Summary of Study ST001607

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 PR001032. The data can be accessed directly via it's Project DOI: 10.21228/M89D63 This work is supported by NIH grant, U2C- DK119886.

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Study IDST001607
Study TitleGenetic background shapes phenotypic response to diet for adiposity in the Collaborative Cross
Study TypeDiet challenge
Study SummaryDefined as chronic excessive accumulation of adiposity, obesity results from long-term imbalance between energy intake and expenditure. The mechanisms behind how caloric imbalance occurs are complex and influenced by numerous biological and environmental factors, especially genetics and diet. Population-based diet recommendations have had limited success partly due to the wide variation in physiological responses across individuals when they consume the same diet. Thus, it is necessary to broaden our understanding of how individual genetics and diet interact relative to the development of obesity for improving weight loss treatment. To determine how consumption of diets with different macronutrient composition alter adiposity and other obesity-related traits in a genetically diverse population, we analyzed body composition, metabolic rate, clinical blood chemistries, and circulating metabolites in 22 strains of mice from the Collaborative Cross (CC), a highly diverse recombinant inbred mouse population, before and after 8 weeks of feeding either a high protein or high fat high sucrose diet. At both baseline and post-diet, adiposity and other obesity-related traits exhibited a broad range of phenotypic variation based on CC strain; diet-induced changes in adiposity and other traits also depended largely on CC strain. In addition to estimating heritability at baseline, we also quantified the effect size of diet for each trait, which varied by trait and experimental diet. Our findings identified CC strains prone to developing obesity, demonstrate the genotypic and phenotypic diversity of the CC for studying complex traits, and highlight the importance of accounting for genetic differences when making dietary recommendations.
Institute
USDA
DepartmentObesity and metabolism research unit
LaboratoryBennett's Lab
Last NameBennett
First NameBrian
Address430 West Health Sciences Dr. Davis, Ca, 95616
Emailbrian.bennett@usda.gov
Phone(530) 754-4417
Submit Date2020-11-05
Total Subjects202
Num Females202
Raw Data AvailableYes
Raw Data File Type(s)wiff
Analysis Type DetailLC-MS
Release Date2020-12-31
Release Version1
Brian Bennett Brian Bennett
https://dx.doi.org/10.21228/M89D63
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR001032
Project DOI:doi: 10.21228/M89D63
Project Title:Genetic background shapes phenotypic response to diet for adiposity in the Collaborative Cross
Project Summary:Defined as chronic excessive accumulation of adiposity, obesity results from long-term imbalance between energy intake and expenditure. The mechanisms behind how caloric imbalance occurs are complex and influenced by numerous biological and environmental factors, especially genetics and diet. Population-based diet recommendations have had limited success partly due to the wide variation in physiological responses across individuals when they consume the same diet. Thus, it is necessary to broaden our understanding of how individual genetics and diet interact relative to the development of obesity for improving weight loss treatment. To determine how consumption of diets with different macronutrient composition alter adiposity and other obesity-related traits in a genetically diverse population, we analyzed body composition, metabolic rate, clinical blood chemistries, and circulating metabolites in 22 strains of mice from the Collaborative Cross (CC), a highly diverse recombinant inbred mouse population, before and after 8 weeks of feeding either a high protein or high fat high sucrose diet. At both baseline and post-diet, adiposity and other obesity-related traits exhibited a broad range of phenotypic variation based on CC strain; diet-induced changes in adiposity and other traits also depended largely on CC strain. In addition to estimating heritability at baseline, we also quantified the effect size of diet for each trait, which varied by trait and experimental diet. Our findings identified CC strains prone to developing obesity, demonstrate the genotypic and phenotypic diversity of the CC for studying complex traits, and highlight the importance of accounting for genetic differences when making dietary recommendations.
Institute:USDA
Department:Obesity and metabolism research unit
Laboratory:Bennett's Lab
Last Name:Bennett
First Name:Brian
Address:430 West Health Sciences Drive, DAVIS, CA, 95616, USA
Email:brian.bennett@usda.gov
Phone:(530) 754-4417

Subject:

Subject ID:SU001684
Subject Type:Mammal
Subject Species:Mus musculus
Taxonomy ID:10090
Genotype Strain:22 strains from the Collaborative Cross (CC) mouse panel
Gender:Female

Factors:

