Summary of Study ST003273

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.

Perform statistical analysis  |  Show all samples  |  Show named metabolites  |  Download named metabolite data  
Download mwTab file (text)   |  Download mwTab file(JSON)   |  Download data files (Contains raw data)
Study IDST003273
Study TitleImpact of serine supplementation following treatment with serine/glycine-depleted diet: Plasma
Study SummaryWe analyzed metabolites in the retina, choroid/RPE, plasma, and paw skin from mice that were previously on control or serine/glycine-depleted diet and then switched over to a control or serine-supplemented diet. This study contains plasma samples.
Institute
Salk Institute for Biological Studies
DepartmentMolecular and Cell Biology Laboratory
LaboratoryMetallo Lab
Last NameLim
First NameEsther
Address10010 N Torrey Pines Rd
Emailewlim2024@gmail.com
Phone(858) 453-4100
Submit Date2024-06-15
Num Groups4
Total Subjects20
Num Males20
Raw Data AvailableYes
Raw Data File Type(s)d
Analysis Type DetailLC-MS
Release Date2024-07-10
Release Version1
Esther Lim Esther Lim
https://dx.doi.org/10.21228/M86V58
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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:SU003393
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:

Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id local_sample_id Treatment Sample source
SA354479LMRI_DietRev_plasma_20J5Plasma Control rescue Mouse plasma
SA354480LMRI_DietRev_plasma_20J4Plasma Control rescue Mouse plasma
SA354481LMRI_DietRev_plasma_20J3Plasma Control rescue Mouse plasma
SA354482LMRI_DietRev_plasma_20J2Plasma Control rescue Mouse plasma
SA354483LMRI_DietRev_plasma_20J1Plasma Control rescue Mouse plasma
SA354489LMRI_DietRev_plasma_20B3Plasma control Mouse plasma
SA354490LMRI_DietRev_plasma_20C3Plasma control Mouse plasma
SA354491LMRI_DietRev_plasma_20C2Plasma control Mouse plasma
SA354492LMRI_DietRev_plasma_20B4Plasma control Mouse plasma
SA354493LMRI_DietRev_plasma_20B2Plasma control Mouse plasma
SA354484LMRI_DietRev_plasma_20H5Plasma High serine rescue Mouse plasma
SA354485LMRI_DietRev_plasma_20H1Plasma High serine rescue Mouse plasma
SA354486LMRI_DietRev_plasma_20H4Plasma High serine rescue Mouse plasma
SA354487LMRI_DietRev_plasma_20H3Plasma High serine rescue Mouse plasma
SA354488LMRI_DietRev_plasma_20H2Plasma High serine rescue Mouse plasma
SA354474LMRI_DietRev_plasma_20D1Plasma -SG diet Mouse plasma
SA354475LMRI_DietRev_plasma_20D2Plasma -SG diet Mouse plasma
SA354476LMRI_DietRev_plasma_20D3Plasma -SG diet Mouse plasma
SA354477LMRI_DietRev_plasma_20D4Plasma -SG diet Mouse plasma
SA354478LMRI_DietRev_plasma_20D5Plasma -SG diet Mouse plasma
Showing results 1 to 20 of 20

Collection:

Collection ID:CO003386
Collection Summary:Blood samples collected into EDTA-coated microvette tubes. EDTA microvettes were spun at 2,000g at 4 °C for 5 min to obtain plasma, and samples stored at −80°C until analysis.
Sample Type:Blood (plasma)

Treatment:

Treatment ID:TR003402
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:SP003400
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 AN005359
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/L

Chromatography:

Chromatography ID:CH004060
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℃
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:MS005089
Analysis ID:AN005359
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
  logo