Summary of Study ST003580
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 PR002210. The data can be accessed directly via it's Project DOI: 10.21228/M8ZG0D 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 | ST003580 |
| Study Title | Metabolomic profiling of normal and fibrotic mouse lungs |
| Study Type | MS quantitative analysis |
| Study Summary | C57BL/6 wild-type (8-10-week old) mice were i.t. injected with saline or bleomycin. 1 to 4 weeks after injection, bronchoalveolar lavage fluid (BALF) was collected with a saline solution. The BALFs samples were processed for untargeted metabolomics. |
| Institute | University of Alabama, Birmingham |
| Department | Medicine |
| Laboratory | Gang Liu Laboratory |
| Last Name | Cui |
| First Name | Huachun |
| Address | BMR2 274, 901 19th St S, Birmingham, AL 35294 |
| hcui@uab.edu | |
| Phone | 205-975-8931 |
| Submit Date | 2024-11-12 |
| Num Groups | 4 |
| Total Subjects | 24 |
| Num Males | 24 |
| Analysis Type Detail | LC-MS |
| Release Date | 2024-12-02 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR002210 |
| Project DOI: | doi: 10.21228/M8ZG0D |
| Project Title: | Metabolomic profiling of normal and fibrotic mouse lungs |
| Project Type: | MS quantitative analysis |
| Project Summary: | Idiopathic pulmonary fibrosis (IPF) is a devastating interstitial lung disease with unclear etiology and limited efficacious treatments. Dysregulated cellular metabolism has been shown to participate in several pathologic processes, however, its role in the pathogenesis of pulmonary fibrosis remains largely unknown. In this study, we used mouse model of bleomycin-induced lung fibrosis and global metabolomics to examine the metabolites differences in control mouse lungs and fibrotic mouse lungs. This metabolomic profiling provides further insights into the pathogenesis of pulmonary injury and fibrosis. |
| Institute: | University of Alabama, Birmingham |
| Department: | Medicine |
| Laboratory: | Gang Liu Laboratory |
| Last Name: | Cui |
| First Name: | Huachun |
| Address: | BMR2 274, 901 19th St S, Birmingham, AL 35294 |
| Email: | hcui@uab.edu |
| Phone: | 205-975-8931 |
Subject:
| Subject ID: | SU003709 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Genotype Strain: | C57BL/6 |
| Age Or Age Range: | 8-10 weeks |
| Gender: | Male |
| Species Group: | Mammals |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | Genotype | Treatment |
|---|---|---|---|---|
| SA389994 | BALF-BLM-1w-1 | BALF | Wild-type | Bleomycin 1 week |
| SA389995 | BALF-BLM-1w-2 | BALF | Wild-type | Bleomycin 1 week |
| SA389996 | BALF-BLM-1w-3 | BALF | Wild-type | Bleomycin 1 week |
| SA389997 | BALF-BLM-1w-4 | BALF | Wild-type | Bleomycin 1 week |
| SA389998 | BALF-BLM-1w-5 | BALF | Wild-type | Bleomycin 1 week |
| SA389999 | BALF-BLM-1w-6 | BALF | Wild-type | Bleomycin 1 week |
| SA390000 | BALF-BLM-2w-2 | BALF | Wild-type | Bleomycin 2 week |
| SA390001 | BALF-BLM-2w-6 | BALF | Wild-type | Bleomycin 2 week |
| SA390002 | BALF-BLM-2w-5 | BALF | Wild-type | Bleomycin 2 week |
| SA390003 | BALF-BLM-2w-4 | BALF | Wild-type | Bleomycin 2 week |
| SA390004 | BALF-BLM-2w-3 | BALF | Wild-type | Bleomycin 2 week |
| SA390005 | BALF-BLM-2w-1 | BALF | Wild-type | Bleomycin 2 week |
| SA390006 | BALF-BLM-4w-2 | BALF | Wild-type | Bleomycin 4 week |
| SA390007 | BALF-BLM-4w-1 | BALF | Wild-type | Bleomycin 4 week |
| SA390008 | BALF-BLM-4w-3 | BALF | Wild-type | Bleomycin 4 week |
| SA390009 | BALF-BLM-4w-4 | BALF | Wild-type | Bleomycin 4 week |
| SA390010 | BALF-BLM-4w-5 | BALF | Wild-type | Bleomycin 4 week |
| SA390011 | BALF-BLM-4w-6 | BALF | Wild-type | Bleomycin 4 week |
| SA390012 | BALF-Control-2 | BALF | Wild-type | Control (saline) |
| SA390013 | BALF-Control-6 | BALF | Wild-type | Control (saline) |
| SA390014 | BALF-Control-5 | BALF | Wild-type | Control (saline) |
| SA390015 | BALF-Control-4 | BALF | Wild-type | Control (saline) |
| SA390016 | BALF-Control-3 | BALF | Wild-type | Control (saline) |
| SA390017 | BALF-Control-1 | BALF | Wild-type | Control (saline) |
| Showing results 1 to 24 of 24 |
Collection:
| Collection ID: | CO003702 |
| Collection Summary: | Mouse bronchoalveolar lavage fluid (BALF) was collected with 1.2 mL saline |
| Sample Type: | Lung |
| Collection Method: | bronchoalveolar lavage |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR003718 |
| Treatment Summary: | Bronchoalveolar lavage fluids were collected from saline or bleomycin injured mouse lungs |
Sample Preparation:
| Sampleprep ID: | SP003716 |
