Summary of Study ST000275

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench,, where it has been assigned Project ID PR000219. The data can be accessed directly via it's Project DOI: 10.21228/M8359Z This work is supported by NIH grant, U2C- DK119886.


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Study IDST000275
Study TitleMetabolic analysis of Parp1 ko/wt Saline & Bleo Mouse Lung Fiboblasts and Human IPF & Normal Lung Fiboblasts (Part 2)
Study TypeGlycolysis/TCA/Nucleotide analysis. Ceramide analysis for parp1 wild type lung tissue/Cells after saline or bleomycin treatment.
Study SummaryThis study is a part of series performed for the same researcher through pilot/feasibility grant program, so the publication is relevant reference for other studies (ST000143, ST000183) This specific experiment is a small pilot study to establish method performance, it includes four biological replicas of identical cell cultures after the identical treatment and a single tissue sample.
University of Michigan
DepartmentDeaprtment of Pathology
LaboratorySem H. Phan
Last NameHu
First NameBiao
AddressAnn Arbor, MI
Submit Date2014-06-11
Num Groups1
Total Subjects5
Study Comments
Raw Data File Type(s)d
Analysis Type DetailLC-MS
Release Date2016-01-13
Release Version1
Biao Hu Biao Hu application/zip

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Project ID:PR000219
Project DOI:doi: 10.21228/M8359Z
Project Title:Metabolic analysis of Parp1 ko/wt Saline & Bleo Mouse Lung Fibroblasts and Human IPF & Normal Lung Fibroblasts
Project Type:Glycolysis/TCA/Nucleotide analysis (tissue/cells)
Project Summary:Hedgehog signaling plays important roles in cell development and differentiation. In this study, the ability of Sonic Hedgehog (SHH) to induce myofibroblast differentiation was analyzed in isolated human lung fibroblasts, and its in vivo significance was evaluated in rodent bleomycin-induced pulmonary fibrosis. The results showed that SHH could induce myofibroblast differentiation in human lung fibroblasts in a Smo- and Gli1-dependent manner. Gel shift analysis, chromatin immunoprecipitation assay, and site-directed mutagenesis revealed that a Gli1 binding consensus in the ?-SMA gene promoter was important for mediating SHH-induced myofibroblast differentiation. Analysis of Hedgehog reemergence in vivo revealed that of all three Hedgehog isoforms, only SHH was significantly induced in bleomycin-injured lung along with Gli1. The induction of SHH was only noted in epithelial cells, and its expression was undetectable in lung fibroblasts or macrophages. Transforming growth factor (TGF)-? induced SHH significantly in cultured alveolar epithelial cells, whereas SHH induced TGF-? in lung fibroblasts. Pulmonary fibrosis and ?-smooth muscle actin (?-SMA) expression were significantly reduced in mice that were Smo deficient only in type I collagen–expressing cells. Thus, the reemergence of SHH in epithelial cells could result in induction of myofibroblast differentiation in a Smo-dependent manner and subsequent Gli1 activation of the ?-SMA promoter.
Institute:University of Michigan
Department:Deaprtment of Pathology
Laboratory:Sem H. Phan
Last Name:Hu
First Name:Biao
Address:Ann Arbor, MI


Subject ID:SU000295
Subject Type:Animal
Subject Species:Mus musculus
Taxonomy ID:10090
Species Group:Mammal


Subject type: Animal; Subject species: Mus musculus (Factor headings shown in green)

mb_sample_id local_sample_id Sample type Genetic background bleomycin
SA012214S00014997Cell culture B6 wt yes
SA012215S00014994Cell culture B6 wt yes
SA012216S00014996Cell culture B6 wt yes
SA012217S00014995Cell culture B6 wt yes
SA012218S00014998Tissue B6 wt yes
Showing results 1 to 5 of 5


Collection ID:CO000289
Collection Summary:-
Sample Type:Cells


Treatment ID:TR000309

Sample Preparation:

Sampleprep ID:SP000303
Sampleprep Summary:-
Sampleprep Protocol Filename:Gly-TCA-nucleotides_analysis_protocol-2015-03-09.docx

Combined analysis:

Analysis ID AN000438 AN000439
Analysis type MS MS
Chromatography type HILIC HILIC
Chromatography system Agilent 1260 Agilent 1260
Column Phenomenex Luna NH2 (150 x 1mm,3um) Phenomenex Luna NH2 (150 x 1mm,3um)
MS instrument type QTOF QTOF
MS instrument name Agilent 6530 QTOF Agilent 6530 QTOF
Units µM (500µl of extraction solvent)


Chromatography ID:CH000307
Methods ID:AQM020
Methods Filename:QTOF-002-HILIC-35min-1mm.m
Instrument Name:Agilent 1260
Column Name:Phenomenex Luna NH2 (150 x 1mm,3um)
Chromatography Type:HILIC


MS ID:MS000379
Analysis ID:AN000438
Instrument Name:Agilent 6530 QTOF
Instrument Type:QTOF
Acquisition Parameters File:Column1_solv1_jetstream+_grad9.m
Processing Parameters File:EX00310-MassHunterQuant-GlyTCA-DataAnalysis-LCMS-Method.m
MS ID:MS000380
Analysis ID:AN000439
Instrument Name:Agilent 6530 QTOF
Instrument Type:QTOF
Acquisition Parameters File:ALPHA_KETO_ACIDS-FULL.M
Processing Parameters File:EX00310-MassHunterQuant-GlyTCA-DataAnalysis-GCMS-Method.m