Summary of Study ST000828
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 PR000219. The data can be accessed directly via it's Project DOI: 10.21228/M8359Z This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST000828 |
| Study Title | Metabolic analysis of Parp1 ko/wt Saline & Bleo Mouse Lung Fiboblasts and Human IPF & Normal Lung Fiboblasts 3 |
| Study Type | MS analysis |
| Study Summary | Glycolysis/TCA/Nucleotide analysis (especially interested in alpha-ketoglutarate) and NAD+ and related metabolite analysis for all samples |
| Institute | University of Michigan |
| Department | Biomedical Research Core Facilities |
| Laboratory | Metabolomics core |
| Last Name | Kachman |
| First Name | Maureen |
| Address | 6300 Brehm Tower, 1000 Wall Street, Ann Arbor, MI 48105-5714 |
| mkachman@med.umich.edu | |
| Phone | (734) 232-8175 |
| Submit Date | 2017-08-02 |
| Num Groups | 6 |
| Total Subjects | 16 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | d |
| Analysis Type Detail | GC-MS/LC-MS |
| Release Date | 2017-10-11 |
| Release Version | 1 |
Select appropriate tab below to view additional metadata details:
Project:
| 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 collagenexpressing 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 |
| Email: | biaohu@med.umich.edu |
| Phone: | 734-7635731 |
Subject:
| Subject ID: | SU001178 |
| Subject Type: | HUMAN |
| Subject Species: | Homo sapiens |
| Taxonomy ID: | 9606 |
| Species Group: | Mammals |
Factors:
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 |
|---|---|---|---|---|---|---|
| SA077749 | S00015476 | Cells | Homo sapiens | N | Y | N |
| SA077750 | S00015478 | Cells | Homo sapiens | N | Y | N |
| SA077751 | S00015479 | Cells | Homo sapiens | N | Y | N |
| SA077752 | S00015475 | Cells | Homo sapiens | N | Y | N |
| SA077753 | S00015477 | Cells | Homo sapiens | N | Y | N |
| SA077754 | S00015482 | Cells | Homo sapiens | Y | N | N |
| SA077755 | S00015483 | Cells | Homo sapiens | Y | N | N |
| SA077756 | S00015484 | Cells | Homo sapiens | Y | N | N |
| SA077757 | S00015481 | Cells | Homo sapiens | Y | N | N |
| SA077758 | S00015480 | Cells | Homo sapiens | Y | N | N |
| SA077759 | S00015469 | Tissues | Mus musculus | N | Y | Y |
| SA077760 | S00015470 | Tissues | Mus musculus | N | Y | Y |
| SA077761 | S00015473 | Tissues | Mus musculus | Y | N | Y |
| SA077762 | S00015472 | Tissues | Mus musculus | Y | N | Y |
| SA077763 | S00015471 | Tissues | Mus musculus | Y | N | Y |
| SA077764 | S00015474 | Tissues | Mus musculus | Y | N | Y |
| Showing results 1 to 16 of 16 |
Collection:
| Collection ID: | CO001172 |
| Collection Summary: | - |
| Sample Type: | Cultured cells |
Treatment:
| 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 | Restek Pinnacle DB Biphenyl (50 x 2.1mm,1.9um,140A) | Restek Pinnacle DB Biphenyl (50 x 2.1mm,1.9um,140A) | Phenomenex Luna NH2 (150 x 1mm,3um) | Agilent DB5-MS (30m × 0.25mm, 0.25um) |
| MS Type | ESI | ESI | ESI | EI |
| MS instrument type | Triple quadrupole | Triple quadrupole | QTOF | Single quadrupole |
| MS instrument name | Agilent 6490A QQQ | Agilent 6490A QQQ | Agilent 6520B QTOF | Agilent 5975 |
| Ion Mode | POSITIVE | POSITIVE | NEGATIVE | POSITIVE |
| Units | counts | uM | uM | uM |
Chromatography:
| Chromatography ID: | CH001312 |
| Instrument Name: | Agilent |
| Column Name: | Restek Pinnacle DB Biphenyl (50 x 2.1mm,1.9um,140A) |
| Column Temperature: | 40 |
| Flow Rate: | 200ul/min |
| Solvent A: | 100% water; 5 mM ammonium acetate,pH 9.9 |
| Solvent B: | 60% acetonitrile/40% isopropanol |
| Chromatography Type: | Phenyl |
| Chromatography ID: | CH001313 |
| Instrument Name: | Agilent |
| Column Name: | Phenomenex Luna NH2 (150 x 1mm,3um) |
| Flow Rate: | 0.075 mL/min |
| Solvent A: | 100% water; 5 mM ammonium acetate, pH 9.9 |
| Solvent B: | 100% acetonitrile |
| 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:
| MS ID: | MS001695 |
| Analysis ID: | AN001834 |
| Instrument Name: | Agilent 6490A QQQ |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | none |
| Ion Mode: | POSITIVE |
| Acquisition Parameters File: | QM033_2mmC18_Ceramide_MRM |
| Analysis Protocol File: | A010_Ceramides.pdf |
| MS ID: | MS001696 |
| Analysis ID: | AN001835 |
| Instrument Name: | Agilent 6490A QQQ |
| Instrument Type: | Triple quadrupole |
| MS Type: | ESI |
| MS Comments: | none |
| Ion Mode: | POSITIVE |
| Acquisition Parameters File: | QM033_2mmC18_Ceramide_MRM |
| Analysis Protocol File: | A010_Ceramides.pdf |
| MS ID: | MS001697 |
| Analysis ID: | AN001836 |
| Instrument Name: | Agilent 6520B QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| MS Comments: | none |
| Ion Mode: | NEGATIVE |
| Acquisition Parameters File: | QTOF-002-HILIC-35min-1mm.m |
| Analysis Protocol File: | A011_Glycolysis-TCA-nucleotides.pdf |
| MS ID: | MS001698 |
| Analysis ID: | AN001837 |
| Instrument Name: | Agilent 5975 |
| Instrument Type: | Single quadrupole |
| MS Type: | EI |
| MS Comments: | none |
| Ion Mode: | POSITIVE |
| Acquisition Parameters File: | ALPHA KETO ACIDS-FULL.M |
| Analysis Protocol File: | A011_Glycolysis-TCA-nucleotides.pdf |
