Summary of Study ST003392

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.

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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.

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Study IDST003392
Study TitleImpact of high-fat diet enriched in cis or trans fatty acids and myriocin on hepatic sphingolipids in Ldlr-/- mice
Study SummaryWe analyzed sphingolipids in the liver of Ldlr-/- mice fed 1) Cis HFD, 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 hepatic sphingolipids while pharmacologically inhibiting the initial rate-limiting enzyme of sphingolipid biosynthesis, serine palmitoyltransferase (SPT), via myriocin.
Institute
Salk Institute for Biological Studies
Last NameGengatharan
First NameJivani
Address10010 N Torrey Pines Rd, La Jolla, CA, 92037, USA
Emailjivani14@gmail.com
Phone(858) 453-4100
Submit Date2024-07-31
Raw Data AvailableYes
Raw Data File Type(s)d
Analysis Type DetailLC-MS
Release Date2024-08-12
Release Version1
Jivani Gengatharan Jivani Gengatharan
https://dx.doi.org/10.21228/M83R6P
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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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:SU003515
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 Sample source Group
SA368352Liver_C8_CisHFD_33Mouse liver Cis HFD
SA368353Liver_C8_CisHFD_13Mouse liver Cis HFD
SA368354Liver_C8_CisHFD_35Mouse liver Cis HFD
SA368355Liver_C8_CisHFD_34Mouse liver Cis HFD
SA368356Liver_C8_CisHFD_12Mouse liver Cis HFD
SA368357Liver_C8_CisHFD_32Mouse liver Cis HFD
SA368358Liver_C8_CisHFD_14Mouse liver Cis HFD
SA368359Liver_C8_CisHFD_31Mouse liver Cis HFD
SA368360Liver_C8_CisHFD_15Mouse liver Cis HFD
SA368361Liver_C8_CisHFDMyr_101Mouse liver Cis HFD + Myriocin
SA368362Liver_C8_CisHFDMyr_102Mouse liver Cis HFD + Myriocin
SA368363Liver_C8_CisHFDMyr_103Mouse liver Cis HFD + Myriocin
SA368364Liver_C8_CisHFDMyr_104Mouse liver Cis HFD + Myriocin
SA368365Liver_C8_CisHFDMyr_105Mouse liver Cis HFD + Myriocin
SA368366Liver_C8_CisHFDMyr_142Mouse liver Cis HFD + Myriocin
SA368367Liver_C8_CisHFDMyr_143Mouse liver Cis HFD + Myriocin
SA368368Liver_C8_CisHFDMyr_144Mouse liver Cis HFD + Myriocin
SA368369Liver_C8_CisHFDMyr_145Mouse liver Cis HFD + Myriocin
SA368370Liver_C8_CisHFDMyr_141Mouse liver Cis HFD + Myriocin
SA368371Liver_C8_TransHFD_83Mouse liver Trans HFD
SA368372Liver_C8_TransHFD_85Mouse liver Trans HFD
SA368373Liver_C8_TransHFD_84Mouse liver Trans HFD
SA368374Liver_C8_TransHFD_45Mouse liver Trans HFD
SA368375Liver_C8_TransHFD_82Mouse liver Trans HFD
SA368376Liver_C8_TransHFD_81Mouse liver Trans HFD
SA368377Liver_C8_TransHFD_44Mouse liver Trans HFD
SA368378Liver_C8_TransHFD_43Mouse liver Trans HFD
SA368379Liver_C8_TransHFD_42Mouse liver Trans HFD
SA368380Liver_C8_TransHFDMyr_61Mouse liver Trans HFD + Myriocin
SA368381Liver_C8_TransHFDMyr_62Mouse liver Trans HFD + Myriocin
SA368382Liver_C8_TransHFDMyr_63Mouse liver Trans HFD + Myriocin
SA368383Liver_C8_TransHFDMyr_64Mouse liver Trans HFD + Myriocin
SA368384Liver_C8_TransHFDMyr_65Mouse liver Trans HFD + Myriocin
SA368385Liver_C8_TransHFDMyr_91Mouse liver Trans HFD + Myriocin
SA368386Liver_C8_TransHFDMyr_92Mouse liver Trans HFD + Myriocin
SA368387Liver_C8_TransHFDMyr_93Mouse liver Trans HFD + Myriocin
SA368388Liver_C8_TransHFDMyr_94Mouse liver Trans HFD + Myriocin
SA368389Liver_C8_TransHFDMyr_95Mouse liver Trans HFD + Myriocin
Showing results 1 to 38 of 38

