Summary of Study ST003384
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 PR002085. The data can be accessed directly via it's Project DOI: 10.21228/M83R6P 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 | ST003384 |
| Study Title | Impact of high-fat diet enriched in cis or trans fatty acids and myriocin on plasma lipidome in Ldlr-/- mice |
| Study Summary | We analyzed LPC (Lysophosphatidylcholines), LPE Lysophosphatidylethanolamines), PC (phosphatidylcholines), PE (phosphatidylethanolamines), DG (diglycerides), TG (triglycerides), and CE (cholesteryl esters) in the plasma of Ldlr-/- mice fed 1) Cis HFD (High Fat Diet), 2) Cis HFD + Myriocin, 3) Trans HFD, or 4) Trans HFD + Myriocin. We aimed to determine how dietary cis and trans monounsaturated fatty acids impact the broader plasma lipidome while pharmacologically inhibiting the initial rate-limiting enzyme of sphingolipid biosynthesis, serine palmitoyltransferase (SPT), via myriocin. |
| Institute | Salk Institute for Biological Studies |
| Last Name | Gengatharan |
| First Name | Jivani |
| Address | 10010 N Torrey Pines Rd, La Jolla, CA, 92037, USA |
| jivani14@gmail.com | |
| Phone | (858) 453-4100 |
| Submit Date | 2024-08-02 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzXML |
| Analysis Type Detail | LC-MS |
| Release Date | 2024-08-12 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002085 |
| Project DOI: | doi: 10.21228/M83R6P |
| Project Title: | Altered sphingolipid biosynthetic flux and lipoprotein trafficking contribute to trans fat-induced atherosclerosis |
| Project Summary: | The goal of the project is to determine the role of sphingolipid metabolism in atherosclerosis induced by dietary trans fat. We analyzed lipid metabolites in Huh7 cells following various fatty acid treatments, with specific focus on cis and trans unsaturated fatty acids. Additionally, we analyzed lipid metabolites in plasma and liver of Ldlr-/- mice fed high-fat diets enriched in cis or trans fatty acids in the presence or absence of myriocin, a pharmacological inhibitor of Serine palmitoyltransferase (SPT), the initial rate-limiting enzyme of sphingolipid biosynthesis. |
| Institute: | Salk Institute for Biological Studies |
| Last Name: | Gengatharan |
| First Name: | Jivani |
| Address: | 10010 N Torrey Pines Rd, La Jolla, CA, 92037, USA |
| Email: | jivani14@gmail.com |
| Phone: | (858) 453-4100 |
Subject:
| Subject ID: | SU003505 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Genotype | Sample source | Group |
|---|---|---|---|---|
| SA367617 | Plasma_C30_CisHFD_33 | Ldlr-/- | Blood plasma | Cis HFD |
| SA367618 | Plasma_C30_CisHFD_12 | Ldlr-/- | Blood plasma | Cis HFD |
| SA367619 | Plasma_C30_CisHFD_35 | Ldlr-/- | Blood plasma | Cis HFD |
| SA367620 | Plasma_C30_CisHFD_34 | Ldlr-/- | Blood plasma | Cis HFD |
| SA367621 | Plasma_C30_CisHFD_11 | Ldlr-/- | Blood plasma | Cis HFD |
| SA367622 | Plasma_C30_CisHFD_32 | Ldlr-/- | Blood plasma | Cis HFD |
