S, Döding A, Meßner M, Troisi F, Ardelt M, Schlüter H, Pachmayr J, Gutiérrez-Gutiérrez Ó, Rudolph KL, Thedieck K, Schulze-Späte U, González-Estévez C, Kosan C, Svatoš A, Kwiatkowski M, Koeberle A. Nat Commun. 2022 May 27;13(1):2982. doi: 10.1038/s41467-022-30374-9.

Subject:

Subject ID:SU001817
Subject Type:Cultured cells
Subject Species:Mus musculus
Taxonomy ID:10090

Factors:

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

mb_sample_id local_sample_id hours treatment concentration
SA162974HP_140311_AP6_10min_#45 - 50.17 CHX 20 µg/ml
SA162975HP_140211_AP4_10m_1h_#45 - 50.17 CHX 20 µg/ml
SA162976HP_140214_AP4und5_48h_10min_#10 - 50.17 CHX 20 µg/ml
SA162977HP_140214_AP4und5_48h_10min_#11 - 60.17 ETO 10 µM
SA162978HP_140311_AP6_10min_#46 - 60.17 ETO 10 µM
SA162979HP_140211_AP4_10m_1h_#46 - 60.17 ETO 10 µM
SA162980HP_140311_AP6_10min_#50 - 100.17 MC 10 µM
SA162981HP_140214_AP4und5_48h_10min_#15 - 100.17 MC 10 µM
SA162982HP_140211_AP4_10m_1h_#50 - 100.17 MC 10 µM
SA162986HP_140214_AP4und5_48h_10min_#14 - 90.17 Serum -
SA162987HP_140211_AP4_10m_1h_#49 - 90.17 Serum -
SA162988HP_140311_AP6_10min_#49 - 90.17 Serum -
SA162983HP_140311_AP6_10min_#44 - 40.17 STS 0.3 µM
SA162984HP_140211_AP4_10m_1h_#44 - 40.17 STS 0.3 µM
SA162985HP_140214_AP4und5_48h_10min_#9 - 40.17 STS 0.3 µM
SA162989HP_140311_AP6_10min_#43 - 30.17 TNFα 10 ng/ml
SA162990HP_140214_AP4und5_48h_10min_#8 - 30.17 TNFα 10 ng/ml
SA162991HP_140211_AP4_10m_1h_#43 - 30.17 TNFα 10 ng/ml
SA162992HP_140311_AP6_10min_#47 - 70.17 TPG 2 µM
SA162993HP_140214_AP4und5_48h_10min_#12 - 70.17 TPG 2 µM
SA162994HP_140211_AP4_10m_1h_#47 - 70.17 TPG 2 µM
SA162995HP_140211_AP4_10m_1h_#48 - 80.17 VAL 10 µM
SA162996HP_140214_AP4und5_48h_10min_#13 - 80.17 VAL 10 µM
SA162997HP_140311_AP6_10min_#48 - 80.17 VAL 10 µM
SA162998HP_140211_AP4_10m_1h_#42 - 20.17 vehicle (DMSO) -
SA162999HP_140311_AP6_10min_#52 - 120.17 vehicle (DMSO) -
SA163000HP_140311_AP6_10min_#42 - 20.17 vehicle (DMSO) -
SA163001HP_140214_AP4und5_48h_10min_#7 - 20.17 vehicle (DMSO) -
SA163002HP_140211_AP4_10m_1h_#52 - 120.17 vehicle (DMSO) -
SA163003HP_140214_AP4und5_48h_10min_#17 - 120.17 vehicle (DMSO) -
SA163004HP_140211_AP4_10min_1h_#10 - 51 CHX 20 µg/ml
SA163005HP_140217_AP5_1h_6h_#45 - 51 CHX 20 µg/ml
SA163006HP_140312_AP6_1h_#45 - 51 CHX 20 µg/ml
SA163007HP_140217_AP5_1h_6h_#46 - 61 ETO 10 µM
SA163008HP_140211_AP4_10min_1h_#11 - 61 ETO 10 µM
SA163009HP_140312_AP6_1h_#46 - 61 ETO 10 µM
SA163010HP_140312_AP6_1h_#50 - 101 MC 10 µM
SA163011HP_140211_AP4_10min_1h_#15 - 101 MC 10 µM
SA163012HP_140217_AP5_1h_6h_#50 - 101 MC 10 µM
SA163016HP_140211_AP4_10min_1h_#14 - 91 Serum -
SA163017HP_140217_AP5_1h_6h_#49 - 91 Serum -
SA163018HP_140312_AP6_1h_#49 - 91 Serum -
SA163013HP_140217_AP5_1h_6h_#44 - 41 STS 0.3 µM
SA163014HP_140312_AP6_1h_#44 - 41 STS 0.3 µM
SA163015HP_140211_AP4_10min_1h_#9 - 41 STS 0.3 µM
SA163019HP_140211_AP4_10min_1h_#8 - 31 TNFα 10 ng/ml
SA163020HP_140312_AP6_1h_#43 - 31 TNFα 10 ng/ml
SA163021HP_140217_AP5_1h_6h_#43 - 31 TNFα 10 ng/ml
SA163022HP_140211_AP4_10min_1h_#12 - 71 TPG 2 µM
SA163023HP_140312_AP6_1h_#47 - 71 TPG 2 µM
SA163024HP_140217_AP5_1h_6h_#47 - 71 TPG 2 µM
SA163025HP_140312_AP6_1h_#48 - 81 VAL 10 µM
SA163026HP_140211_AP4_10min_1h_#13 - 81 VAL 10 µM
SA163027HP_140217_AP5_1h_6h_#48 - 81 VAL 10 µM
SA163028HP_140217_AP5_1h_6h_#42 - 21 vehicle (DMSO) -
