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.

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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.

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Study IDST002547
Study TitleC57bl/6 mice subjected to either PBS or bleomycin treatment to develop fibrosis
Study SummaryC57bl/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 NameSun
First NameRamon
Address1200 Newell Drive, ARB, Gainesville, FL, 32610, USA
Emailramonsun@ufl.edu
Phone8594733233
Submit Date2023-04-06
Raw Data AvailableYes
Raw Data File Type(s)d
Analysis Type DetailLC-MS
Release Date2023-04-20
Release Version1
Ramon Sun Ramon Sun
https://dx.doi.org/10.21228/M8QF0W
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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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
SA255674WT_Bleo_1Bleomycin
SA255675WT_Bleo_5Bleomycin
SA255676WT_Bleo_4Bleomycin
SA255677WT_Bleo_2Bleomycin
SA255678WT_Bleo_3Bleomycin
SA255679WT_PBS_5PBS
SA255680WT_PBS_4PBS
SA255681WT_PBS_1PBS
SA255682WT_PBS_2PBS
SA255683WT_PBS_3PBS
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
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