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.
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 | ST003392 |
| Study Title | Impact of high-fat diet enriched in cis or trans fatty acids and myriocin on hepatic sphingolipids in Ldlr-/- mice |
| Study Summary | We 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 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 | 2024-07-31 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | d |
| 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: | SU003515 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Species Group: | Mammals |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Group |
|---|---|---|
| SA368352 | Liver_C8_CisHFD_33 | Cis HFD |
| SA368353 | Liver_C8_CisHFD_13 | Cis HFD |
| SA368354 | Liver_C8_CisHFD_35 | Cis HFD |
| SA368355 | Liver_C8_CisHFD_34 | Cis HFD |
| SA368356 | Liver_C8_CisHFD_12 | Cis HFD |
| SA368357 | Liver_C8_CisHFD_32 | Cis HFD |
| SA368358 | Liver_C8_CisHFD_14 | Cis HFD |
| SA368359 | Liver_C8_CisHFD_31 | Cis HFD |
| SA368360 | Liver_C8_CisHFD_15 | Cis HFD |
| SA368361 | Liver_C8_CisHFDMyr_101 | Cis HFD + Myriocin |
| SA368362 | Liver_C8_CisHFDMyr_102 | Cis HFD + Myriocin |
| SA368363 | Liver_C8_CisHFDMyr_103 | Cis HFD + Myriocin |
| SA368364 | Liver_C8_CisHFDMyr_104 | Cis HFD + Myriocin |
| SA368365 | Liver_C8_CisHFDMyr_105 | Cis HFD + Myriocin |
| SA368366 | Liver_C8_CisHFDMyr_142 | Cis HFD + Myriocin |
| SA368367 | Liver_C8_CisHFDMyr_143 | Cis HFD + Myriocin |
| SA368368 | Liver_C8_CisHFDMyr_144 | Cis HFD + Myriocin |
| SA368369 | Liver_C8_CisHFDMyr_145 | Cis HFD + Myriocin |
| SA368370 | Liver_C8_CisHFDMyr_141 | Cis HFD + Myriocin |
| SA368371 | Liver_C8_TransHFD_83 | Trans HFD |
| SA368372 | Liver_C8_TransHFD_85 | Trans HFD |
| SA368373 | Liver_C8_TransHFD_84 | Trans HFD |
| SA368374 | Liver_C8_TransHFD_45 | Trans HFD |
| SA368375 | Liver_C8_TransHFD_82 | Trans HFD |
| SA368376 | Liver_C8_TransHFD_81 | Trans HFD |
| SA368377 | Liver_C8_TransHFD_44 | Trans HFD |
| SA368378 | Liver_C8_TransHFD_43 | Trans HFD |
| SA368379 | Liver_C8_TransHFD_42 | Trans HFD |
| SA368380 | Liver_C8_TransHFDMyr_61 | Trans HFD + Myriocin |
| SA368381 | Liver_C8_TransHFDMyr_62 | Trans HFD + Myriocin |
| SA368382 | Liver_C8_TransHFDMyr_63 | Trans HFD + Myriocin |
| SA368383 | Liver_C8_TransHFDMyr_64 | Trans HFD + Myriocin |
| SA368384 | Liver_C8_TransHFDMyr_65 | Trans HFD + Myriocin |
| SA368385 | Liver_C8_TransHFDMyr_91 | Trans HFD + Myriocin |
| SA368386 | Liver_C8_TransHFDMyr_92 | Trans HFD + Myriocin |
| SA368387 | Liver_C8_TransHFDMyr_93 | Trans HFD + Myriocin |
| SA368388 | Liver_C8_TransHFDMyr_94 | Trans HFD + Myriocin |
| SA368389 | Liver_C8_TransHFDMyr_95 | 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. |
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 |
Analysis:
| Analysis ID: | AN005566 |
| Analysis Type: | MS |
| Chromatography ID: | CH004230 |
| Num Factors: | 4 |
| Num Metabolites: | 61 |
| Units: | Peak area |
