Summary of Study ST002339
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 PR001502. The data can be accessed directly via it's Project DOI: 10.21228/M8JD81 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 | ST002339 |
| Study Title | Myriocin rescue of serine-associated hepatic lipid diversity |
| Study Summary | We analyzed hepatic polar and lipid metabolites in mice (C57BL/6J) in response to two dietary interventions. The first was: 1) low fat (LFD), 2) serine/glycine-free LFD (-SG LFD), high fat (HFD), and serine/glycine-free HFD (-SG HFD). And the second was: 1) low fat (LFD), high fat (HFD), serine/glycine-free HFD (-SG HFD), and serine/glycine-free HFD (-SG HFD) with myriocin (0.3 mg/kg every other day) treatment. The goal of the study was to determine the impact of dietary serine/glycine restriction and myriocin treatment on the hepatic lipidome. |
| Institute | Salk Institute for Biological Studies |
| Department | Molecular and Cell Biology Laboratory |
| Laboratory | Metallo Lab |
| Last Name | Handzlik |
| First Name | Michal |
| Address | 10010 N Torrey Pines Rd, La Jolla, California, 92037, USA |
| mhandzlik@salk.edu | |
| Phone | 2069601945 |
| Submit Date | 2022-11-10 |
| Num Groups | LFD, -SG LFD, HFD, -SG HFD, LFD+Veh, HFD+Veh, -SG HFD+Veh, -SG HFD+Myr |
| Total Subjects | 88 |
| Num Males | 88 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzXML |
| Analysis Type Detail | LC-MS |
| Release Date | 2024-01-01 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001502 |
| Project DOI: | doi: 10.21228/M8JD81 |
| Project Title: | Serine and lipid metabolism |
| Project Summary: | We analyzed hepatic polar and lipid metabolites in mice (C57BL/6J) in response to two dietary interventions. The first was: 1) low fat (LFD), 2) serine/glycine-free LFD (-SG LFD), high fat (HFD), and serine/glycine-free HFD (-SG HFD). And the second was: 1) low fat (LFD), high fat (HFD), serine/glycine-free HFD (-SG HFD), and serine/glycine-free HFD (-SG HFD) with myriocin (0.3 mg/kg every other day) treatment. The goal of the study was to determine the impact of dietary serine/glycine restriction and myriocin treatment on the hepatic lipidome. |
| Institute: | Salk Institute for Biological Studies |
| Department: | Molecular and Cell Biology Laboratory |
| Laboratory: | Metallo Lab |
| Last Name: | Handzlik |
| First Name: | Michal |
| Address: | 10010 N Torrey Pines Rd, La Jolla, California, 92037, USA |
| Email: | mhandzlik@salk.edu |
| Phone: | 2069601945 |
| Funding Source: | R01CA234245 |
Subject:
| Subject ID: | SU002428 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Genotype Strain: | C57BL/6J |
| Age Or Age Range: | 8-32-week-old |
| Weight Or Weight Range: | 25-50 |
| Gender: | Male |
| Animal Animal Supplier: | JAX |
| Animal Housing: | 5/cage |
| Animal Light Cycle: | 12h dark/12 h light |
| Animal Feed: | Special diets; see group labeling |
| Animal Water: | Ad libitum |
| Species Group: | Mammals |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Group |
|---|---|---|
| SA235018 | 317 | High fat diet + vehicle |
| SA235019 | 316 | High fat diet + vehicle |
| SA235020 | 314 | High fat diet + vehicle |
| SA235021 | 318 | High fat diet + vehicle |
| SA235022 | 315 | High fat diet + vehicle |
| SA235023 | 320 | High fat diet + vehicle |
| SA235024 | 323 | High fat diet + vehicle |
| SA235025 | 322 | High fat diet + vehicle |
| SA235026 | 321 | High fat diet + vehicle |
| SA235027 | 313 | High fat diet + vehicle |
| SA235028 | 319 | High fat diet + vehicle |
| SA235029 | 324 | High fat diet + vehicle |
| SA235030 | 304 | Low fat diet + vehicle |
| SA235031 | 305 | Low fat diet + vehicle |
| SA235032 | 303 | Low fat diet + vehicle |
| SA235033 | 301 | Low fat diet + vehicle |
