Summary of Study ST000275
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 | ST000275 |
| Study Title | Metabolic analysis of Parp1 ko/wt Saline & Bleo Mouse Lung Fiboblasts and Human IPF & Normal Lung Fiboblasts (Part 2) |
| Study Type | Glycolysis/TCA/Nucleotide analysis. Ceramide analysis for parp1 wild type lung tissue/Cells after saline or bleomycin treatment. |
| Study Summary | This 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. |
| Institute | University of Michigan |
| Department | Deaprtment of Pathology |
| Laboratory | Sem H. Phan |
| Last Name | Hu |
| First Name | Biao |
| Address | Ann Arbor, MI |
| biaohu@med.umich.edu | |
| Phone | 734-7635731 |
| Submit Date | 2014-06-11 |
| Num Groups | 1 |
| Total Subjects | 5 |
| Study Comments | http://www.atsjournals.org/doi/full/10.1165/rcmb.2014-0108OC#.Vmb9VVWrRhE |
| Raw Data File Type(s) | d |
| Analysis Type Detail | LC-MS |
| Release Date | 2016-01-13 |
| 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: | SU000295 |
| Subject Type: | Animal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Species Group: | Mammal |
Factors:
Subject type: Animal; Subject species: Mus musculus (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample type | Genetic background | bleomycin |
|---|---|---|---|---|
| SA012214 | S00014997 | Cell culture | B6 wt | yes |
| SA012215 | S00014994 | Cell culture | B6 wt | yes |
| SA012216 | S00014996 | Cell culture | B6 wt | yes |
| SA012217 | S00014995 | Cell culture | B6 wt | yes |
| SA012218 | S00014998 | Tissue | B6 wt | yes |
| Showing results 1 to 5 of 5 |
Collection:
| Collection ID: | CO000289 |
| Collection Summary: | - |
| Sample Type: | Cells |
Treatment:
| 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 Type | ESI | ESI |
| MS instrument type | QTOF | QTOF |
| MS instrument name | Agilent 6530 QTOF | Agilent 6530 QTOF |
| Ion Mode | NEGATIVE | POSITIVE |
| Units | µM (500µl of extraction solvent) |
Chromatography:
| 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:
| MS ID: | MS000379 |
| Analysis ID: | AN000438 |
| Instrument Name: | Agilent 6530 QTOF |
| Instrument Type: | QTOF |
| MS Type: | ESI |
| Ion Mode: | NEGATIVE |
| 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 |
| MS Type: | ESI |
| Ion Mode: | POSITIVE |
| Acquisition Parameters File: | ALPHA_KETO_ACIDS-FULL.M |
| Processing Parameters File: | EX00310-MassHunterQuant-GlyTCA-DataAnalysis-GCMS-Method.m |
