Summary of Study ST003317
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 PR002064. The data can be accessed directly via it's Project DOI: 10.21228/M8TF97 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 | ST003317 |
| Study Title | Effects of LDAH deficiency on the lipidome of oxLDL-treated mouse peritoneal macrophages |
| Study Summary | Lipid droplet-associated hydrolase (LDAH) has a lipase structure and high affinity for lipid droplets of macrophages/foam cells. However, LDAH's functions and lipid substrates remain poorly understood. Mouse peritoneal macrophages from LDAH-knockout mice and their wild-type control littermates were harvested 5 days after aged 3% thioglycolate injection. 4–5 million cells were plated in 60mm culture dishes, and cultured overnight in DMEM supplemented with 10% heat-inactivated fetal bovine serum (FBS). The media was replaced by DMEM-1% FBS supplemented with Hi-TBAR oxLDL (50 μg/ml, Alfa Aesar J65261) for 48h. |
| Institute | Albany Medical College |
| Department | MCP |
| Laboratory | Paul |
| Last Name | Paul |
| First Name | Antoni |
| Address | 47 New Scotland Avenue, MC-8, Albany, NY-12208 |
| paula@amc.edu | |
| Phone | 518-262-1158 |
| Submit Date | 2024-07-06 |
| Num Groups | 2 |
| Total Subjects | 9 |
| Analysis Type Detail | LC-MS |
| Release Date | 2024-07-18 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002064 |
| Project DOI: | doi: 10.21228/M8TF97 |
| Project Title: | Effects of LDAH deficiency on the lipidome of oxLDL-treated mouse peritoneal macrophages |
| Project Summary: | Lipid droplet-associated hydrolase (LDAH) has a lipase structure and high affinity for lipid droplets of macrophages/foam cells. However, LDAH's functions and lipid substrates remain poorly understood. In this project we treated mouse peritoneal macrophages isolated from LDAH-deficient mice and wild-type littermate controls with oxidized low-density lipoprotein (oxLDL) and analyzed the effects of LDAH deficiency on their lipidome. |
| Institute: | Albany Medical College |
| Department: | MCP |
| Laboratory: | Paul |
| Last Name: | Paul |
| First Name: | Antoni |
| Address: | 47 New Scotland Avenue, MC-8, albany, NY-12208 |
| Email: | paula@amc.edu |
| Phone: | 518-262-1158 |
Subject:
| Subject ID: | SU003438 |
| Subject Type: | Cultured cells |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Genotype Strain: | LDAH wild-type and LDAH-knockout mice in C57BL/6 background |
Factors:
Subject type: Cultured cells; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | Genotype |
|---|---|---|---|
| SA359541 | K2 | Peritoneal Macrophages | LDAH-Knockout |
| SA359542 | K1 | Peritoneal Macrophages | LDAH-Knockout |
| SA359543 | K3 | Peritoneal Macrophages | LDAH-Knockout |
| SA359544 | K4 | Peritoneal Macrophages | LDAH-Knockout |
| SA359545 | W1 | Peritoneal Macrophages | Wild-type |
| SA359546 | W2 | Peritoneal Macrophages | Wild-type |
| SA359547 | W3 | Peritoneal Macrophages | Wild-type |
| SA359548 | W4 | Peritoneal Macrophages | Wild-type |
| SA359549 | W5 | Peritoneal Macrophages | Wild-type |
| Showing results 1 to 9 of 9 |
Collection:
| Collection ID: | CO003431 |
| Collection Summary: | Cells were collected, centrifuged, and washed 3x in cold PBS. Cells were immediately frozen and stored at -80C. |
| Sample Type: | Peritoneal macrophages |
Treatment:
| Treatment ID: | TR003447 |
| Treatment Summary: | Cells were treated with Hi-TBAR oxLDL (50 μg/ml, Alfa Aesar J65261) for 48h in DMEM-1% FBS. |
Sample Preparation:
| Sampleprep ID: | SP003445 |
| Sampleprep Summary: | Monophasic lipid extracts were diluted into isopropanol: methanol (2:1,v:v) containing 20 mM ammonium formate and analyzed by flow injection high resolution/accurate MS and tandem MS. |
Combined analysis:
| Analysis ID | AN005431 |
|---|---|
| Analysis type | MS |
| Chromatography type | None (Direct infusion) |
| Chromatography system | none |
| Column | none |
| MS Type | ESI |
| MS instrument type | Orbitrap |
| MS instrument name | Thermo Velos LTQ Orbitrap |
| Ion Mode | POSITIVE |
| Units | Normalized intensity |
Chromatography:
| Chromatography ID: | CH004120 |
| Chromatography Summary: | Lipids were analyzed by flow injection high resolution/accurate MS and tandem MS. Lipid species were identified using the Lipid Mass Spectrum Analysis (LIMSA) v.1.0 software linear fit algorithm, in conjunction with a user-defined database of hypothetical lipid compounds for automated peak finding and correction of 13C isotope effects. Relative quantification of lipid abundance between samples was performed by normalization of target lipid ion peak areas to the di-myristoyl phosphatidylcholine internal standard. |
| Instrument Name: | none |
| Column Name: | none |
| Column Temperature: | none |
| Flow Gradient: | none |
| Flow Rate: | none |
| Solvent A: | none |
| Solvent B: | none |
| Chromatography Type: | None (Direct infusion) |
MS:
| MS ID: | MS005157 |
| Analysis ID: | AN005431 |
| Instrument Name: | Thermo Velos LTQ Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Lipid sample was introduced via nanoESI to a high resolution / accurate mass Thermo Scientific model LTQ Orbitrap Velos mass spectrometer (San Jose, CA) using an Advion Triversa Nanomate nESI source (Advion, Ithaca, NY) operating with a spray voltage of 1.4 kV and a gas pressure of 0.3 psi. The ion source interface settings (inlet temperature of 100°C and S-Lens value of 50%) were optimized to maximize the sensitivity of the precursor ions while minimizing ‘in-source’ fragmentation. |
| Ion Mode: | POSITIVE |
