Summary of Study ST004413
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 PR002788. The data can be accessed directly via it's Project DOI: 10.21228/M88V81 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 | ST004413 |
| Study Title | Plasma metabolomics characterization of mouse models of Down syndrome Dp16 and Dp16-2xIfnrs versus WT mice |
| Study Summary | Metabolomics of plasma at baseline from adult mice comparing WT, the Dp16 Down syndrome mouse model, and Dp16-2xIfnrs, where genome editing has been utilized to correct the dosage of the Ifnr locus within a mouse model of DS. Within this data and lipidomics data collected on the same samples (see study part 1), bile acids were the pathway most elevated in Dp16 animals, with 12 of 17 significantly elevated. Dp16-2xIfnrs animals retained elevated levels of plasma bile acids. |
| Institute | University of Colorado Anschutz Medical Campus |
| Last Name | Haines |
| First Name | Julie |
| Address | 12801 E 17th Ave, Room 1303, Aurora, Colorado, 80045, USA |
| julie.haines@cuanschutz.edu | |
| Phone | 3037243339 |
| Submit Date | 2025-12-02 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzXML, raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2025-12-05 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002788 |
| Project DOI: | doi: 10.21228/M88V81 |
| Project Title: | Altered hepatic metabolism manifests in levels of circulating bile acids in Down Syndrome |
| Project Summary: | Trisomy 21 (T21) gives rise to Down syndrome (DS), the most commonly occurring chromosomal abnormality in humans. T21 affects nearly every organ and tissue system in the body, predisposing individuals with DS to congenital heart defects, autoimmunity, and Alzheimer’s disease, among other co-occurring conditions. Here, using multi-omic analysis of plasma from more than 400 people, we report broad metabolic changes in the population with DS typified by increased bile acid levels and protein signatures of liver dysfunction. In a mouse model of DS, we demonstrate conservation of perturbed bile acid metabolism accompanied by liver pathology. Bulk RNA-sequencing revealed widespread impacts of the Dp16 model on hepatic metabolism and inflammation, while single-cell transcriptomics highlighted cell types associated with these observations. Modulation of dietary fat profoundly impacted gene expression, bile acids, and liver pathology. Overall, these data represent evidence for altered hepatic metabolism in DS that could be modulated by diet. |
| Institute: | University of Colorado Anschutz Medical Campus |
| Laboratory: | Lab of Angelo D'Alessandro in collaboration with labs of Kelly Sullivan and Joaquin Espinosa |
| Last Name: | Haines |
| First Name: | Julie |
| Address: | 12801 E 17th Ave, Room 1303, Aurora, Colorado, 80045, USA |
| Email: | julie.haines@cuanschutz.edu |
| Phone: | 3037243339 |
Subject:
| Subject ID: | SU004572 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Gender: | Male and female |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Chromosome 21 status | Sex | Sample source |
|---|---|---|---|---|
| SA522170 | F2-51-14- | Dp16-2xIfnrs | Female | plasma |
| SA522171 | F2-51-17- | Dp16-2xIfnrs | Female | plasma |
| SA522172 | F2-51-16- | Dp16-2xIfnrs | Female | plasma |
| SA522173 | F2-51-15- | Dp16-2xIfnrs | Female | plasma |
| SA522174 | F2-51-18- | Dp16-2xIfnrs | Female | plasma |
| SA522175 | F2-51-21- | Dp16-2xIfnrs | Male | plasma |
| SA522176 | F2-51-23- | Dp16-2xIfnrs | Male | plasma |
| SA522177 | F2-51-22- | Dp16-2xIfnrs | Male | plasma |
| SA522178 | F2-51-20- | Dp16-2xIfnrs | Male | plasma |