| SA367623 | Plasma_C30_CisHFD_15 | Ldlr-/- | Blood plasma | Cis HFD |
| SA367624 | Plasma_C30_CisHFD_14 | Ldlr-/- | Blood plasma | Cis HFD |
| SA367625 | Plasma_C30_CisHFD_31 | Ldlr-/- | Blood plasma | Cis HFD |
| SA367626 | Plasma_C30_CisHFD_13 | Ldlr-/- | Blood plasma | Cis HFD |
| SA367627 | Plasma_C30_CisHFDMyr_142 | Ldlr-/- | Blood plasma | Cis HFD + Myriocin |
| SA367628 | Plasma_C30_CisHFDMyr_145 | Ldlr-/- | Blood plasma | Cis HFD + Myriocin |
| SA367629 | Plasma_C30_CisHFDMyr_144 | Ldlr-/- | Blood plasma | Cis HFD + Myriocin |
| SA367630 | Plasma_C30_CisHFDMyr_143 | Ldlr-/- | Blood plasma | Cis HFD + Myriocin |
| SA367631 | Plasma_C30_CisHFDMyr_141 | Ldlr-/- | Blood plasma | Cis HFD + Myriocin |
| SA367632 | Plasma_C30_CisHFDMyr_105 | Ldlr-/- | Blood plasma | Cis HFD + Myriocin |
| SA367633 | Plasma_C30_CisHFDMyr_104 | Ldlr-/- | Blood plasma | Cis HFD + Myriocin |
| SA367634 | Plasma_C30_CisHFDMyr_103 | Ldlr-/- | Blood plasma | Cis HFD + Myriocin |
| SA367635 | Plasma_C30_CisHFDMyr_102 | Ldlr-/- | Blood plasma | Cis HFD + Myriocin |
| SA367636 | Plasma_C30_CisHFDMyr_101 | Ldlr-/- | Blood plasma | Cis HFD + Myriocin |
| SA367637 | Plasma_C30_TransHFD_82 | Ldlr-/- | Blood plasma | Trans HFD |
| SA367638 | Plasma_C30_TransHFD_85 | Ldlr-/- | Blood plasma | Trans HFD |
| SA367639 | Plasma_C30_TransHFD_84 | Ldlr-/- | Blood plasma | Trans HFD |
| SA367640 | Plasma_C30_TransHFD_83 | Ldlr-/- | Blood plasma | Trans HFD |
| SA367641 | Plasma_C30_TransHFD_44 | Ldlr-/- | Blood plasma | Trans HFD |
| SA367642 | Plasma_C30_TransHFD_81 | Ldlr-/- | Blood plasma | Trans HFD |
| SA367643 | Plasma_C30_TransHFD_45 | Ldlr-/- | Blood plasma | Trans HFD |
| SA367644 | Plasma_C30_TransHFD_43 | Ldlr-/- | Blood plasma | Trans HFD |
| SA367645 | Plasma_C30_TransHFD_42 | Ldlr-/- | Blood plasma | Trans HFD |
| SA367646 | Plasma_C30_TransHFD_41 | Ldlr-/- | Blood plasma | Trans HFD |
| SA367647 | Plasma_C30_TransHFDMyr_61 | Ldlr-/- | Blood plasma | Trans HFD + Myriocin |
| SA367648 | Plasma_C30_TransHFDMyr_62 | Ldlr-/- | Blood plasma | Trans HFD + Myriocin |
| SA367649 | Plasma_C30_TransHFDMyr_63 | Ldlr-/- | Blood plasma | Trans HFD + Myriocin |
| SA367650 | Plasma_C30_TransHFDMyr_64 | Ldlr-/- | Blood plasma | Trans HFD + Myriocin |
| SA367651 | Plasma_C30_TransHFDMyr_65 | Ldlr-/- | Blood plasma | Trans HFD + Myriocin |
| SA367652 | Plasma_C30_TransHFDMyr_91 | Ldlr-/- | Blood plasma | Trans HFD + Myriocin |
| SA367653 | Plasma_C30_TransHFDMyr_92 | Ldlr-/- | Blood plasma | Trans HFD + Myriocin |
| SA367654 | Plasma_C30_TransHFDMyr_93 | Ldlr-/- | Blood plasma | Trans HFD + Myriocin |
| SA367655 | Plasma_C30_TransHFDMyr_94 | Ldlr-/- | Blood plasma | Trans HFD + Myriocin |
| SA367656 | Plasma_C30_TransHFDMyr_95 | Ldlr-/- | Blood plasma | Trans HFD + Myriocin |
| Showing results 1 to 40 of 40 |
Collection:
| Collection ID: | CO003498 |
| Collection Summary: | Blood was collected in EDTA-coated tubes (Sarstedt Inc.) and centrifuged at 2000g for 5 min. The supernatant was transferred to a new Eppendorf tube and stored at -80°C until analysis. |
