Summary of Study ST003379

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	ST003379
Study Title	Impact of high-fat diet enriched in cis or trans fatty acids and myriocin on hepatic 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 liver 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 hepatic 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
Email	jivani14@gmail.com
Phone	(858) 453-4100
Submit Date	2024-07-31
Raw Data Available	Yes
Raw Data File Type(s)	mzXML
Analysis Type Detail	LC-MS
Release Date	2024-08-12
Release Version	1

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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:	SU003500
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
SA367246	Liver_C30_CisHFD_33	Ldlr-/-	Mouse liver	Cis HFD
SA367247	Liver_C30_CisHFD_12	Ldlr-/-	Mouse liver	Cis HFD
SA367248	Liver_C30_CisHFD_35	Ldlr-/-	Mouse liver	Cis HFD
SA367249	Liver_C30_CisHFD_34	Ldlr-/-	Mouse liver	Cis HFD
SA367250	Liver_C30_CisHFD_11	Ldlr-/-	Mouse liver	Cis HFD
SA367251	Liver_C30_CisHFD_32	Ldlr-/-	Mouse liver	Cis HFD
SA367252	Liver_C30_CisHFD_15	Ldlr-/-	Mouse liver	Cis HFD
SA367253	Liver_C30_CisHFD_14	Ldlr-/-	Mouse liver	Cis HFD
SA367254	Liver_C30_CisHFD_31	Ldlr-/-	Mouse liver	Cis HFD
SA367255	Liver_C30_CisHFD_13	Ldlr-/-	Mouse liver	Cis HFD
SA367256	Liver_C30_CisHFDMyr_142	Ldlr-/-	Mouse liver	Cis HFD + Myriocin
SA367257	Liver_C30_CisHFDMyr_145	Ldlr-/-	Mouse liver	Cis HFD + Myriocin
SA367258	Liver_C30_CisHFDMyr_144	Ldlr-/-	Mouse liver	Cis HFD + Myriocin
SA367259	Liver_C30_CisHFDMyr_143	Ldlr-/-	Mouse liver	Cis HFD + Myriocin
SA367260	Liver_C30_CisHFDMyr_141	Ldlr-/-	Mouse liver	Cis HFD + Myriocin
SA367261	Liver_C30_CisHFDMyr_105	Ldlr-/-	Mouse liver	Cis HFD + Myriocin
SA367262	Liver_C30_CisHFDMyr_104	Ldlr-/-	Mouse liver	Cis HFD + Myriocin
SA367263	Liver_C30_CisHFDMyr_103	Ldlr-/-	Mouse liver	Cis HFD + Myriocin
SA367264	Liver_C30_CisHFDMyr_102	Ldlr-/-	Mouse liver	Cis HFD + Myriocin
SA367265	Liver_C30_CisHFDMyr_101	Ldlr-/-	Mouse liver	Cis HFD + Myriocin
SA367266	Liver_C30_TransHFD_82	Ldlr-/-	Mouse liver	Trans HFD
SA367267	Liver_C30_TransHFD_85	Ldlr-/-	Mouse liver	Trans HFD
SA367268	Liver_C30_TransHFD_84	Ldlr-/-	Mouse liver	Trans HFD
SA367269	Liver_C30_TransHFD_83	Ldlr-/-	Mouse liver	Trans HFD
SA367270	Liver_C30_TransHFD_44	Ldlr-/-	Mouse liver	Trans HFD
SA367271	Liver_C30_TransHFD_81	Ldlr-/-	Mouse liver	Trans HFD
SA367272	Liver_C30_TransHFD_45	Ldlr-/-	Mouse liver	Trans HFD
SA367273	Liver_C30_TransHFD_43	Ldlr-/-	Mouse liver	Trans HFD
SA367274	Liver_C30_TransHFD_42	Ldlr-/-	Mouse liver	Trans HFD
SA367275	Liver_C30_TransHFD_41	Ldlr-/-	Mouse liver	Trans HFD
SA367276	Liver_C30_TransHFDMyr_61	Ldlr-/-	Mouse liver	Trans HFD + Myriocin
SA367277	Liver_C30_TransHFDMyr_62	Ldlr-/-	Mouse liver	Trans HFD + Myriocin
SA367278	Liver_C30_TransHFDMyr_63	Ldlr-/-	Mouse liver	Trans HFD + Myriocin
SA367279	Liver_C30_TransHFDMyr_64	Ldlr-/-	Mouse liver	Trans HFD + Myriocin
SA367280	Liver_C30_TransHFDMyr_65	Ldlr-/-	Mouse liver	Trans HFD + Myriocin
SA367281	Liver_C30_TransHFDMyr_91	Ldlr-/-	Mouse liver	Trans HFD + Myriocin
SA367282	Liver_C30_TransHFDMyr_92	Ldlr-/-	Mouse liver	Trans HFD + Myriocin
SA367283	Liver_C30_TransHFDMyr_93	Ldlr-/-	Mouse liver	Trans HFD + Myriocin
SA367284	Liver_C30_TransHFDMyr_94	Ldlr-/-	Mouse liver	Trans HFD + Myriocin
SA367285	Liver_C30_TransHFDMyr_95	Ldlr-/-	Mouse liver	Trans HFD + Myriocin

Showing results 1 to 40 of 40

Showing results 1 to 40 of 40

Collection:

Collection ID:	CO003493
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:	TR003509
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.

Treatment ID:

TR003509

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:	SP003507
Sampleprep Summary:	Frozen liver (10-20 mg) was spiked with 2 ug 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). 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 Scientific). The remaining homogenate was transferred to a new Eppendorf tube and 1 mL chloroform was added. 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 liver were resuspended in 100 µl 65:30:5 ACN: IPA:H2O, 5 µL of sample was injected.

Sampleprep ID:

SP003507

Sampleprep Summary:

Frozen liver (10-20 mg) was spiked with 2 ug 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). 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 Scientific). The remaining homogenate was transferred to a new Eppendorf tube and 1 mL chloroform was added. 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 liver were resuspended in 100 µl 65:30:5 ACN: IPA:H2O, 5 µL of sample was injected.

Combined analysis:

Analysis ID	AN005534
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:	CH004208
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:	MS005259
Analysis ID:	AN005534
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