Summary of Study ST004414

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.

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 IDST004414
Study TitlePlasma metabolomics characterization of the impact of high fat diet on the Down syndrome mouse model Dp16 versus WT mice
Study SummaryWT or Dp16 mice were fed control or high-fat diet for 8 weeks beginning at 28 days of age. Plasma was obtained at sacrifice and metabolites and oxylipins were measured by mass spectrometry. HFD-fed Dp16 animals revealed a strong dysregulation in bile acid metabolism not seen in HFD-fed WT animals.
Institute
University of Colorado Anschutz Medical Campus
Last NameHaines
First NameJulie
Address12801 E 17th Ave, Room 1303, Aurora, Colorado, 80045, USA
Emailjulie.haines@cuanschutz.edu
Phone3037243339
Submit Date2025-12-02
Raw Data AvailableYes
Raw Data File Type(s)mzXML, raw(Thermo)
Analysis Type DetailLC-MS
Release Date2025-12-05
Release Version1
Julie Haines Julie Haines
https://dx.doi.org/10.21228/M88V81
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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:SU004573
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 Genotype Diet Sample source
SA52220217Dp16 Control Plasma
SA52220346Dp16 Control Plasma
SA52220444Dp16 Control Plasma
SA52220542Dp16 Control Plasma
SA5222066Dp16 Control Plasma
SA5222077Dp16 Control Plasma
SA52220822Dp16 Control Plasma
SA52220921Dp16 Control Plasma
SA52221020Dp16 Control Plasma
SA52221118Dp16 Control Plasma
SA52221236Dp16 HFD Plasma
SA52221335Dp16 HFD Plasma
SA52221432Dp16 HFD Plasma
SA52221530Dp16 HFD Plasma
SA52221627Dp16 HFD Plasma
SA5222171Dp16 HFD Plasma
SA52221812Dp16 HFD Plasma
SA5222195Dp16 HFD Plasma
SA5222203Dp16 HFD Plasma
SA52222114Dp16 HFD Plasma
SA52222213Dp16 HFD Plasma
SA5222239Dp16 HFD Plasma
SA52222410Dp16 HFD Plasma
SA52222519WT Control Plasma
SA52222640WT Control Plasma
SA52222741WT Control Plasma
SA52222824WT Control Plasma
SA52222943WT Control Plasma
SA52223037WT Control Plasma
SA52223125WT Control Plasma
SA52223245WT Control Plasma
SA52223323WT Control Plasma
SA5222348WT Control Plasma
SA5222354WT HFD Plasma
SA52223639WT HFD Plasma
SA52223716WT HFD Plasma
SA52223838WT HFD Plasma
SA52223934WT HFD Plasma
SA52224031WT HFD Plasma
SA52224111WT HFD Plasma
SA52224229WT HFD Plasma
SA52224328WT HFD Plasma
SA52224426WT HFD Plasma
SA5222452WT HFD Plasma
SA52224615WT HFD Plasma
SA52224733WT HFD Plasma
Showing results 1 to 46 of 46

Collection:

Collection ID:CO004566
Collection Summary:Blood was collected from 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:TR004582
Treatment Summary:WT or Dp16 mice had ad libitum access to either a low-fat diet (6 kcal% fat, D12450J, Research Diets, New Brunswick, NJ) or high-fat diet (60 kcal% fat, D12492, Research Diets) for 8 weeks, beginning at 28 days of age.

Sample Preparation:

Sampleprep ID:SP004579
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 degrees. 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:CH005591
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:CH005592
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
  
Chromatography ID:CH005593
Chromatography Summary:Negative C18 oxylipins
Instrument Name:Thermo Vanquish
Column Name:Waters ACQUITY UPLC BEH C18 (100 x 2.1 mm, 1.7 µm)
Column Temperature:60℃
Flow Gradient:0-0.5 min 0% B, 0.5-1 min 0-25% B, 1-2.5 min increase to 40% B, 2.5-2.6 min increase to 55% B, 2.6-4.5 min increase to 70% B, 4.5-4.6 min increase to 100% B, 4.6-6 min hold at 100% B, 6-6.1 min decrease to 0% B, 6.1-7 min hold at 0% B
Flow Rate:0.35 ml/min
Solvent A:20% water/80% acetonitrile; 5 mM ammonium acetate
Solvent B:80% isopropanol/15% acetonitrile/5% water; 5 mM ammonium acetate
Chromatography Type:Reversed phase

Analysis:

Analysis ID:AN007382
Analysis Type:MS
Chromatography ID:CH005591
Num Factors:4
Num Metabolites:96
Units:peak area
  
Analysis ID:AN007383
Analysis Type:MS
Chromatography ID:CH005592
Num Factors:4
Num Metabolites:76
Units:peak area
  
Analysis ID:AN007384
Analysis Type:MS
Chromatography ID:CH005593
Num Factors:4
Num Metabolites:17
Units:peak area
  logo