Summary of Study ST003383

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 IDST003383
Study TitleImpact of high-fat diet enriched in cis or trans fatty acids and myriocin on the plasma lipoprotein profile of sphingolipids in Ldlr-/- mice
Study SummaryWe analyzed sphingolipids in plasma lipoprotein fractions 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 sphingolipid enrichment in circulating lipoproteins 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 Date2024-08-02
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

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:SU003504
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
SA367353FPLC_C3_8Ldlr-/- Blood plasma Cis HFD
SA367354FPLC_C2_16Ldlr-/- Blood plasma Cis HFD
SA367355FPLC_C2_17Ldlr-/- Blood plasma Cis HFD
SA367356FPLC_C2_18Ldlr-/- Blood plasma Cis HFD
SA367357FPLC_C2_19Ldlr-/- Blood plasma Cis HFD
SA367358FPLC_C2_20Ldlr-/- Blood plasma Cis HFD
SA367359FPLC_C2_21Ldlr-/- Blood plasma Cis HFD
SA367360FPLC_C2_22Ldlr-/- Blood plasma Cis HFD
SA367361FPLC_C3_1Ldlr-/- Blood plasma Cis HFD
SA367362FPLC_C3_2Ldlr-/- Blood plasma Cis HFD
SA367363FPLC_C3_3Ldlr-/- Blood plasma Cis HFD
SA367364FPLC_C3_4Ldlr-/- Blood plasma Cis HFD
SA367365FPLC_C3_5Ldlr-/- Blood plasma Cis HFD
SA367366FPLC_C3_6Ldlr-/- Blood plasma Cis HFD
SA367367FPLC_C3_7Ldlr-/- Blood plasma Cis HFD
SA367368FPLC_C3_9Ldlr-/- Blood plasma Cis HFD
SA367369FPLC_C2_14Ldlr-/- Blood plasma Cis HFD
SA367370FPLC_C3_10Ldlr-/- Blood plasma Cis HFD
SA367371FPLC_C3_11Ldlr-/- Blood plasma Cis HFD
SA367372FPLC_C3_12Ldlr-/- Blood plasma Cis HFD
SA367373FPLC_C3_13Ldlr-/- Blood plasma Cis HFD
SA367374FPLC_C3_14Ldlr-/- Blood plasma Cis HFD
SA367375FPLC_C3_15Ldlr-/- Blood plasma Cis HFD
SA367376FPLC_C3_16Ldlr-/- Blood plasma Cis HFD
SA367377FPLC_C3_17Ldlr-/- Blood plasma Cis HFD
SA367378FPLC_C3_18Ldlr-/- Blood plasma Cis HFD
SA367379FPLC_C3_19Ldlr-/- Blood plasma Cis HFD
SA367380FPLC_C3_20Ldlr-/- Blood plasma Cis HFD
SA367381FPLC_C3_21Ldlr-/- Blood plasma Cis HFD
SA367382FPLC_C3_22Ldlr-/- Blood plasma Cis HFD
SA367383FPLC_C1_2Ldlr-/- Blood plasma Cis HFD
SA367384FPLC_C2_15Ldlr-/- Blood plasma Cis HFD
SA367385FPLC_C1_1Ldlr-/- Blood plasma Cis HFD
SA367386FPLC_C2_13Ldlr-/- Blood plasma Cis HFD
SA367387FPLC_C1_17Ldlr-/- Blood plasma Cis HFD
SA367388FPLC_C1_3Ldlr-/- Blood plasma Cis HFD
SA367389FPLC_C1_4Ldlr-/- Blood plasma Cis HFD
SA367390FPLC_C1_5Ldlr-/- Blood plasma Cis HFD
SA367391FPLC_C1_6Ldlr-/- Blood plasma Cis HFD
SA367392FPLC_C1_7Ldlr-/- Blood plasma Cis HFD
SA367393FPLC_C1_8Ldlr-/- Blood plasma Cis HFD
SA367394FPLC_C1_9Ldlr-/- Blood plasma Cis HFD
SA367395FPLC_C1_10Ldlr-/- Blood plasma Cis HFD
SA367396FPLC_C1_11Ldlr-/- Blood plasma Cis HFD
SA367397FPLC_C1_12Ldlr-/- Blood plasma Cis HFD
SA367398FPLC_C1_13Ldlr-/- Blood plasma Cis HFD
SA367399FPLC_C1_14Ldlr-/- Blood plasma Cis HFD
SA367400FPLC_C1_15Ldlr-/- Blood plasma Cis HFD
SA367401FPLC_C1_16Ldlr-/- Blood plasma Cis HFD
SA367402FPLC_C2_12Ldlr-/- Blood plasma Cis HFD
SA367403FPLC_C1_18Ldlr-/- Blood plasma Cis HFD
SA367404FPLC_C2_5Ldlr-/- Blood plasma Cis HFD
SA367405FPLC_C2_11Ldlr-/- Blood plasma Cis HFD
SA367406FPLC_C2_10Ldlr-/- Blood plasma Cis HFD
SA367407FPLC_C2_9Ldlr-/- Blood plasma Cis HFD
SA367408FPLC_C2_8Ldlr-/- Blood plasma Cis HFD
SA367409FPLC_C2_6Ldlr-/- Blood plasma Cis HFD
SA367410FPLC_C2_7Ldlr-/- Blood plasma Cis HFD
SA367411FPLC_C2_4Ldlr-/- Blood plasma Cis HFD
SA367412FPLC_C2_3Ldlr-/- Blood plasma Cis HFD
SA367413FPLC_C2_2Ldlr-/- Blood plasma Cis HFD
SA367414FPLC_C2_1Ldlr-/- Blood plasma Cis HFD
SA367415FPLC_C1_22Ldlr-/- Blood plasma Cis HFD
