Summary of Study ST002547
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 PR001640. The data can be accessed directly via it's Project DOI: 10.21228/M8QF0W 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 | ST002547 |
| Study Title | C57bl/6 mice subjected to either PBS or bleomycin treatment to develop fibrosis |
| Study Summary | C57bl/6 mice subjected to either PBS or bleomycin treatment. By day 21, lung fibrosis will develop. We resected the lung and performed LC-QTOF analysis on small molecule metabolites between the two groups. |
| Institute | University of Florida |
| Last Name | Sun |
| First Name | Ramon |
| Address | 1200 Newell Drive, ARB, Gainesville, FL, 32610, USA |
| ramonsun@ufl.edu | |
| Phone | 8594733233 |
| Submit Date | 2023-04-06 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | d |
| Analysis Type Detail | LC-MS |
| Release Date | 2023-04-20 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| Project ID: | PR001640 |
| Project DOI: | doi: 10.21228/M8QF0W |
| Project Title: | LCMS analysis of WT mice treated with PBS or bleomycin |
| Project Summary: | C57bl/6 mice were treated with either PBS or bleomycin and waited for 21 days to develop fibrosis. Mouse lungs were resected following by LC-QTOF analysis. |
| Institute: | University of Florida |
| Last Name: | Sun |
| First Name: | Ramon |
| Address: | 1200 Newell Drive, ARB, Gainesville, FL, 32610, USA |
| Email: | ramonsun@ufl.edu |
| Phone: | 8594733233 |
Subject:
| Subject ID: | SU002647 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Species Group: | Mammals |
Factors:
Subject type: Mammal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Treatment |
|---|---|---|
| SA255674 | WT_Bleo_1 | Bleomycin |
| SA255675 | WT_Bleo_5 | Bleomycin |
| SA255676 | WT_Bleo_4 | Bleomycin |
| SA255677 | WT_Bleo_2 | Bleomycin |
| SA255678 | WT_Bleo_3 | Bleomycin |
| SA255679 | WT_PBS_5 | PBS |
| SA255680 | WT_PBS_4 | PBS |
| SA255681 | WT_PBS_1 | PBS |
| SA255682 | WT_PBS_2 | PBS |
| SA255683 | WT_PBS_3 | PBS |
| Showing results 1 to 10 of 10 |
Collection:
| Collection ID: | CO002640 |
| Collection Summary: | Approximately 20mg of pulverized, frozen tissue was extracted in 3ml ice-cold 60% acetonitrile by extensively vortexing. Next, 1ml chloroform was added to each sample and samples were mixed by manual shaking followed by centrifuging at 3,200g for 20 minutes at 4°C. The aqueous layer was moved to a new tube and lyophilized. The middle layer containing protein and insoluble material was transferred to a new tube, washed twice with 50% methanol, once with 100% methanol, and briefly dried in a speed-vac. After drying, the insoluble material was hydrolyzed by heating samples in 3N HCl at 95°C for 2 hours. 100% methanol was added to hydrolysate to achieve a final concentration of 50% methanol, samples mixed, centrifuged at 18,000g for 10 min at 4°C, then supernatant dried on a speed vac. |
| Sample Type: | Lung |
| Storage Conditions: | -80℃ |
Treatment:
| Treatment ID: | TR002659 |
| Treatment Summary: | mice were treated with either PBS or bleomycin. |
Sample Preparation:
| Sampleprep ID: | SP002653 |
| Sampleprep Summary: | Approximately 20mg of pulverized, frozen tissue was extracted in 3ml ice-cold 60% acetonitrile by extensively vortexing. Next, 1ml chloroform was added to each sample and samples were mixed by manual shaking followed by centrifuging at 3,200g for 20 minutes at 4°C. The aqueous layer was moved to a new tube and lyophilized. The middle layer containing protein and insoluble material was transferred to a new tube, washed twice with 50% methanol, once with 100% methanol, and briefly dried in a speed-vac. After drying, the insoluble material was hydrolyzed by heating samples in 3N HCl at 95°C for 2 hours. 100% methanol was added to hydrolysate to achieve a final concentration of 50% methanol, samples mixed, centrifuged at 18,000g for 10 min at 4°C, then supernatant dried on a speed vac. |
| Processing Storage Conditions: | -80℃ |
| Extract Storage: | -80℃ |
Chromatography:
| Chromatography ID: | CH003108 |
| Instrument Name: | Agilent 1290 Infinity |
| Column Name: | Agilent InfinityLab Poroshell 120 EC-C8 (150 x 2.1mm,2.7um) |
| Column Temperature: | 40 |
| Flow Gradient: | 0-15 min linear ramp 90%B to 30%B, 15-18 min isocratic flow of 30%B, 18-19 min linear ramp from 30%B to 90%B, and 19-27 min column regeneration with isocratic flow of 90%B |
| Flow Rate: | 0.25ml/min |
| Solvent A: | 100% water; 10mM ammonium acetate |
| Solvent B: | 100% acetonitrile |
| Chromatography Type: | HILIC |
Analysis:
| Analysis ID: | AN004194 |
| Analysis Type: | MS |
| Chromatography ID: | CH003108 |
| Num Factors: | 2 |
| Num Metabolites: | 23 |
| Units: | normalized abundance |
