> Gene Expression Database
ERG Transcriptome
CPDR tumor-benign 80 genechip dataset
From 40 patients specimens were obtained under an IRB-approved protocol from patients treated with radical prostatectomy (RP) at Walter Reed Army Medical Center (WRAMC). From over 300 patients two groups were selected which had prostate tumors with either well differentiated (WD) or poorly differentiated (PD) after radical RP. The PD group had Gleason score 8-9, seminal vesicle invasion, and poorly differentiated tumor cells; the WD group had Gleason score 6-7, no seminal vesicle invasion, and well to moderately differentiated tumor cells. LCM compatible specimens were selected from age and race (Caucasians) matched PD or WD patients with no family history of CaP.
Note: yearly PSA screening is mandatory for military health care recipients.
(right click to download .txt files - convert txt files to MS Excel format by opening the txt document from within the Excel application.)
Abstract |
Publications | 
Well Differentiated Normals 1-20 (txt file) |
Well Differentiated Tumors 1-20 (txt file)
Poorly Differentiated Normals 21-40 (txt file) |
Poorly Differentiated Tumors 21-40 (txt file)
VCaP Cell Response to ERG siRNA
VCaP Human prostate tumor cell line, was obtained from the American Type Culture Collection (ATCC, Rockville, MD) and were maintained in growth medium and under conditions recommended by the supplier. For hormone treatment the R1881 synthetic androgen analogue, was used (New England Nuclear, Boston, MA). Small interference RNA (siRNA) oligo duplex against human ERG (Locus ID: GXL_163565, Accession: NM_004440) was designed as follows: ERG siRNA, 5’-TGATGTTGATAAAGCCTTATT -3’ (Dharmacon, Lafayette, CO). Non-target (NT) siRNA duplexes (D-001206-13-20) were from Dharmacon (Lafayette, CO). VCaP cells were seeded into 10 cm tissue culture dishes in the appropriate medium with 10% cFBS for three days. Transfection of siRNA was carried out with Lipofectamine 2000 (Invitrogen, Carlsbad, CA). Twelve hours after transfection of si RNAs, VCaP cells were treated with 100pM R1881, incubated for 24h or 48h and processed for microarray analysis. Total RNA was isolated and five micrograms of RNA from each of the VCaP transfectants were biotin labeled and GeneChip® HG U133 Plus 2.0 chips were hybridized with the labeled probes. Expression data were normalized by Robust Multi-array Averages (RMA) and fold changes in ERGsi/NT (24h) and ERGsi/NT (48h) treatment groups were calculated. A two folds cut-off criterion was applied for subsequent pathway analysis by the Bibliosphere Software using the functional co-citation-based analysis function (Genomatix GmbH, Munich, Germany) (Scherf et al., 2005).
(right click to download .txt files - convert txt files to MS Excel format by opening the txt document from within the Excel application.)
Publications |
CPDR NT 24h (txt file) |
CPDR NT 48h (txt file) | CPDR Si1 24h (txt file) |
CPDR Si1 48h (txt file)