| Sampleprep Summary: | BALFs were collected with 1.2 mL saline. Samples were centrifuged at 500 x g to deplete cells and debris, flash frozen and stored at -80°C until processed. Samples were prepared using the automated MicroLab STAR® system from Hamilton Company. Several recovery standards were added prior to the first step in the extraction process for QC purposes. To remove protein, dissociate small molecules bound to protein or trapped in the precipitated protein matrix, and to recover chemically diverse metabolites, proteins were precipitated with methanol under vigorous shaking for 2 min (Glen Mills GenoGrinder 2000) followed by centrifugation. The resulting extract was divided into five fractions: two for analysis by two separate reverse phase (RP)/UPLC-MS/MS methods with positive ion mode electrospray ionization (ESI), one for analysis by RP/UPLC-MS/MS with negative ion mode ESI, one for analysis by HILIC/UPLC-MS/MS with negative ion mode ESI, and one sample was reserved for backup. Samples were placed briefly on a TurboVap® (Zymark) to remove the organic solvent. The sample extracts were stored overnight under nitrogen before preparation for analysis. |
| Processing Storage Conditions: | -80℃ |
Combined analysis:
| Analysis ID | AN005879 | AN005880 | AN005881 | AN005882 |
|---|---|---|---|---|
| Analysis type | MS | MS | MS | MS |
| Chromatography type | Reversed phase | Reversed phase | Reversed phase | HILIC |
| Chromatography system | Waters Acquity | Waters Acquity | Waters Acquity | Waters Acquity |
| Column | Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um) | Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um) | Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7μm) | Waters ACQUITY UPLC BEH Amide (150 x 2.1mm,1.7μm) |
| MS Type | ESI | ESI | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap | Orbitrap | Orbitrap |
| MS instrument name | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap | Thermo Q Exactive Orbitrap |
| Ion Mode | POSITIVE | POSITIVE | NEGATIVE | NEGATIVE |
| Units | Peak Area | Peak Area | Peak Area | Peak Area |
Chromatography:
| Chromatography ID: | CH004465 |
| Chromatography Summary: | Low pH polar (LC/MS Pos early) |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um) |
| Column Temperature: | 40-50 |
| Flow Gradient: | Linear gradient from 5% B to 80% B over 3.35 minutes |
| Flow Rate: | 0.35 mL/min |
| Solvent A: | 100% water; 0.1% formic acid; 0.05% Pentafluoropropionic Acid, pH ~2.5 |
| Solvent B: | 100% methanol; 0.1% formic acid; 0.05% Pentafluoropropionic Acid, pH ~2.5 |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH004466 |
| Chromatography Summary: | Low pH Lipophilic (LC/MS Pos late) |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7um) |
| Column Temperature: | 40-50 |
| Flow Gradient: | Linear gradient from 40% B to 99.5% B over 1.0 minute, hold 99.5% B for 2.4 minutes. |
| Flow Rate: | 0.60 mL/min |
| Solvent A: | 100% water; 0.1% formic acid; 0.05% Pentafluoropropionic Acid, pH ~2.5 |
| Solvent B: | 50% methanol/50% acetonitrile; 0.1% formic acid; 0.05% Pentafluoropropionic Acid, pH ~2.5 |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH004467 |
| Chromatography Summary: | High pH (LC/MS Neg) |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters ACQUITY UPLC BEH C18 (100 x 2.1mm,1.7μm) |
| Column Temperature: | 40-50 |
| Flow Gradient: | Linear gradient from 0.5 to 70% B over 4.0 minutes, then rapid gradient to 99%B in 0.5 minutes. |
| Flow Rate: | 0.35 mL/min |
| Solvent A: | 100% water; 6.5 mM ammonium bicarbonate, pH 8 |
| Solvent B: | 95% methanol/5% water; 6.5 mM ammonium bicarbonate |
| Chromatography Type: | Reversed phase |
| Chromatography ID: | CH004468 |
| Chromatography Summary: | HILIC (LC/MS Polar) |
| Instrument Name: | Waters Acquity |
| Column Name: | Waters ACQUITY UPLC BEH Amide (150 x 2.1mm,1.7μm) |
| Column Temperature: | 40-50 |
| Flow Gradient: | Linear gradient from 5% B to 50% B in 3.5 minutes, then linear gradient from 50% B to 95% B in 2 minutes minutes. |
| Flow Rate: | 0.50 mL/min |
| Solvent A: | 15% water/5% methanol/80% acetonitrile; 10 mM ammonium formate, (effective pH 10.16 with ammonium hydroxide) |
| Solvent B: | 50% water/50% acetonitrile; 10 mM ammonium formate, (effective pH 10.60 with ammonium hydroxide) |
| Chromatography Type: | HILIC |
MS:
| MS ID: | MS005599 |
| Analysis ID: | AN005879 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Metabolon (LC/MS Pos early) |
| Ion Mode: | POSITIVE |
| MS ID: | MS005600 |
| Analysis ID: | AN005880 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Metabolon (LC/MS Pos late) |
| Ion Mode: | POSITIVE |
| MS ID: | MS005601 |
| Analysis ID: | AN005881 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Metabolon (LC/MS Neg) |
| Ion Mode: | NEGATIVE |
| MS ID: | MS005602 |
| Analysis ID: | AN005882 |
| Instrument Name: | Thermo Q Exactive Orbitrap |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Metabolon (LC/MS Polar) |
| Ion Mode: | NEGATIVE |