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

mb_sample_id local_sample_id Diet TimePoint
SA136047P 238AIN-76A baseline
SA136048P 237AIN-76A baseline
SA136049P 240AIN-76A baseline
SA136050P 242AIN-76A baseline
SA136051P 243AIN-76A baseline
SA136052P 236AIN-76A baseline
SA136053P 234AIN-76A baseline
SA136054P 228AIN-76A baseline
SA136055P 230AIN-76A baseline
SA136056P 231AIN-76A baseline
SA136057P 233AIN-76A baseline
SA136058P 245AIN-76A baseline
SA136059P 249AIN-76A baseline
SA136060P 261AIN-76A baseline
SA136061P 260AIN-76A baseline
SA136062P 263AIN-76A baseline
SA136063P 264AIN-76A baseline
SA136064P 266AIN-76A baseline
SA136065P 258AIN-76A baseline
SA136066P 257AIN-76A baseline
SA136067P 227AIN-76A baseline
SA136068P 251AIN-76A baseline
SA136069P 252AIN-76A baseline
SA136070P 254AIN-76A baseline
SA136071P 246AIN-76A baseline
SA136072P 224AIN-76A baseline
SA136073P 197AIN-76A baseline
SA136074P 195AIN-76A baseline
SA136075P 198AIN-76A baseline
SA136076P 200AIN-76A baseline
SA136077P 201AIN-76A baseline
SA136078P 191AIN-76A baseline
SA136079P 189AIN-76A baseline
SA136080P 183AIN-76A baseline
SA136081P 185AIN-76A baseline
SA136082P 186AIN-76A baseline
SA136083P 188AIN-76A baseline
SA136084P 203AIN-76A baseline
SA136085P 204AIN-76A baseline
SA136086P 216AIN-76A baseline
SA136087P 218AIN-76A baseline
SA136088P 219AIN-76A baseline
SA136089P 221AIN-76A baseline
SA136090P 215AIN-76A baseline
SA136091P 213AIN-76A baseline
SA136092P 207AIN-76A baseline
SA136093P 209AIN-76A baseline
SA136094P 210AIN-76A baseline
SA136095P 212AIN-76A baseline
SA136096P 267AIN-76A baseline
SA136097P 269AIN-76A baseline
SA136098P 119AIN-76A baseline
SA136099P 116AIN-76A baseline
SA136100P 120AIN-76A baseline
SA136101P 126AIN-76A baseline
SA136102P 137AIN-76A baseline
SA136103P 114AIN-76A baseline
SA136104P 104AIN-76A baseline
SA136105P 92AIN-76A baseline
SA136106P 93AIN-76A baseline
SA136107P 96AIN-76A baseline
SA136108P 98AIN-76A baseline
SA136109P 164AIN-76A baseline
SA136110P 176AIN-76A baseline
SA136111P 255AIN-76A baseline
SA136112P 275AIN-76A baseline
SA136113P 2AIN-76A baseline
SA136114P 320AIN-76A baseline
SA136115P 248AIN-76A baseline
SA136116P 225AIN-76A baseline
SA136117P 192AIN-76A baseline
SA136118P 194AIN-76A baseline
SA136119P 206AIN-76A baseline
SA136120P 222AIN-76A baseline
SA136121P 87AIN-76A baseline
SA136122P 86AIN-76A baseline
SA136123P 284AIN-76A baseline
SA136124P 282AIN-76A baseline
SA136125P 285AIN-76A baseline
SA136126P 302AIN-76A baseline
SA136127P 303AIN-76A baseline
SA136128P 281AIN-76A baseline
SA136129P 279AIN-76A baseline
SA136130P 270AIN-76A baseline
SA136131P 272AIN-76A baseline
SA136132P 273AIN-76A baseline
SA136133P 278AIN-76A baseline
SA136134P 305AIN-76A baseline
SA136135P 306AIN-76A baseline
SA136136P 344AIN-76A baseline
SA136137P 352AIN-76A baseline
SA136138P 353AIN-76A baseline
SA136139P 74AIN-76A baseline
SA136140P 343AIN-76A baseline
SA136141P 338AIN-76A baseline
SA136142P 321AIN-76A baseline
SA136143P 334AIN-76A baseline
SA136144P 335AIN-76A baseline
SA136145P 337AIN-76A baseline
SA136146P 182AIN-76A baseline
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Collection:

Collection ID:CO001677
Collection Summary:Blood was drawn from the mice after a 2-week acclimation period (baseline) and after 8 weeks (postdiet) on either a high protein (H-Protein) or high fat high sucrose (H-Sucrose). Blood samples were collected via retro-orbital bleed with heparinized capillary tubes into EDTA tubes, placed on ice, and centrifuged at 6000 rpm for 10 minutes at 4°C for plasma collection. Plasma was then transferred to 1.5 ml Eppendorf tubes and stored at -80°C.
Sample Type:Blood (plasma)
Collection Method:retro-orbital bleed with heparinized capillary tubes
Storage Conditions:Described in summary
Collection Vials:EDTA tubes

