Summary of Study ST002344
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 | ST002344 |
| Study Title | The impact of dietary serine/glycine restriction and myriocin treatment on hepatic sphingolipid diversity during prolonged high fat diet feeding. |
| Study Summary | We wanted to determine the impact of dietary serine/glycine restriction on hepatic sphingolipidome. |
| 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 | 80 |
| Num Males | 80 |
| 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: | SU002433 |
| 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 |
|---|---|---|
| SA235281 | L_155 | High fat diet + myriocin |
| SA235282 | L_154 | High fat diet + myriocin |
| SA235283 | L_142 | High fat diet + myriocin |
| SA235284 | L_156 | High fat diet + myriocin |
| SA235285 | L_152 | High fat diet + myriocin |
| SA235286 | L_153 | High fat diet + myriocin |
| SA235287 | L_157 | High fat diet + myriocin |
| SA235288 | L_160 | High fat diet + myriocin |
| SA235289 | L_159 | High fat diet + myriocin |
| SA235290 | L_158 | High fat diet + myriocin |
| SA235291 | L_145 | High fat diet + vehicle |
| SA235292 | L_144 | High fat diet + vehicle |
| SA235293 | L_143 | High fat diet + vehicle |
| SA235294 | L_146 | High fat diet + vehicle |
| SA235295 | L_149 | High fat diet + vehicle |
| SA235296 | L_151 | High fat diet + vehicle |
| SA235297 | L_150 | High fat diet + vehicle |
| SA235298 | L_131 | High fat diet + vehicle |
| SA235299 | L_147 | High fat diet + vehicle |
| SA235300 | L_141 | High fat diet + vehicle |
| SA235301 | L_117 | Low fat diet + myriocin |
| SA235302 | L_118 | Low fat diet + myriocin |
| SA235303 | L_119 | Low fat diet + myriocin |
| SA235304 | L_116 | Low fat diet + myriocin |
| SA235305 | L_115 | Low fat diet + myriocin |
| SA235306 | L_111 | Low fat diet + myriocin |
| SA235307 | L_113 | Low fat diet + myriocin |
| SA235308 | L_114 | Low fat diet + myriocin |
| SA235309 | L_120 | Low fat diet + myriocin |
| SA235310 | L_112 | Low fat diet + myriocin |
| SA235311 | L_106 | Low fat diet + vehicle |
| SA235312 | L_108 | Low fat diet + vehicle |
| SA235313 | L_109 | Low fat diet + vehicle |
| SA235314 | L_105 | Low fat diet + vehicle |
| SA235315 | L_104 | Low fat diet + vehicle |
| SA235316 | L_102 | Low fat diet + vehicle |
| SA235317 | L_103 | Low fat diet + vehicle |
| SA235318 | L_110 | Low fat diet + vehicle |
| SA235319 | L_107 | Low fat diet + vehicle |
| SA235320 | L_101 | Low fat diet + vehicle |
| SA235321 | L_175 | Serine/glycine-free high fat diet + myriocin |
| SA235322 | L_174 | Serine/glycine-free high fat diet + myriocin |
| SA235323 | L_173 | Serine/glycine-free high fat diet + myriocin |
| SA235324 | L_176 | Serine/glycine-free high fat diet + myriocin |
| SA235325 | L_172 | Serine/glycine-free high fat diet + myriocin |
| SA235326 | L_177 | Serine/glycine-free high fat diet + myriocin |
| SA235327 | L_180 | Serine/glycine-free high fat diet + myriocin |
| SA235328 | L_179 | Serine/glycine-free high fat diet + myriocin |
| SA235329 | L_178 | Serine/glycine-free high fat diet + myriocin |
| SA235330 | L_165 | Serine/glycine-free high fat diet + vehicle |
| SA235331 | L_163 | Serine/glycine-free high fat diet + vehicle |
| SA235332 | L_166 | Serine/glycine-free high fat diet + vehicle |
| SA235333 | L_164 | Serine/glycine-free high fat diet + vehicle |
| SA235334 | L_169 | Serine/glycine-free high fat diet + vehicle |
| SA235335 | L_125 | Serine/glycine-free high fat diet + vehicle |
| SA235336 | L_170 | Serine/glycine-free high fat diet + vehicle |
| SA235337 | L_139 | Serine/glycine-free high fat diet + vehicle |
| SA235338 | L_167 | Serine/glycine-free high fat diet + vehicle |
| SA235339 | L_161 | Serine/glycine-free high fat diet + vehicle |
| SA235340 | L_140 | Serine/glycine-free low fat diet + myriocin |
| SA235341 | L_133 | Serine/glycine-free low fat diet + myriocin |
| SA235342 | L_148 | Serine/glycine-free low fat diet + myriocin |
| SA235343 | L_132 | Serine/glycine-free low fat diet + myriocin |
| SA235344 | L_168 | Serine/glycine-free low fat diet + myriocin |
| SA235345 | L_134 | Serine/glycine-free low fat diet + myriocin |
| SA235346 | L_137 | Serine/glycine-free low fat diet + myriocin |
| SA235347 | L_135 | Serine/glycine-free low fat diet + myriocin |
| SA235348 | L_136 | Serine/glycine-free low fat diet + myriocin |
| SA235349 | L_128 | Serine/glycine-free low fat diet + vehicle |
| SA235350 | L_129 | Serine/glycine-free low fat diet + vehicle |
| SA235351 | L_130 | Serine/glycine-free low fat diet + vehicle |
| SA235352 | L_127 | Serine/glycine-free low fat diet + vehicle |
| SA235353 | L_122 | Serine/glycine-free low fat diet + vehicle |
| SA235354 | L_123 | Serine/glycine-free low fat diet + vehicle |
| SA235355 | L_121 | Serine/glycine-free low fat diet + vehicle |
| SA235356 | L_124 | Serine/glycine-free low fat diet + vehicle |
| SA235357 | L_162 | Serine/glycine-free low fat diet + vehicle |
| SA235358 | L_126 | Serine/glycine-free low fat diet + vehicle |
| Showing results 1 to 78 of 78 |
Collection:
| Collection ID: | CO002426 |
| 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: | TR002445 |
| Treatment Summary: | Animals were subjected to 8 different dietary interventions: 1. Low fat diet + vehicle 2. Low fat diet + myriocin 3. Serine/glycine-free low fat diet + vehicle 4. Serine/glycine-free low fat diet + myriocin 5. High fat diet + vehicle 6. High fat fat diet + myriocin 7. Serine/glycine-free high fat diet + vehicle 7. Serine/glycine-free high fat diet + myriocin |
Sample Preparation:
| Sampleprep ID: | SP002439 |
| 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 | AN003828 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | 6460C |
| Column | Peeke Scientific Spectra 3um C8SR (150 x 3mm) |
| 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: | CH002833 |
| 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: | 6460C |
| Column Name: | Peeke Scientific Spectra 3um C8SR (150 x 3mm) |
| 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: | MS003570 |
| Analysis ID: | AN003828 |
| Instrument Name: | Agilent 6460 QQQ |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | Mass Hunter |
| Ion Mode: | POSITIVE |
