Summary of Study ST000143

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 IDST000143
Study TitleMetabolic analysis of Normal Mouse Lung Fiboblasts with/without TGFbeta treatment (Part 1)
Study TypeGlycolysis/TCA/Nucleotide analysis (tissue/cells)
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, see the project for this study. 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
DepartmentBiomedical Research Core Facilities
LaboratoryMetabolomics core
Last NameKachman
First NameMaureen
Address6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Submit Date2015-03-13
Num Groups4
Total Subjects21
Raw Data AvailableYes
Raw Data File Type(s)d
Uploaded File Size5.2 G
Analysis Type DetailGC-MS/LC-MS
Release Date2015-03-13
Release Version1
Maureen Kachman Maureen Kachman application/zip

Select appropriate tab below to view additional metadata details:


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:SU000162
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 Genotype Treatment
SA007974S00014569parp1 ko bleomycin
SA007975S00014578parp1 ko bleomycin
SA007976S00014579parp1 ko bleomycin
SA007977S00014580parp1 ko bleomycin
SA007978S00014559parp1 ko bleomycin
SA007979S00014568parp1 ko bleomycin
SA007980S00014557parp1 ko bleomycin
SA007981S00014558parp1 ko bleomycin
SA007982S00014577parp1 ko saline
SA007983S00014555parp1 ko saline
SA007984S00014575parp1 ko saline
SA007985S00014576parp1 ko saline
SA007986S00014554parp1 ko saline
SA007987S00014556parp1 ko saline
SA007988S00014567parp1 ko saline
SA007989S00014566parp1 ko saline
SA007990S00014564parp1 wt bleomycin
SA007991S00014563parp1 wt bleomycin
SA007992S00014574parp1 wt bleomycin
SA007993S00014572parp1 wt bleomycin
SA007994S00014573parp1 wt bleomycin
SA007995S00014565parp1 wt bleomycin
SA007996S00014583parp1 wt saline
SA007997S00014581parp1 wt saline
SA007998S00014582parp1 wt saline
SA007999S00014571parp1 wt saline
SA008000S00014561parp1 wt saline
SA008001S00014562parp1 wt saline
SA008002S00014570parp1 wt saline
SA008003S00014560parp1 wt saline
Showing results 1 to 30 of 30


Collection ID:CO000148
Collection Summary:-
Sample Type:Tissues


Treatment ID:TR000167

Sample Preparation:

Sampleprep ID:SP000162
Sampleprep Summary:-
Sampleprep Protocol Filename:Gly-TCA-nucleotides_analysis_protocol-2015-03-09.docx

Combined analysis:

Analysis ID AN000226 AN000227
Analysis type MS MS
Chromatography type HILIC GC
Chromatography system Agilent 1260 Agilent 7890A
Column Phenomenex Luna NH2 (150 x 1mm,3um) Agilent DB5-MS (30m × 0.25mm, 0.25um)
MS instrument type QTOF Single quadrupole
MS instrument name Agilent 6520 QTOF Agilent 5975C
Units uM uM


Chromatography ID:CH000157
Methods ID:AQM020
Instrument Name:Agilent 1260
Column Name:Phenomenex Luna NH2 (150 x 1mm,3um)
Chromatography Type:HILIC
Chromatography ID:CH001298
Methods ID:AQM011
Instrument Name:Agilent 7890A
Column Name:Agilent DB5-MS (30m × 0.25mm, 0.25um)
Chromatography Type:GC


MS ID:MS000177
Analysis ID:AN000226
Instrument Name:Agilent 6520 QTOF
Instrument Type:QTOF
Acquisition Parameters
Processing Parameters
MS ID:MS000178
Analysis ID:AN000227
Instrument Name:Agilent 5975C
Instrument Type:Single quadrupole
MS Type:EI
Tube Lens Voltage:Positive
Acquisition Parameters
Processing Parameters