Summary of Study ST003757

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 PR002341. The data can be accessed directly via it's Project DOI: 10.21228/M81N8S This work is supported by NIH grant, U2C- DK119886. See: https://www.metabolomicsworkbench.org/about/howtocite.php

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Study IDST003757
Study TitleUntargeted lipidomics of gemcitabine-resistant PDAC cells
Study SummaryIn this work we developed gemcitabine (GEMC) resistant (GEMR) PDAC cell lines from Panc1 and MiaPaCa2 cells. This dataset contains results and raw data for untargeted lipidomics of Panc1 cells, including control (CON), and GEMR cells alongside internal quality controls (iQC) and blank samples for background subtraction (as described under sample prep). Untargeted lipidomics enabled the quantification of more than 400 distinct molecular lipid species within Panc1 & MiaPaCa2 control (CON) & GEMR cells from 12 different classes of lipid, with 77 molecular species being differentially abundant between Panc1 control and GEMR cells following unpaired t test. Data were analysed using MS-DIAL 4.9.
Institute
Victor Chang Cardiac Research Institute
Last NameHancock
First NameSarah
AddressLevel 7 Lowy Packer Building, 405 Liverpool Street, Darlinghurst, NSW 2010 Australia
Emails.hancock@victorchang.edu.au
Phone+61414537526
Submit Date2025-02-18
Raw Data AvailableYes
Raw Data File Type(s)mzML
Analysis Type DetailLC-MS
Release Date2025-03-21
Release Version1
Sarah Hancock Sarah Hancock
https://dx.doi.org/10.21228/M81N8S
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

Project ID:PR002341
Project DOI:doi: 10.21228/M81N8S
Project Title:Untargeted lipidomics of gemcitabine-resistant PDAC cells
Project Summary:Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive disease with few treatment options and poor survivability. In this work we sought to characterise metabolic adaptations to gemcitabine (GEMC)-based chemotherapy exposure to discover new therapeutic targets for improving treatment efficacy. We show that GEMC resistance (GEMR) upregulates de novo lipogenesis in Panc1 and MiaPaCa2 cells.
Institute:Victor Chang Cardiac Research Institute
Last Name:Hancock
First Name:Sarah
Address:Lowy Packer Building, 405 Liverpool Street, Darlinghurst, NSW, 2010, Australia
Email:s.hancock@victorchang.edu.au
Phone:+61414537526

Subject:

Subject ID:SU003890
Subject Type:Cultured cells
Subject Species:Homo sapiens
Taxonomy ID:9606
Cell Strain Details:Panc1

Factors:

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

mb_sample_id local_sample_id Sample source group group
SA409045Blank_cells_neg_20210814030609- Blank Blank
SA409046Blank_cells_neg- Blank Blank
SA409047Blank_cells_pos_20210813215440- Blank Blank
SA409048Blank_cells_pos- Blank Blank
SA409049iQC_cells_neg_20210814033722- pool iQC
SA409050iQC_cells_pos- pool iQC
SA409051iQC_cells_pos_20210813222552- pool iQC
SA409052iQC_cells_neg- pool iQC
SA409053Panc1_CON_p3_posPancreas Panc1 cells CON
SA409054Panc1_CON_p3_negPancreas Panc1 cells CON
SA409055Panc1_CON_p2_posPancreas Panc1 cells CON
SA409056Panc1_CON_p1_posPancreas Panc1 cells CON
SA409057Panc1_CON_p1_negPancreas Panc1 cells CON
SA409058Panc1_CON_p2_negPancreas Panc1 cells CON
SA409059Panc1_GEMR_p1_negPancreas Panc1 cells GEMR
SA409060Panc1_GEMR_p1_posPancreas Panc1 cells GEMR
SA409061Panc1_GEMR_p2_negPancreas Panc1 cells GEMR
SA409062Panc1_GEMR_p2_posPancreas Panc1 cells GEMR
SA409063Panc1_GEMR_p3_negPancreas Panc1 cells GEMR
SA409064Panc1_GEMR_p3_posPancreas Panc1 cells GEMR
Showing results 1 to 20 of 20

Collection:

Collection ID:CO003883
Collection Summary:Samples were obtained from established immortalised adherent human pancreatic ductal adenocarcinoma cells (Panc1). Cells were cultured in high glucose DMEM containing 4.5 g/L glucose and 4 mM glutamine and were supplemented with 10% FCS. Cells were cultured under 5% CO2 at 37ºC and routinely passaged every 2-3 days (when ~80-90% confluent). Cell lines were regularly screened for mycoplasma infection.
Sample Type:Pancreas

Treatment:

Treatment ID:TR003899
Treatment Summary:Panc1 GEMR cells were produced by serial treatment with escalating doses of gemcitabine for approximately 12 weeks. The final concentration of GEMC for Panc1 cells was 150 nM, resulting in a half-maximal inhibitory concentration of 720.5 nM (approximately 2.5 times increase over control (CON) cells, 273.3 nM)

Sample Preparation:

