Summary of Study ST000295

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 IDST000295
Study TitleMetabolic analysis of Human and Mouse Lung Fiboblasts
Study SummaryMetabolic analysis of Parp1 ko/wt Saline & Bleo Mouse Lung Fiboblasts and Human Normal Lung Fiboblasts with TGFbeta and Fizz2 treatment. Glycolysis/TCA/Nucleotide analysis and NAD+ and related metabolite analysis for all samples
University of Michigan
DepartmentBiomedical Research Core Facilities
LaboratoryMetabolomics core
Last NameKachman
First NameMaureen
Address6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714
Phone(734) 232-8175
Submit Date2014-10-16
Num Groups6
Total Subjects35
Raw Data AvailableYes
Raw Data File Type(s)d
Analysis Type DetailLC-MS
Release Date2016-06-18
Release Version1
Maureen Kachman Maureen Kachman 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:SU000315
Subject Type:Human/animal
Subject Species:Mus musculus;Homo sapiens
Taxonomy ID:10090;9606
Species Group:Mammal


Subject type: Human/animal; Subject species: Mus musculus;Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Species Genotype Treatment
SA013430S00016620Homo sapiens WT Fizz2
SA013431S00016622Homo sapiens WT Fizz2
SA013432S00016621Homo sapiens WT Fizz2
SA013433S00016623Homo sapiens WT Fizz2
SA013434S00016624Homo sapiens WT Fizz2
SA013435S00016613Homo sapiens WT None
SA013436S00016612Homo sapiens WT None
SA013437S00016610Homo sapiens WT None
SA013438S00016614Homo sapiens WT None
SA013439S00016611Homo sapiens WT None
SA013440S00016618Homo sapiens WT TGFb
SA013441S00016619Homo sapiens WT TGFb
SA013442S00016615Homo sapiens WT TGFb
SA013443S00016617Homo sapiens WT TGFb
SA013444S00016616Homo sapiens WT TGFb
SA013445S00016609Mus musculus PARP1 knockout bleomycin
SA013446S00016608Mus musculus PARP1 knockout bleomycin
SA013447S00016607Mus musculus PARP1 knockout bleomycin
SA013448S00016606Mus musculus PARP1 knockout bleomycin
SA013449S00016605Mus musculus PARP1 knockout bleomycin
SA013450S00016601Mus musculus PARP1 knockout saline
SA013451S00016600Mus musculus PARP1 knockout saline
SA013452S00016602Mus musculus PARP1 knockout saline
SA013453S00016603Mus musculus PARP1 knockout saline
SA013454S00016604Mus musculus PARP1 knockout saline
SA013455S00016596Mus musculus WT bleomycin
SA013456S00016595Mus musculus WT bleomycin
SA013457S00016597Mus musculus WT bleomycin
SA013458S00016599Mus musculus WT bleomycin
SA013459S00016598Mus musculus WT bleomycin
SA013460S00016591Mus musculus WT saline
SA013461S00016592Mus musculus WT saline
SA013462S00016594Mus musculus WT saline
SA013463S00016590Mus musculus WT saline
SA013464S00016593Mus musculus WT saline
Showing results 1 to 35 of 35


Collection ID:CO000309
Collection Summary:-
Sample Type:Cells


Treatment ID:TR000329
Treatment Summary:-

Sample Preparation:

Sampleprep ID:SP000323
Sampleprep Summary:-
Sampleprep Protocol Filename:Glycolysis-TCA-nucleotides-20150324.docx

Combined analysis:

Analysis ID AN000472 AN000473
Analysis type MS MS
Chromatography type Reversed phase HILIC
Chromatography system Agilent 1260 Agilent 1260
Column Waters XBridge C18 (50 x 2.1mm,3um) Phenomenex Luna NH2 (150 x 1mm,3um)
MS instrument type Triple quadrupole QTOF
MS instrument name Agilent 6410A QQQ Agilent 6520 QTOF
Units ng/ug protein pmol/µg protein


Chromatography ID:CH000335
Methods ID:DQM0152
Methods Filename:Ceramides-20150305.docx
Instrument Name:Agilent 1260
Column Name:Waters XBridge C18 (50 x 2.1mm,3um)
Chromatography Type:Reversed phase
Chromatography ID:CH000336
Methods ID:DQM0010
Methods Filename:Glycolysis-TCA-nucleotides-20150324.docx
Instrument Name:Agilent 1260
Column Name:Phenomenex Luna NH2 (150 x 1mm,3um)
Chromatography Type:HILIC


MS ID:MS000412
Analysis ID:AN000472
Instrument Name:Agilent 6410A QQQ
Instrument Type:Triple quadrupole
MS Comments:Ceramides MS(+)
Analysis Protocol File:Ceramides-20150305.docx
MS ID:MS000413
Analysis ID:AN000473
Instrument Name:Agilent 6520 QTOF
Instrument Type:QTOF
MS Comments:TCA MS(-)
Analysis Protocol File:Glycolysis-TCA-nucleotides-20150324.docx