Summary of study ST000828

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 IDST000828
Study TitleMetabolic analysis of Parp1 ko/wt Saline & Bleo Mouse Lung Fiboblasts and Human IPF & Normal Lung Fiboblasts 3
Study TypeMS analysis
Study SummaryGlycolysis/TCA/Nucleotide analysis (especially interested in alpha-ketoglutarate) 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 Date2017-08-02
Num Groups6
Total Subjects16
Raw Data AvailableYes
Analysis Type DetailGC/LC-MS
Release Date2017-10-11
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:SU001178
Subject Type:HUMAN
Subject Species:Homo sapiens
Taxonomy ID:9606


Subject type: HUMAN; Subject species: Homo sapiens (Factor headings shown in green)

mb_sample_id local_sample_id Sample type Species bleomycin/IPF saline/HLF wt B6
SA077749S00015476Cells Homo sapiens N Y N
SA077750S00015478Cells Homo sapiens N Y N
SA077751S00015479Cells Homo sapiens N Y N
SA077752S00015475Cells Homo sapiens N Y N
SA077753S00015477Cells Homo sapiens N Y N
SA077754S00015482Cells Homo sapiens Y N N
SA077755S00015483Cells Homo sapiens Y N N
SA077756S00015484Cells Homo sapiens Y N N
SA077757S00015481Cells Homo sapiens Y N N
SA077758S00015480Cells Homo sapiens Y N N
SA077759S00015469Tissues Mus musculus N Y Y
SA077760S00015470Tissues Mus musculus N Y Y
SA077761S00015473Tissues Mus musculus Y N Y
SA077762S00015472Tissues Mus musculus Y N Y
SA077763S00015471Tissues Mus musculus Y N Y
SA077764S00015474Tissues Mus musculus Y N Y
Showing results 1 to 16 of 16


Collection ID:CO001172
Collection Summary:-
Sample Type:Cultured cells


Treatment ID:TR001193
Treatment Summary:-

Sample Preparation:

Sampleprep ID:SP001186
Sampleprep Summary:-
Sampleprep Protocol Filename:A010-Ceramides.pdf

Combined analysis:

Analysis ID AN001834 AN001835 AN001836 AN001837
Analysis type MS MS MS MS
Chromatography type Phenyl Phenyl HILIC GC
Chromatography system Agilent Agilent Agilent Agilent GC_7890N
Column Pinnacle DB Biphenyl, 140A, 1.9mkm, 2.1mm X 50mm (Restek) Pinnacle DB Biphenyl, 140A, 1.9mkm, 2.1mm X 50mm (Restek) Phenomenex Luna NH2 (150 x 1mm, 3um) Agilent DB5-MS (30m × 0.25mm, 0.25um)
MS instrument type Triple quadrupole Triple quadrupole QTOF Single quadrupole
MS instrument name Agilent 6490A QQQ Agilent 6490A QQQ Agilent 6520B QTOF Agilent 5975
Units counts uM uM uM


Chromatography ID:CH001312
Instrument Name:Agilent
Column Name:Pinnacle DB Biphenyl, 140A, 1.9mkm, 2.1mm X 50mm (Restek)
Chromatography Type:Phenyl
Chromatography ID:CH001313
Instrument Name:Agilent
Column Name:Phenomenex Luna NH2 (150 x 1mm, 3um)
Chromatography Type:HILIC
Chromatography ID:CH001314
Instrument Name:Agilent GC_7890N
Column Name:Agilent DB5-MS (30m × 0.25mm, 0.25um)
Chromatography Type:GC


MS ID:MS001695
Analysis ID:AN001834
Instrument Name:Agilent 6490A QQQ
Instrument Type:Triple quadrupole
MS Comments:none
MS ID:MS001696
Analysis ID:AN001835
Instrument Name:Agilent 6490A QQQ
Instrument Type:Triple quadrupole
MS Comments:none
MS ID:MS001697
Analysis ID:AN001836
Instrument Name:Agilent 6520B QTOF
Instrument Type:QTOF
MS Comments:none
MS ID:MS001698
Analysis ID:AN001837
Instrument Name:Agilent 5975
Instrument Type:Single quadrupole
MS Type:EI
MS Comments:none