PXD000624

PXD000624 is an original dataset announced via ProteomeXchange.

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.
HostingRepository	PRIDE
AnnounceDate	2014-10-23
AnnouncementXML	Submission_2014-10-23_02:48:36.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD000624
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Wei Yang
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	6x(13)C: 4x(15)N labeled L-arginine; monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue; (18)O label at both C-terminal oxygens; 6x(13)C labeled residue; 6x(13)C: 2x(15)N labeled L-lysine
Instrument	LTQ Orbitrap; instrument model: LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2013-12-06 01:48:42	ID requested
1	2014-08-04 02:40:39	announced
⏵ 2	2014-10-23 02:48:37	announced	Updated project metadata.

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, 12():44(2014) [pubmed]

curator keyword: Biomedical

submitter keyword: SILAC, Quantitive Proteomics, LC-MS/MS, MaxQuant, PDGF, smooth muscle cells

Wei Yang
contact affiliation	Cedars-Sinai Medical Center
contact email	omician@gmail.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD000624
     1. Label: PRIDE project
     2. Name: SILAC analysis of PDGF-treated primary bladder smooth muscle cells