Treatment:

Treatment ID:TR001697
Treatment Summary:Approximately 4-5 mice were assigned to either the high protein (H-Protein) or high fat high sucrose (H-Sucrose) diet per strain for 8 weeks.
Treatment:Diet challenge

Sample Preparation:

Sampleprep ID:SP001690
Sampleprep Summary:Baseline and post-diet circulating trimethylamine N-oxide (TMAO), choline, phosphocholine, betaine, and carnitine were quantified using liquid chromatography–mass spectrometry (LC-MS) methods described by Wang et al. (2014) with modifications (Wang et al., 2014. Analytical Biochemistry 455 (June 2014): 35–40. https://doi.org/10.1016/j.ab.2014.03.016.). Briefly, samples (20 µl plasma) were aliquoted to a 2 ml Eppendorf tube and mixed with 80 µl of 5 µM surrogate standard comprised of deuterated analytes in methanol. Standards ranging from 0 µM to 100 µM of non-deuterated analytes in methanol were run in order to establish analyte standard curves. Two-fold serial dilutions of a 100 µM stock solution in methanol was used to make 13 standards. To prepare standards for sample quantification, 80 µl of 5 µM SSTD and 20 µl of each standard were aliquoted directly to the glass inserts in HPLC vials and briefly vortexed. Prior to acquisition, samples and standards were vortexed for 30 seconds and centrifuged at 18,000 g at 10°C for 10 min. Supernatant (5 µl) was transferred to 150 µl glass inserts in High Performance Liquid Chromatography (HPLC) vials and analyzed by injection onto a silica column (150 by 2 mm, 3 um particle Silica (2) with 100 Angstrom; Catalog #00F-41620-B0, Phenomenex, Torrance, CA) at a flow rate of 0.25 ml/min using a Waters Acquity UPLC (Waters, Milford, MA) interfaced with an API 4000 Q-TRAP mass spectrometer (AB SCIEX, Framingham, MA). A discontinuous gradient was generated to resolve the analytes by mixing solvent A (0.1% acetic acid in water) with solvent B (0.1% acetic acid in methanol) at different ratios starting from 2% B linearly to 15% B over 5 min, then linearly to 100% B to 6.25 min, then hold to 8 min, and then back to 2% B at 6.25 min and held until 10 min.
Sampleprep Protocol Filename:phoebeyam_SP_protocol.pdf

Combined analysis:

Analysis ID AN002640
Analysis type MS
Chromatography type Normal phase
Chromatography system Waters Acquity UPLC
Column Luna Silica (150 x 2mm,3m)
MS Type ESI
MS instrument type Triple quadrupole
MS instrument name ABI Sciex API 4000 QTrap
Ion Mode POSITIVE
Units micromolar

Chromatography:

Chromatography ID:CH001950
Chromatography Comments:Phenomenex Luna 3 µm Silica (2) 100 Å, LC Column 150 x 2 mm
Instrument Name:Waters Acquity UPLC
Column Name:Luna Silica (150 x 2mm,3m)
Column Temperature:Room Temperature
Flow Rate:0.25 ml/min
Sample Injection:5 µL
Solvent A:100% water; 0.1% acetic acid
Solvent B:100% methanol; 0.1% acetic acid
Weak Wash Solvent Name:70% water, 20% methanol, 10% 2-propanol
Strong Wash Solvent Name:50:50 Acetonitrile:Methanol
Chromatography Type:Normal phase

MS:

MS ID:MS002452
Analysis ID:AN002640
Instrument Name:ABI Sciex API 4000 QTrap
Instrument Type:Triple quadrupole
MS Type:ESI
MS Comments:Analytes were monitored using electrospray ionization in positive-ion mode with multiple reaction monitoring (MRM) of precursor and characteristic production transitions as shown in MS_protocol.pdf. The parameters for the ion monitoring were as follows: spray voltage, 4.5 kV; curtain gas, 15; GS1, 60; GS2, 50; CAD gas, medium; Nitrogen (99.95% purity) was used as the source and collision gas. Integration and quantification of values was done using Analyst 1.6.2 software (AB SCIEX, Singapore). Standard linearity was calculated using linear regression model. Please see LC_protocol.pdf and MS_protocol.pdf for additional details.
Ion Mode:POSITIVE
Analysis Protocol File:phoebeyam_LC_protocol.pdf
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