Project PXD000624

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Biomedical Dataset
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Summary

Title

SILAC analysis of PDGF-treated primary bladder smooth muscle cells

Description

SILAC analysis of human primary bladder smooth muscle cells treated with platelet-derived growth factor for 0, 4, and 24 h. Platelet-derived growth factor-BB (PDGF-BB) is a mitogen and motogen that has been implicated in the proliferation, migration and synthetic activities of smooth muscle cells (SMC) that characterize pathologic tissue remodeling in hollow organs. To explore the signals induced by PDGF on a global scale, we performed expression profiling and quantitative proteomics analysis of PDGF-treated human visceral SMC. 1695 genes and 241 proteins were identified as differentially expressed in PDGF-treated primary bladder SMC versus non-treated cells. Analysis of gene expression data revealed MYC, JUN, EGR1, MYB and RUNX1 as the transcription factors most significantly networked with upregulated genes; DDIT3, NFAT5, and SOX5 were most networked with downregulated genes. For protein identification and quantification, raw mass spectrometric data were analyzed with MaxQuant software (version 1.0.13.13). The parameters were set as follows. In the Quant module, SILAC triplets was selected; oxidation (M) and acetyl (Protein N-term) were set as variable modification; carbamidomethyl (C) was set as fixed modification; concatenated IPI human database (version 3.52) (74,190 forward sequences and 74,190 reverse sequences) was used for database searching; all other parameters were default. Tandem mass spectra were searched by Mascot (version 2.2.0.4) (Matrix Science, Boston, MA). In the Identify module, all parameters were default, except that maximal peptide posterior error probability was set as 0.05. False discovery rates for protein and peptide identifications were both set at 0.01.

Sample Processing Protocol

See details in reference(s) : 25080971

Data Processing Protocol

See details in reference(s) : 25080971

Contact

Wei Yang, Cedars-Sinai Medical Center

Submission Date

06/12/2013

Publication Date

04/08/2014

Publication

    Yang W, Ramachandran A, You S, Jeong H, Morley S, Mulone MD, Logvinenko T, Kim J, Hwang D, Freeman MR, Adam RM. Integration of proteomic and transcriptomic profiles identifies a novel PDGF-MYC network in human smooth muscle cells. Cell Commun Signal. 2014 Aug 1;12(1):44 PubMed: 25080971

Assay

Showing 1 - 4 of 4 results
# Accession Title Proteins Peptides Unique Peptides Spectra Identified Spectra View in Reactome
1 33005 Triplex SILAC analysis of pBSMCs_iso 1830 13886 2464 39218 7925
2 33006 Triplex SILAC analysis of pBSMCs_sil0 3049 56235 8812 56181 34023
3 33007 Triplex SILAC analysis of pBSMCs_sil1 2770 52028 8751 57195 32400
4 33008 Triplex SILAC analysis of pBSMCs_sil2 2686 44341 8061 53155 28829