| SA522179 | F2-51-19- | Dp16-2xIfnrs | Male | plasma |
| SA522180 | F2-51-04- | Dp16 | Female | plasma |
| SA522181 | F2-51-03- | Dp16 | Female | plasma |
| SA522182 | F2-51-02- | Dp16 | Female | plasma |
| SA522183 | F2-51-05- | Dp16 | Female | plasma |
| SA522184 | F2-51-06- | Dp16 | Female | plasma |
| SA522185 | F2-51-11- | Dp16 | Male | plasma |
| SA522186 | F2-51-10- | Dp16 | Male | plasma |
| SA522187 | F2-51-08- | Dp16 | Male | plasma |
| SA522188 | F2-51-09- | Dp16 | Male | plasma |
| SA522189 | F2-51-12- | Dp16 | Male | plasma |
| SA522190 | F2-51-13- | Dp16 | Male | plasma |
| SA522191 | F2-51-07- | Dp16 | Male | plasma |
| SA522192 | F2-51-24- | WT | Female | plasma |
| SA522193 | F2-51-26- | WT | Female | plasma |
| SA522194 | F2-51-27- | WT | Female | plasma |
| SA522195 | F2-51-28- | WT | Female | plasma |
| SA522196 | F2-51-25- | WT | Female | plasma |
| SA522197 | F2-51-29- | WT | Male | plasma |
| SA522198 | F2-51-30- | WT | Male | plasma |
| SA522199 | F2-51-31- | WT | Male | plasma |
| SA522200 | F2-51-32- | WT | Male | plasma |
| SA522201 | F2-51-33- | WT | Male | plasma |
| Showing results 1 to 32 of 32 |
Collection:
| Collection ID: | CO004565 |
| Collection Summary: | Blood was collected from WT, Dp16, or Dp16-2xIfnrs mice via a cardiac puncture post euthanasia into lithium heparin tubes (Sarstedt). Plasma was isolated from whole blood via centrifugation for 15 minutes at 700g, then the supernatant was isolated and spun again for 15 minutes at 2100g. |
| Sample Type: | Blood (plasma) |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR004581 |
| Treatment Summary: | No treatments were performed for this lipidomics study. The Dp16-2xIfnrs mouse model was previously described in PMID 37277650. |
Sample Preparation:
| Sampleprep ID: | SP004578 |
| Sampleprep Summary: | Plasma specimens were thawed on ice then a 10 µL aliquot was diluted with 240 µL cold 5:3:2 methanol:acetonitrile:water. Samples were vortexed for 30 minutes at 4℃. Insoluble material was then pelleted by centrifugation (18,000 g, 10 min) then supernatants were collected. |
| Processing Storage Conditions: | 4℃ |
| Extract Storage: | -80℃ |
Chromatography:
| Chromatography ID: | CH005589 |
| Chromatography Summary: | Negative C18 metabolomics |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Phenomenex Kinetex C18 (150 x 2.1 mm, 1.7 µm) |
| Column Temperature: | 45℃ |
| Flow Gradient: | 0-0.5 min 0% B, 0.5-1.1 min 0-100% B, 1.1-2.75 min hold at 100% B, 2.75-3 min 100-0% B, 3-5 min hold at 0% B. |
| Flow Rate: | 0.45 mL/min |
| Sample Injection: | 10 µL |
| Solvent A: | 95% water/5% acetonitrile; 1 mM ammonium acetate |
| Solvent B: | 95% acetonitrile, 5% water, 1 mM ammonium acetate |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH005590 |
| Chromatography Summary: | Positive C18 metabolomics |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Phenomenex Kinetex C18 (150 x 2.1 mm, 1.7 µm) |
| Column Temperature: | 45℃ |
| Flow Gradient: | 0-0.5 min 5% B, 0.5-1.1 min 5-95% B, 1.1-2.75 min hold at 95% B, 2.75-3 min 95-5% B, 3-5 min hold at 5% B |
| Flow Rate: | 0.45 mL/min |
| Sample Injection: | 10 µL |
| Solvent A: | water, 0.1% formic acid |
| Solvent B: | acetonitrile, 0.1% formic acid |
| Chromatography Type: | Reversed phase |
Analysis:
| Analysis ID: | AN007380 |
| Analysis Type: | MS |
| Chromatography ID: | CH005589 |
| Num Factors: | 6 |
| Num Metabolites: | 60 |
| Units: | peak area |
| Analysis ID: | AN007381 |
| Analysis Type: | MS |
| Chromatography ID: | CH005590 |
| Num Factors: | 6 |
| Num Metabolites: | 71 |
| Units: | peak area |
