Summary of Study ST003525
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 PR002169. The data can be accessed directly via it's Project DOI: 10.21228/M88236 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 | ST003525 |
| Study Title | Metabolic and Proteomic Divergence is Present in Spleens and Livers from Berkeley Sickle Cell Anemia and beta-thalassemia mice |
| Study Summary | Steady state metabolomics of liver tissue from the Berkeley sickle cell disease (Berk-SS), heterozygous B1/B2 globin gene deletion (HbbTh3/+) a known beta-Thalassemia model, and wildtype (WT, C57/Bl6) murine models. |
| 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 | 2024-10-18 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML, raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2025-04-18 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002169 |
| Project DOI: | doi: 10.21228/M88236 |
| Project Title: | Metabolic and Proteomic Divergence is Present in Spleens and Livers from Berkeley Sickle Cell Anemia and beta-thalassemia mice |
| Project Summary: | Sickle cell disease and beta-thalassemia are two of the most prevalent hemoglobinopathies worldwide. Both occur due to genetic mutations within the HBB gene and are characterized by red blood cell dysfunction, anemia, and end-organ injury. The spleen and liver are the primary organs where erythrophagocytosis, engulfing the red blood cells, occurs in these diseases. Understanding metabolism and protein composition within these tissues can therefore inform the extent of hemolysis and disease progression. Here, we utilized a multi-omics approach to highlight metabolomic and proteomic differences in the spleen and liver, which are responsible for clearing diseased red blood cells in sickle cell and beta-Thalassemia. The Berkley sickle cell disease (Berk-SS), heterozygous B1/B2 globin gene deletion (HbbTh3/+), a known beta-thalassemia model, and wildtype (WT, C57/Bl6) murine models were evaluated in this report. This analysis showed Berk-SS and HbbTh3/+ shared distinct antioxidant and immunosuppressive splenic phenotypes compared to WT mice with divergence in purine metabolism, gluconeogenesis, and glycolysis. In contrast, Berk-SS mice have a distinct liver pro-inflammatory phenotype not shared by HbbTh3/+ or WT mice. Together, these data emphasize that metabolic and proteomic reprogramming of the spleen and livers in Berk-SS and HbbTh3/+mice may be relevant to the individual disease processes. |
| Institute: | University of Colorado Anschutz Medical Campus |
| Laboratory: | Lab of Angelo D'Alessandro in collaboration with lab of David Irwin |
| 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: | SU003654 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Gender: | Not applicable |
| Species Group: | Mammals |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Genotype |
|---|---|---|
| SA387176 | F2-96-19 | Aged Berk |
| SA387177 | F2-96-20 | Aged Berk |
| SA387178 | F2-96-18 | Aged Berk |
| SA387179 | F2-96-17 | Aged Berk |
| SA387180 | F2-96-13 | Aged Berk |
| SA387181 | F2-96-12 | Aged Berk |
| SA387182 | F2-96-11 | Aged Berk |
| SA387183 | F2-96-10 | Aged Berk |
| SA387166 | F2-96-30 | Aged B-Thals |
| SA387167 | F2-96-29 | Aged B-Thals |
| SA387168 | F2-96-28 | Aged B-Thals |
| SA387169 | F2-96-27 | Aged B-Thals |
| SA387170 | F2-96-26 | Aged B-Thals |
| SA387171 | F2-96-25 | Aged B-Thals |
| SA387172 | F2-96-24 | Aged B-Thals |
| SA387173 | F2-96-23 | Aged B-Thals |
| SA387174 | F2-96-22 | Aged B-Thals |
| SA387175 | F2-96-21 | Aged B-Thals |
| SA387184 | F2-96-02 | WT (b-thal negative) |
| SA387185 | F2-96-09 | WT (b-thal negative) |
| SA387186 | F2-96-08 | WT (b-thal negative) |
| SA387187 | F2-96-07 | WT (b-thal negative) |
| SA387188 | F2-96-06 | WT (b-thal negative) |
| SA387189 | F2-96-05 | WT (b-thal negative) |
| SA387190 | F2-96-04 | WT (b-thal negative) |
| SA387191 | F2-96-03 | WT (b-thal negative) |
| SA387192 | F2-96-01 | WT (b-thal negative) |
| Showing results 1 to 27 of 27 |
Collection:
| Collection ID: | CO003647 |
| Collection Summary: | Animals were euthanized via carbon dioxide exposure then exsanguinated via cardiac puncture. Tissues were removed and snap frozen in liquid nitrogen. Frozen tissue was then pulverized on dry ice, weighed, and then placed in 2 mL Eppendorf safe-lock tube in a 4°C room. |
| Sample Type: | Liver |
Treatment:
| Treatment ID: | TR003663 |
| Treatment Summary: | Both mice are commercially available through Jackson Laboratory (strain #000996 for Beta Thal, Strain # 003342 for the Berkeley). No treatment, baseline (steady state) characterization only. |
Sample Preparation:
| Sampleprep ID: | SP003661 |
| Sampleprep Summary: | Metabolites from tissue specimens were extracted at 15 mg per mL using ice cold 5:3:2 methanol:acetonitrile:water (v/v/v) with vigorous vortexing at 4°C followed by centrifugation as described for 10 min at 18,000 g at 4°C and stored at −80°C until analysis. |
| Processing Storage Conditions: | 4℃ |
| Extract Storage: | -80℃ |
Chromatography:
| Chromatography ID: | CH004393 |
| Chromatography Summary: | Negative C18 |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Phenomenex Kinetex C18 (150 x 2.1 mm,1.7 µm) |
| Column Temperature: | 45°C |
| 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: | 450 µL/min |
| Sample Injection: | 6 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: | CH004394 |
| Chromatography Summary: | Positive C18 |
| Instrument Name: | Thermo Vanquish |
| Column Name: | Phenomenex Kinetex C18 (150 x 2.1 mm,1.7 µm) |
| Column Temperature: | 45°C |
| 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: | 450 µL/min |
| Sample Injection: | 6 µL |
| Solvent A: | 100% Water; 0.1% formic acid |
| Solvent B: | 100% Acetonitrile; 0.1% formic acid |
| Chromatography Type: | Reversed phase |
Analysis:
| Analysis ID: | AN005788 |
| Analysis Type: | MS |
| Chromatography ID: | CH004393 |
| Num Factors: | 3 |
| Num Metabolites: | 93 |
| Units: | peak area |
| Analysis ID: | AN005789 |
| Analysis Type: | MS |
| Chromatography ID: | CH004394 |
| Num Factors: | 3 |
| Num Metabolites: | 121 |
| Units: | peak area |
