Summary of Study ST002343
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 | ST002343 |
| Study Title | The impact of myriocin and dietary serine restriction on paw skin sphingolipid diversity |
| Study Summary | We analyzed paw skin 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 | 2022-11-11 |
| Num Groups | LFD, -SG LFD, HFD, -SG HFD, LFD+Veh, HFD+Veh, -SG HFD+Veh, -SG HFD+Myr |
| Total Subjects | 47 |
| Num Males | 47 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | d |
| 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: | SU002432 |
| 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 |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Group |
|---|---|---|
| SA235234 | 317 | High fat diet + vehicle |
| SA235235 | 316 | High fat diet + vehicle |
| SA235236 | 314 | High fat diet + vehicle |
| SA235237 | 318 | High fat diet + vehicle |
| SA235238 | 315 | High fat diet + vehicle |
| SA235239 | 320 | High fat diet + vehicle |
| SA235240 | 323 | High fat diet + vehicle |
| SA235241 | 322 | High fat diet + vehicle |
| SA235242 | 321 | High fat diet + vehicle |
| SA235243 | 313 | High fat diet + vehicle |
| SA235244 | 319 | High fat diet + vehicle |
| SA235245 | 324 | High fat diet + vehicle |
| SA235246 | 304 | Low fat diet + vehicle |
| SA235247 | 305 | Low fat diet + vehicle |
| SA235248 | 303 | Low fat diet + vehicle |
| SA235249 | 301 | Low fat diet + vehicle |
| SA235250 | 312 | Low fat diet + vehicle |
| SA235251 | 306 | Low fat diet + vehicle |
| SA235252 | 302 | Low fat diet + vehicle |
| SA235253 | 311 | Low fat diet + vehicle |
| SA235254 | 307 | Low fat diet + vehicle |
| SA235255 | 310 | Low fat diet + vehicle |
| SA235256 | 309 | Low fat diet + vehicle |
| SA235257 | 308 | Low fat diet + vehicle |
| SA235258 | 342 | Serine/glycine-free high fat diet + myriocin |
| SA235259 | 343 | Serine/glycine-free high fat diet + myriocin |
| SA235260 | 338 | Serine/glycine-free high fat diet + myriocin |
| SA235261 | 340 | Serine/glycine-free high fat diet + myriocin |
| SA235262 | 341 | Serine/glycine-free high fat diet + myriocin |
| SA235263 | 346 | Serine/glycine-free high fat diet + myriocin |
| SA235264 | 337 | Serine/glycine-free high fat diet + myriocin |
| SA235265 | 348 | Serine/glycine-free high fat diet + myriocin |
| SA235266 | 347 | Serine/glycine-free high fat diet + myriocin |
| SA235267 | 345 | Serine/glycine-free high fat diet + myriocin |
| SA235268 | 344 | Serine/glycine-free high fat diet + myriocin |
| SA235269 | 331 | Serine/glycine-free high fat diet + vehicle |
| SA235270 | 328 | Serine/glycine-free high fat diet + vehicle |
| SA235271 | 327 | Serine/glycine-free high fat diet + vehicle |
| SA235272 | 326 | Serine/glycine-free high fat diet + vehicle |
| SA235273 | 325 | Serine/glycine-free high fat diet + vehicle |
| SA235274 | 329 | Serine/glycine-free high fat diet + vehicle |
| SA235275 | 330 | Serine/glycine-free high fat diet + vehicle |
| SA235276 | 335 | Serine/glycine-free high fat diet + vehicle |
| SA235277 | 334 | Serine/glycine-free high fat diet + vehicle |
| SA235278 | 333 | Serine/glycine-free high fat diet + vehicle |
| SA235279 | 332 | Serine/glycine-free high fat diet + vehicle |
| SA235280 | 336 | Serine/glycine-free high fat diet + vehicle |
| Showing results 1 to 47 of 47 |
Collection:
| Collection ID: | CO002425 |
| Collection Summary: | Paw skin samples were collected using Wollenberger clamps pre-cooled to the temperature of liquid nitrogen and stored at -80 C until analysis. |
| Sample Type: | Paw skin |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR002444 |
| Treatment Summary: | Animals were subjected to 4 different conditions for a period of 24 weeks: 1) low fat diet, 2) high fat diet, 3) serine/glycine-free high fat diet, and 4) serine/glycine-free high fat diet with myriocin. |
Sample Preparation:
| Sampleprep ID: | SP002438 |
| 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 | AN003827 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | Agilent 6460C |
| Column | Spectra 3 μm C8SR 150 × 3 mm inner diameter, Peeke Scientific |
| MS Type | ESI |
| MS instrument type | Triple quadrupole |
| MS instrument name | Agilent 6460 QQQ |
| Ion Mode | POSITIVE |
| Units | normalized ion count/mg protein |
Chromatography:
| Chromatography ID: | CH002832 |
| Chromatography Summary: | The gradient elution program consisted of the following profile: 0 min, 82% B; 3 min, 82% B; 4 min, 90% B, 18 min, 99% B; 25 min, 99%, 27 min, 82% B, 30 min, 82% B. |
| Instrument Name: | Agilent 6460C |
| Column Name: | Spectra 3 μm C8SR 150 × 3 mm inner diameter, Peeke Scientific |
| Column Temperature: | 40 |
| 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: | MS003569 |
| Analysis ID: | AN003827 |
| Instrument Name: | Agilent 6460 QQQ |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | Mass Hunter |
| Ion Mode: | POSITIVE |
