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MB Sample ID: SA354422
| Local Sample ID: | LMRI_DietRev_Skin_20J2 |
| Subject ID: | SU003391 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Genotype Strain: | C57BL/6J |
| Age Or Age Range: | 12-16 months |
| Weight Or Weight Range: | 25-45 g |
| Gender: | Male |
| Animal Animal Supplier: | The Scripps Research Institute Vivarium |
| Animal Housing: | 5/cage |
| Animal Light Cycle: | 12h dark/12 h light |
| Animal Feed: | Special diets; see group labeling |
| Animal Water: | Ad libitum |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU003391 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Genotype Strain: | C57BL/6J |
| Age Or Age Range: | 12-16 months |
| Weight Or Weight Range: | 25-45 g |
| Gender: | Male |
| Animal Animal Supplier: | The Scripps Research Institute Vivarium |
| Animal Housing: | 5/cage |
| Animal Light Cycle: | 12h dark/12 h light |
| Animal Feed: | Special diets; see group labeling |
| Animal Water: | Ad libitum |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| LMRI_DietRev_Skin_20J2 | SA354422 | FL041362 | Paw skin Control rescue | Treatment |
| LMRI_DietRev_Skin_20J2 | SA354422 | FL041362 | Mouse paw skin | Sample source |
Collection:
| Collection ID: | CO003384 |
| Collection Summary: | Tissues were collected using Wollenberger clamps pre-cooled to the temperature of liquid nitrogen and stored at -80°C until analysis |
| Sample Type: | Skin |
Treatment:
| Treatment ID: | TR003400 |
| Treatment Summary: | Mice were fed control or serine/glycine-depleted (-SG) diet for 12 months. After 12 months, a subset of the mice that were on the -SG diet were switched back to either the control or supplemented diet for 4 months. |
Sample Preparation:
| Sampleprep ID: | SP003398 |
| Sampleprep Summary: | For sphingolipid extraction from retina and choroid/RPE, frozen tissue was homogenized with a ball mill (Retsch Mixer Mill MM 400) at 30 Hz for 3 min in 500 μl of −20°C methanol, 400 μl of ice-cold saline, and 100 μl of ice-cold MilliQ water, spiked with deuterated internal standards as described earlier. The mixture was then transferred into a 2-ml Eppendorf tube containing 1 ml of chloroform. The tubes were vortexed for 5 min and centrifuged at 16,000g at 4°C for 5 min. The lower 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 and resuspended in 50 μl of 0.2% formic acid and 1 mM ammonium formate in methanol. Last, the tubes were sonicated in a bath sonicator for 10 min and spun at 16,000g for 10 min at 4°C. For plasma, 50 μl of plasma was extracted with 500 μl of −20°C methanol, 400 μl of saline, and 100 μl of water spiked with deuterated internal standards. Chloroform (1 ml) was then added to the tubes. The tubes were vortexed for 5 min and centrifuged at 16,000g at 4°C for 5 min. The lower organic phase was collected, and 2 μl of formic acid was added to the remaining polar phase, which was reextracted with 1 ml of chloroform. Combined organic phases were dried and resuspended in 100 μl of 0.2% formic acid and 1 mM ammonium formate in methanol. Next, the tubes were sonicated in a bath sonicator for 10 min and spun at 16,000g for 10 min at 4°C |
| Processing Storage Conditions: | Room temperature |
| Extract Storage: | 4℃ |
Combined analysis:
| Analysis ID | AN005357 |
|---|---|
| Analysis type | MS |
| Chromatography type | Reversed phase |
| Chromatography system | Agilent 6460 |
| Column | Peeke Scientific Spectra C8SR (150 x 3.0 mm, 3μm) |
| MS Type | ESI |
| MS instrument type | Triple quadrupole |
| MS instrument name | Agilent 6460 QQQ |
| Ion Mode | POSITIVE |
| Units | Normalized ion count/mg of protein |
Chromatography:
| Chromatography ID: | CH004058 |
| 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 6460 |
| 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; and 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 |
MS:
| MS ID: | MS005087 |
| Analysis ID: | AN005357 |
| Instrument Name: | Agilent 6460 QQQ |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | Software: Agilent MassHunter Sphingolipid species were analyzed by selective reaction monitoring of the transition from precursor to product ions at associated optimized collision energies, and fragmentor voltages are provided elsewhere (https://doi.org/10.1007/978-1-60761-322-0_22). The m/z values of the precursor and product ions are provided in the metabolite metadata section. |
| Ion Mode: | POSITIVE |
