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 |
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℃ |
Combined analysis:
| Analysis ID | AN004194 |
|---|---|
| Analysis type | MS |
| Chromatography type | HILIC |
| Chromatography system | Agilent 1290 Infinity |
| Column | Agilent InfinityLab Poroshell 120 EC-C8 (150 x 2.1mm,2.7um) |
| MS Type | ESI |
| MS instrument type | QTOF |
| MS instrument name | Agilent 6545 QTOF |
| Ion Mode | NEGATIVE |
| Units | normalized abundance |
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 |
MS:
| MS ID: | MS003941 |
| Analysis ID: | AN004194 |
| Instrument Name: | Agilent 6545 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | Metabolites were measured using an Agilent 6545 quadrapole-time of flight mass spectrometer (MS) coupled to an Agilent 1290 Infinity II UHPLC. Individual samples and standards were acquired with full scan MS in negative mode. Peaks for the deprotonated [M-H]¬- ions were extracted and integrated using Agilent Qualitative Analysis software. |
| Ion Mode: | NEGATIVE |