SA163029HP_140211_AP4_10min_1h_#7 - 21 vehicle (DMSO) -
SA163030HP_140312_AP6_1h_#42 - 21 vehicle (DMSO) -
SA163031HP_140312_AP6_1h_#52 - 121 vehicle (DMSO) -
SA163032HP_140211_AP4_10min_1h_#17 - 121 vehicle (DMSO) -
SA163033HP_140217_AP5_1h_6h_#52 - 121 vehicle (DMSO) -
SA163034HP_140213_AP4_6h_24_restart_#30 - 524 CHX 20 µg/ml
SA163035HP_140227_AP5_24h_48h_#45 - 524 CHX 20 µg/ml
SA163036HP_140314_AP6_24h_#19 - 524 CHX 20 µg/ml
SA163037HP_140314_AP6_24h_#20 - 624 ETO 10 µM
SA163038HP_140227_AP5_24h_48h_#46 - 624 ETO 10 µM
SA163039HP_140213_AP4_6h_24_restart_#31 - 624 ETO 10 µM
SA163040HP_140213_AP4_6h_24_restart_#35 - 1024 MC 10 µM
SA163041HP_140227_AP5_24h_48h_#50 - 1024 MC 10 µM
SA163042HP_140314_AP6_24h_#24 - 1024 MC 10 µM
SA163046HP_140227_AP5_24h_48h_#49 - 924 Serum -
SA163047HP_140213_AP4_6h_24_restart_#34 - 924 Serum -
SA163048HP_140314_AP6_24h_#23 - 924 Serum -
SA163043HP_140314_AP6_24h_#18 - 424 STS 0.3 µM
SA163044HP_140213_AP4_6h_24_restart_#29 - 424 STS 0.3 µM
SA163045HP_140227_AP5_24h_48h_#44 - 424 STS 0.3 µM
SA163049HP_140227_AP5_24h_48h_#43 - 324 TNFα 10 ng/ml
SA163050HP_140314_AP6_24h_#17 - 324 TNFα 10 ng/ml
SA163051HP_140213_AP4_6h_24_restart_#28 - 324 TNFα 10 ng/ml
SA163052HP_140227_AP5_24h_48h_#47 - 724 TPG 2 µM
SA163053HP_140314_AP6_24h_#21 - 724 TPG 2 µM
SA163054HP_140213_AP4_6h_24_restart_#32 - 724 TPG 2 µM
SA163055HP_140227_AP5_24h_48h_#48 - 824 VAL 10 µM
SA163056HP_140213_AP4_6h_24_restart_#33 - 824 VAL 10 µM
SA163057HP_140314_AP6_24h_#22 - 824 VAL 10 µM
SA163058HP_140213_AP4_6h_24_restart_#37 - 1224 vehicle (DMSO) -
SA163059HP_140213_AP4_6h_24_restart_#27 - 224 vehicle (DMSO) -
SA163060HP_140314_AP6_24h_#16 - 224 vehicle (DMSO) -
SA163061HP_140314_AP6_24h_#26 - 1224 vehicle (DMSO) -
SA163062HP_140227_AP5_24h_48h_#42 - 224 vehicle (DMSO) -
SA163063HP_140227_AP5_24h_48h_#52 - 1224 vehicle (DMSO) -
SA163064HP_140214_AP4and5_48h_10min_#45 - 548 CHX 20 µg/ml
SA163065HP_140228_AP5_24h_48h_#19 - 548 CHX 20 µg/ml
SA163066HP_140321_Betti_AP6_48h_#58 - 548 CHX 20 µg/ml
SA163067HP_140214_AP4and5_48h_10min_#46 - 648 ETO 10 µM
SA163068HP_140321_Betti_AP6_48h_#59 - 648 ETO 10 µM
SA163069HP_140228_AP5_24h_48h_#20 - 648 ETO 10 µM
SA163070HP_140321_Betti_AP6_48h_#63 - 1048 MC 10 µM
SA163071HP_140214_AP4and5_48h_10min_#50 - 1048 MC 10 µM
SA163072HP_140228_AP5_24h_48h_#24 - 1048 MC 10 µM
SA163076HP_140228_AP5_24h_48h_#23 - 948 Serum -
Showing page 1 of 2     Results:    1  2  Next     Showing results 1 to 100 of 150

Collection:

Collection ID:CO001810
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:TR001830
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, TNFα (10 ng/ml), 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:SP001823
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 and subjected to UPLC-MS/MS.
Extract Storage:-20℃

Combined analysis:

Analysis ID AN002833
Analysis type MS
Chromatography type Reversed phase
Chromatography system Waters Acquity H-Class
Column Waters Acquity 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 intensities

Chromatography:

Chromatography ID:CH002096
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 UHPLC.
Instrument Name:Waters Acquity H-Class
Column Name:Waters Acquity BEH C8 (100 x 2.1mm,1.7um)
Chromatography Type:Reversed phase

MS:

MS ID:MS002626
Analysis ID:AN002833
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