Sampleprep ID:SP003896
Sampleprep Summary:Lipids were extracted from cells grown to 80-90% confluency in 6 well plates using a modified methyl tert-butyl ether (MTBE) method. Adherent cells were washed with ice-cold PBS and scraped into methanol containing 0.01% butylated hydroxytoluene and 100 pmol each of internal standards (phosphatidylcholine 19:0/19:0, phosphatidylethanolamine 17:0/17:0, phosphatidylserine 17:0/17:0, lysophosphatidylcholine 17:0, lysophosphatidylethanolamine 14:0, phosphatidylglycerol 17:0/17:0, phosphatidic acid 17:0/17:0, ceramide d18:1/17:0, dihydrosphingomyelin 12:0, cholesteryl ester 22:1, diacylglycerol 17:0/17:0, D5-triacylglycerol 16:0/16:0/16:0 and cardiolipin 14:0/14:0/14:0/14:0). An empty well was also scraped for use in background subtraction. To this, MTBE was added at a ratio of 3:1 v/v, and extracts were rotated overnight at 4ºC. Following overnight rotation, 1 part of ice-cold 150 mM ammonium acetate was added, samples were vortexed vigorously and centrifuged at 2000 x g for 5 min. The upper organic phase containing lipids was transferred into a 1.5 mL autosampler vial and dried under N2 at 37ºC Dried lipids were reconstituted in chloroform:methanol:water (60:30:4.5 v/v/v), transferred to a sleeved vial, and stored at -20ºC until analysis. The aqueous phase containing the protein pellet was dried under N2 and digested with 1M NaOH overnight at 4ºC. Digested protein was diluted 1:2 v/v with water and protein concentration was determined using a Pierce BCA assay kit (ThermoFisher Scientific)

Combined analysis:

Analysis ID AN006168 AN006169
Chromatography ID CH004684 CH004684
MS ID MS005873 MS005874
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Thermo Dionex Ultimate 3000 Thermo Dionex Ultimate 3000
Column Waters ACQUITY UPLC CSH C18 (100 x 2.1 mm, 1.7 μm) Waters ACQUITY UPLC CSH C18 (100 x 2.1 mm, 1.7 μm)
MS Type ESI ESI
MS instrument type Orbitrap Orbitrap
MS instrument name Thermo Q Exactive HF hybrid Orbitrap Thermo Q Exactive HF hybrid Orbitrap
Ion Mode POSITIVE NEGATIVE
Units nmol/mg protein nmol/mg protein

Chromatography:

Chromatography ID:CH004684
Instrument Name:Thermo Dionex Ultimate 3000
Column Name:Waters ACQUITY UPLC CSH C18 (100 x 2.1 mm, 1.7 μm)
Column Temperature:60°C
Flow Gradient:0.1-1.5 min 68% A (32% B), 1.4-4 min 55% A (45% B), 4-5 min 48% A (52% B), 5-8 min 42% A (58% B), 8-11 min 34% A (66% B), 11-14 min 30% A (70% B), 14-18 min 25% A (75% B), 18-21 min 3% A (97% B), 21-25 min 3% A (97% B), 25.1-30 min 68% A (32% B).
Flow Rate:0.26 mL/min
Solvent A:60% Acetonitrile/40% Water; 10 mM Ammonium Formate; 0.1% Formic acid
Solvent B:10% Acetonitrile/90% Isopropanol; 10 mM Ammonium Formate; 0.1% Formic acid
Chromatography Type:Reversed phase

MS:

MS ID:MS005873
Analysis ID:AN006168
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Source conditions were as follows: a spray voltage 4.0 kV in positive ion mode and 3.5 kV in negative ion mode, capillary temperature 290°C, S lens RF 50, and auxiliary gas heater temperature of 250°C. Nitrogen was used as both source and collision gas, with the sheath gas flow rate set at 20 and the auxiliary gas flow rate at 5 (arbitrary units). Data were acquired in full scan/data-dependent MS2 mode (full-scan resolution 70,000 FWHM, max ion injection time 50 ms, scan range m/z 200–1,500), with the 10 most abundant ions being subjected to collision-induced dissociation using an isolation window of 1.5 Da and a normalized stepped collision energy of 15/27 eV. Product ions were detected at a resolution of 17,500. An exclusion list for background ions was developed using extraction blanks, and mass calibration was performed in both positive and negative ionization modes before analysis to ensure mass accuracy of 5 ppm in full-scan mode.
Ion Mode:POSITIVE
  
MS ID:MS005874
Analysis ID:AN006169
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments:Source conditions were as follows: a spray voltage 4.0 kV in positive ion mode and 3.5 kV in negative ion mode, capillary temperature 290°C, S lens RF 50, and auxiliary gas heater temperature of 250°C. Nitrogen was used as both source and collision gas, with the sheath gas flow rate set at 20 and the auxiliary gas flow rate at 5 (arbitrary units). Data were acquired in full scan/data-dependent MS2 mode (full-scan resolution 70,000 FWHM, max ion injection time 50 ms, scan range m/z 200–1,500), with the 10 most abundant ions being subjected to collision-induced dissociation using an isolation window of 1.5 Da and a normalized stepped collision energy of 15/27 eV. Product ions were detected at a resolution of 17,500. An exclusion list for background ions was developed using extraction blanks, and mass calibration was performed in both positive and negative ionization modes before analysis to ensure mass accuracy of 5 ppm in full-scan mode.
Ion Mode:NEGATIVE
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