| SA235034 | 312 | Low fat diet + vehicle |
| SA235035 | 306 | Low fat diet + vehicle |
| SA235036 | 302 | Low fat diet + vehicle |
| SA235037 | 311 | Low fat diet + vehicle |
| SA235038 | 307 | Low fat diet + vehicle |
| SA235039 | 310 | Low fat diet + vehicle |
| SA235040 | 309 | Low fat diet + vehicle |
| SA235041 | 308 | Low fat diet + vehicle |
| SA235042 | 342 | Serine/glycine-free high fat diet + myriocin |
| SA235043 | 343 | Serine/glycine-free high fat diet + myriocin |
| SA235044 | 338 | Serine/glycine-free high fat diet + myriocin |
| SA235045 | 340 | Serine/glycine-free high fat diet + myriocin |
| SA235046 | 341 | Serine/glycine-free high fat diet + myriocin |
| SA235047 | 346 | Serine/glycine-free high fat diet + myriocin |
| SA235048 | 337 | Serine/glycine-free high fat diet + myriocin |
| SA235049 | 348 | Serine/glycine-free high fat diet + myriocin |
| SA235050 | 347 | Serine/glycine-free high fat diet + myriocin |
| SA235051 | 345 | Serine/glycine-free high fat diet + myriocin |
| SA235052 | 344 | Serine/glycine-free high fat diet + myriocin |
| SA235053 | 331 | Serine/glycine-free high fat diet + vehicle |
| SA235054 | 328 | Serine/glycine-free high fat diet + vehicle |
| SA235055 | 327 | Serine/glycine-free high fat diet + vehicle |
| SA235056 | 326 | Serine/glycine-free high fat diet + vehicle |
| SA235057 | 325 | Serine/glycine-free high fat diet + vehicle |
| SA235058 | 329 | Serine/glycine-free high fat diet + vehicle |
| SA235059 | 330 | Serine/glycine-free high fat diet + vehicle |
| SA235060 | 335 | Serine/glycine-free high fat diet + vehicle |
| SA235061 | 334 | Serine/glycine-free high fat diet + vehicle |
| SA235062 | 333 | Serine/glycine-free high fat diet + vehicle |
| SA235063 | 332 | Serine/glycine-free high fat diet + vehicle |
| SA235064 | 336 | Serine/glycine-free high fat diet + vehicle |
| Showing results 1 to 47 of 47 |
Collection:
| Collection ID: | CO002421 |
| Collection Summary: | Liver samples were collected using Wollenberger clamps pre-cooled to the temperature of liquid nitrogen and stored at -80 C until analysis. |
| Sample Type: | Liver |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR002440 |
| Treatment Summary: | Animals were subjected to 4 different conditions for a period of 24 weeks: 1) low fat diet + vehicle, 2) high fat diet + vehicle, 3) serine/glycine-free high fat diet + vehicle, and 4) serine/glycine-free high fat diet + myriocin. |
Sample Preparation:
| Sampleprep ID: | SP002434 |
| Sampleprep Summary: | Samples were extracted with 400 ul of methanol (-20 C), 100 ul of water (ice-cold), 400 saline (ice-cold), and 1000 ul of chloroform (-20 C). |
| Processing Storage Conditions: | Room temperature |
| Extract Storage: | 4℃ |
Combined analysis:
| Analysis ID | AN003822 |
|---|---|
| Chromatography ID | CH002828 |
| MS ID | MS003564 |
| 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 | Ion trap |
| MS instrument name | Thermo Q Exactive Orbitrap |
| Ion Mode | POSITIVE |
| Units | normalized ion count/mg protein |
Chromatography:
| Chromatography ID: | CH002828 |
| Chromatography Summary: | 30% to 43% B from 3-8 min, then from 43% to 50% B from 8-9 min, then 50-90% B from 9-18 min, then 90-99% B from 18-26 min, then held at 99% B from 26-30 min, before returning to 30% B in 6 min and held for a further 4 min |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Thermo Accucore C30 (150 x 2.1mm,2.6um) |
| Column Temperature: | 40 |
| Flow Rate: | 0.2 ml/min |
| Solvent A: | 40% water/60% acetonitrile; 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: | MS003564 |
| Analysis ID: | AN003822 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Ion trap |
| MS Type: | ESI |
| MS Comments: | El-MAVEN |
| Ion Mode: | POSITIVE |
