Summary of Study ST003269
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 PR002030. The data can be accessed directly via it's Project DOI: 10.21228/M86V58 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 | ST003269 |
| Study Title | WT and PHGDH(+/-) mice fed control or -SG diet: Retina samples |
| Study Summary | We analyzed metabolites in the retina, choroid/RPE, and plasma from WT and PHGDH heterozygous mice that were fed either a control or serine/glycine-deprived diet. This study contains retina samples. |
| Institute | Salk Institute for Biological Studies |
| Last Name | Lim |
| First Name | Esther |
| Address | 10010 N Torrey Pines Rd, La Jolla, CA, 92037, USA |
| ewlim2024@gmail.com | |
| Phone | (858) 453-4100 |
| Submit Date | 2024-06-15 |
| Num Groups | 4 |
| Total Subjects | 20 |
| Num Males | 20 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | d |
| Analysis Type Detail | LC-MS |
| Release Date | 2024-07-10 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002030 |
| Project DOI: | doi: 10.21228/M86V58 |
| Project Title: | Metabolomic changes in mouse tissues following modulation of serine through the diet |
| Project Summary: | We analyzed metabolites in the retina, choroid/RPE, and plasma from WT and PHGDH heterozygous mice that were fed either a control or serine/glycine-deprived diet. Additionally, we also analyzed metabolites from the retina, choroid/RPE, paw skin, and plasma from mice that were previously on either a control or serine/glycine-deprived diet and then switched back to a control or serine-supplemented diet. |
| Institute: | Salk Institute |
| Department: | Molecular and Cell Biology Laboratory |
| Laboratory: | Metallo Lab |
| Last Name: | Lim |
| First Name: | Esther |
| Address: | 10010 N Torrey Pines Rd, La Jolla, CA, 92037, USA |
| Email: | ewlim2024@gmail.com |
| Phone: | (858) 453-4100 |
| Funding Source: | R01CA234245 |
Subject:
| Subject ID: | SU003389 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Genotype Strain: | C57BL/6J |
| Age Or Age Range: | 12-16 weeks |
| Weight Or Weight Range: | 20-30g |
| Gender: | Male |
| Animal Animal Supplier: | Phgdh floxed/floxed from the Shigeki Furuya Lab; E2a-Cre mice from 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 | Genotype | Treatment | Sample source |
|---|---|---|---|---|
| SA354374 | R_L3B | PHGDH+/- | Control diet | Mouse retina |
| SA354375 | R_L3E | PHGDH+/- | Control diet | Mouse retina |
| SA354376 | R_L3D | PHGDH+/- | Control diet | Mouse retina |
| SA354377 | R_L3C | PHGDH+/- | Control diet | Mouse retina |
| SA354378 | R_L3A | PHGDH+/- | Control diet | Mouse retina |
| SA354379 | R_L4B | PHGDH+/- | Serine/glycine-depleted diet | Mouse retina |
| SA354380 | R_L4A | PHGDH+/- | Serine/glycine-depleted diet | Mouse retina |
| SA354381 | R_L4C | PHGDH+/- | Serine/glycine-depleted diet | Mouse retina |
| SA354382 | R_L4D | PHGDH+/- | Serine/glycine-depleted diet | Mouse retina |
| SA354383 | R_L4E | PHGDH+/- | Serine/glycine-depleted diet | Mouse retina |
| SA354384 | R_L7E | Wild-type | Control diet | Mouse retina |
| SA354385 | R_L7B | Wild-type | Control diet | Mouse retina |
| SA354386 | R_L7D | Wild-type | Control diet | Mouse retina |
| SA354387 | R_L7C | Wild-type | Control diet | Mouse retina |
| SA354388 | R_L7A | Wild-type | Control diet | Mouse retina |
| SA354389 | R_L8B | Wild-type | Serine/glycine-depleted diet | Mouse retina |
| SA354390 | R_L8C | Wild-type | Serine/glycine-depleted diet | Mouse retina |
| SA354391 | R_L8D | Wild-type | Serine/glycine-depleted diet | Mouse retina |
| SA354392 | R_L8E | Wild-type | Serine/glycine-depleted diet | Mouse retina |
| SA354393 | R_L8A | Wild-type | Serine/glycine-depleted diet | Mouse retina |
| Showing results 1 to 20 of 20 |
Collection:
| Collection ID: | CO003382 |
| 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: | Retina |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR003398 |
| Treatment Summary: | In this cohort, there were wildtype (WT) and PHGDH heterozygous (PHGDH +/-) mice that were put on either a control amino acid or serine/glycine-depleted diet. |
Sample Preparation:
| Sampleprep ID: | SP003396 |
| 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 | AN005355 |
|---|---|
| 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: | CH004056 |
| 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: | MS005085 |
| Analysis ID: | AN005355 |
| 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 |