| Sample Type: | Blood (plasma) |
Treatment:
| Treatment ID: | TR003514 |
| Treatment Summary: | Four-five-week-old Ldlr-/- C57BL/6J male and female mice (JAX# 002207) were fed with irradiated 60% high fat diets (HFD) prepared by Dyets for 16 weeks. These diets include Cis Unsaturated HFD (105063GI), Cis Unsaturated HFD with 2.2 mg/kg Myriocin Added (105064GI), Trans Unsaturated HFD (105061GI), and Trans Unsaturated HFD with 2.2 mg/kg Myriocin Added (105061GI). The Trans Unsaturated HFD was designed with 100% Primex, a partially hydrogenated vegetable oil, and the Cis Unsaturated HFD was designed with 34% lard and 66% olive oil. |
Sample Preparation:
| Sampleprep ID: | SP003512 |
| Sampleprep Summary: | Plasma (10 µL) was spiked with 1 µg of each of the following internal standards: 18:1-d7 cholesteryl ester (Avanti Polar Lipids, Cat #791645), 15:0-18:1(d7) phosphatidylcholine (Avanti Polar Lipids, Cat #791637), 15:0-18:1(d7) phosphatidylethanolamine (Avanti Polar Lipids, Cat #791638), 18:1(d7) lysophosphatidylcholine (Avanti Polar Lipids, Cat#791643), 18:1(d7) lysophosphatidylethanolamine (Avanti Polar Lipids, Cat #791644), 15:0-18:1(d7) diacylglycerol (Avanti Polar Lipids, Cat #791647), 15:0-18:1(d7)-15:0 triacylglycerol (Avanti Polar Lipids, Cat #791648). 0.5 mL methanol, 0.5 mL H2O, and 1 mL chloroform were added directly. Samples were vortexed for 5 min, centrifuged for 5 min at 4˚C at 15,000g. The organic phase was collected and 2 μL of formic acid was added to the remaining polar phase which was re-extracted with 1 mL of chloroform. Combined organic phases were dried under nitrogen. After dried extracts for plasma were resuspended in 60 µL 65:30:5 ACN: IPA:H2O, 5 µL of sample was injected. |
Combined analysis:
| Analysis ID | AN005542 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | Thermo Vanquish |
| Column | Thermo Accucore C30 (150 x 2.1mm,2.6um) |
| MS Type | ESI |
| MS instrument type | Orbitrap |
| MS instrument name | Thermo Q Exactive Orbitrap |
| Ion Mode | POSITIVE |
| Units | Peak area |
Chromatography:
| Chromatography ID: | CH004214 |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Thermo Accucore C30 (150 x 2.1mm,2.6um) |
| Column Temperature: | 40˚C |
| Flow Gradient: | 0 min, 30% B; 3 min, 30% B; 8 min, 43% B; 9 min, 50% B; 18 min, 90% B; 26 min, 99% B; 30 min, 99%B; 36 min, 30% B |
| Flow Rate: | 0.2 mL/min |
| Solvent A: | 60% Acetonitrile/40% Water; 0.1% Formic acid; 10 mM ammonium formate |
| Solvent B: | 90% Isopropanol/10% Acetonitrile; 0.1% Formic acid; 10 mM ammonium formate |
| Chromatography Type: | Reversed phase |
MS:
| MS ID: | MS005267 |
| Analysis ID: | AN005542 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Lipids were identified in EL-MAVEN using exact mass of precursor ion in MS1 chromatogram and product ion in MS2 spectra. Lipids were quantified using peak areas in MS1 chromatogram. |
| Ion Mode: | POSITIVE |