Collection:

Collection ID:CO003508
Collection Summary:Tissues were collected after mice were fasted for 6 hours. Mice were anesthetized with isoflurane and tissues were freeze-clamped immediately using Wollenberger clamps pre-cooled to the temperature of liquid nitrogen and stored at -80°C until analysis.
Sample Type:Liver

Treatment:

Treatment ID:TR003524
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:SP003522
Sampleprep Summary:Frozen liver (20-30 mg) was spiked with the following internal standards: 20 pmol sphinganine-d7 (Avanti Polar Lipids, Cat# 860658), deoxysphinganine-d3 (Avanti Polar Lipids, Cat# 860474), 100 pmol d18:0-d7/13:0 dihydroceramide (Avanti Polar Lipids, Cat# 330726), 200 pmol d18:1-d7/15:0 ceramide (Avanti Polar Lipids, Cat# 860681), 100 pmol d18:1-d7/15:0 glucosylceramide (Avanti Polar Lipids, Cat# 330729), 100 pmol d18:1-d7/15:0 lactosylceramide (Avanti Polar Lipids, Cat# 330727), 200 pmol sphingosine-d7 (Avanti Polar Lipids, Cat# 860657), and 200 pmol d18:1/18:1-d9 sphingomyelin (Avanti Polar Lipids, Cat# 791649). Tissue was homogenized with 0.5 mL methanol and 0.5 mL H2O. Homogenate aliquot of 100 µL was taken to determine protein content using the BCA protein assay (Thermo Fisher Scientific). The remaining homogenate was transferred to a new Eppendorf tube and 1 mL chloroform was added. Samples were vortexed for 5 min and 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 liver and plasma were resuspended in 100 µl Buffer B, 5 µL of sample was injected.

Combined analysis:

Analysis ID AN005566
Analysis type MS
Chromatography type Reversed phase
Chromatography system Agilent 1260 Infinity II
Column Peeke Scientific Spectra C8SR (150 x 3.0 mm, 3μm)
MS Type ESI
MS instrument type Triple quadrupole
MS instrument name Agilent 6460 QQQ
Ion Mode POSITIVE
Units Peak area

Chromatography:

Chromatography ID:CH004230
Instrument Name:Agilent 1260 Infinity II
Column Name:Peeke Scientific Spectra C8SR (150 x 3.0 mm, 3μm)
Column Temperature:40˚C
Flow Gradient:0 min, 82% B; 3 min, 82% B; 4 min, 90% B; 18 min, 99% B; 25 min, 99% B; 27 min, 82% B; 30 min, 82% B
Flow Rate:0.5 mL/min
Solvent A:100% water; 0.2% formic acid; 2 mM ammonium formate
Solvent B:100% methanol; 0.2% formic acid; 1 mM ammonium formate
Chromatography Type:Reversed phase

MS:

MS ID:MS005291
Analysis ID:AN005566
Instrument Name:Agilent 6460 QQQ
Instrument Type:Triple quadrupole
MS Type:ESI
MS Comments:Sphingolipid species were analyzed by multiple reaction monitoring of the transition from precursor to product ions at associated optimized collision energies, and fragmentor voltages using Agilent Masshunter. The m/z values of the precursor and product ions are provided in the metabolite metadata section.
Ion Mode:POSITIVE
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