SA367416FPLC_C1_21Ldlr-/- Blood plasma Cis HFD
SA367417FPLC_C1_20Ldlr-/- Blood plasma Cis HFD
SA367418FPLC_C1_19Ldlr-/- Blood plasma Cis HFD
SA367419FPLC_CM5_22Ldlr-/- Blood plasma Cis HFD + Myriocin
SA367420FPLC_CM6_5Ldlr-/- Blood plasma Cis HFD + Myriocin
SA367421FPLC_CM6_4Ldlr-/- Blood plasma Cis HFD + Myriocin
SA367422FPLC_CM6_3Ldlr-/- Blood plasma Cis HFD + Myriocin
SA367423FPLC_CM6_2Ldlr-/- Blood plasma Cis HFD + Myriocin
SA367424FPLC_CM6_1Ldlr-/- Blood plasma Cis HFD + Myriocin
SA367425FPLC_CM5_15Ldlr-/- Blood plasma Cis HFD + Myriocin
SA367426FPLC_CM5_21Ldlr-/- Blood plasma Cis HFD + Myriocin
SA367427FPLC_CM5_20Ldlr-/- Blood plasma Cis HFD + Myriocin
SA367428FPLC_CM5_19Ldlr-/- Blood plasma Cis HFD + Myriocin
SA367429FPLC_CM5_18Ldlr-/- Blood plasma Cis HFD + Myriocin
SA367430FPLC_CM5_17Ldlr-/- Blood plasma Cis HFD + Myriocin
SA367431FPLC_CM5_16Ldlr-/- Blood plasma Cis HFD + Myriocin
SA367432FPLC_CM6_7Ldlr-/- Blood plasma Cis HFD + Myriocin
SA367433FPLC_CM6_6Ldlr-/- Blood plasma Cis HFD + Myriocin
SA367434FPLC_CM6_15Ldlr-/- Blood plasma Cis HFD + Myriocin
SA367435FPLC_CM6_8Ldlr-/- Blood plasma Cis HFD + Myriocin
SA367436FPLC_CM6_9Ldlr-/- Blood plasma Cis HFD + Myriocin
SA367437FPLC_CM6_10Ldlr-/- Blood plasma Cis HFD + Myriocin
SA367438FPLC_CM6_11Ldlr-/- Blood plasma Cis HFD + Myriocin
SA367439FPLC_CM6_12Ldlr-/- Blood plasma Cis HFD + Myriocin
SA367440FPLC_CM6_13Ldlr-/- Blood plasma Cis HFD + Myriocin
SA367441FPLC_CM6_14Ldlr-/- Blood plasma Cis HFD + Myriocin
SA367442FPLC_CM6_16Ldlr-/- Blood plasma Cis HFD + Myriocin
SA367443FPLC_CM6_17Ldlr-/- Blood plasma Cis HFD + Myriocin
SA367444FPLC_CM6_18Ldlr-/- Blood plasma Cis HFD + Myriocin
SA367445FPLC_CM6_19Ldlr-/- Blood plasma Cis HFD + Myriocin
SA367446FPLC_CM6_20Ldlr-/- Blood plasma Cis HFD + Myriocin
SA367447FPLC_CM6_21Ldlr-/- Blood plasma Cis HFD + Myriocin
SA367448FPLC_CM6_22Ldlr-/- Blood plasma Cis HFD + Myriocin
SA367449FPLC_CM5_13Ldlr-/- Blood plasma Cis HFD + Myriocin
SA367450FPLC_CM5_14Ldlr-/- Blood plasma Cis HFD + Myriocin
SA367451FPLC_CM5_12Ldlr-/- Blood plasma Cis HFD + Myriocin
SA367452FPLC_CM4_2Ldlr-/- Blood plasma Cis HFD + Myriocin
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Collection:

Collection ID:CO003497
Collection Summary:Blood was collected in EDTA-coated tubes (Sarstedt Inc.) and centrifuged at 2000g for 5 min. The plasma supernatant was transferred to a new Eppendorf tube and stored at -80°C until analysis. Plasma from 9 mice were combined into 3 pooled samples (n=3) and separated via gel-filtration fast-protein liquid chromatography (FPLC). Samples were run on a GE Superose 6 10/30 GL column in 0.15 M sodium chloride containing 1 mM ethylenediaminetetraacetic acid and 0.02% sodium azide with pH 7.4. Fractions of 0.5 mL were collected at a flow rate of 0.5 mL/min.
Sample Type:Blood (plasma)

Treatment:

Treatment ID:TR003513
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:SP003511
Sampleprep Summary:Plasma lipoprotein fractions (100 µL) was spiked with 0.5 µL of UltimateSPLASH One Mix (Avanti Polar Lipids, Cat #330820). 0.5 mL methanol, 0.5 mL H2O, and 1 mL chloroform were added directly. 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 were resuspended in 70 µL Buffer B, 5 µL of sample was injected.

Combined analysis:

Analysis ID AN005541
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:CH004213
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:MS005266
Analysis ID:AN005541
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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