|
| Status |
Public on Jun 27, 2008 |
| Title |
Prostate_HGPIN, Rep 4 |
| Sample type |
RNA |
| |
|
| Source name |
Prostate HGPIN Lesion
|
| Organism |
Mus musculus |
| Characteristics |
Strain: mixed 129XC57Bl/6, Gender: male, Tissue: prostate
Age (Months): 10.5
Genotyping: Nkx3.1+/-;Pten+/-
|
| Treatment protocol |
To obtain androgen-independent lesions, mice were castrated at 7 to 14 months of age.
|
| Growth protocol |
Mutant animals were bred on a mixed 129xC57Bl/6 background. Double heterozgotes (Nkx 3.1+/—; Pten+/—) were mated to obtain desired genotypic combinations.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared from the LCM samples using the PicoPure RNA isolation kit (Arcturus), followed by RNA linear amplification.
|
| Label |
biotin
|
| Label protocol |
The RNA was labelied using Small Sample Labeling Protocol VII (Affymetrix).Samples were labeled using a BioArray High Yield RNA transcript labeling kit (Enzo Life Scientific).
|
| |
|
| Hybridization protocol |
Hybridization was carried out at 45°C for 16 hours in 200 µl of cocktail containing 20 µg of biotinilated RNA probe according to the Affymetrix Standard Protocol; post hybridization washing and antibody enhancement staining were performed using EukGE-WS2v4 protocol on Affymetrix Fluidics Station.
|
| Scan protocol |
GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
|
| Description |
high-grade prostate intraepithelial neoplasia
|
| Data processing |
GeneChip CEL files underwent normalization using GeneChip Robust Multichip Analysis (RMA) in Bioconductor/R. Differential regulation was defined as probe sets that passed an ANOVA (P<0.1, variances assumed equal; False Detection Rate P<0.1 using Benjamani and Hochberg multiple testing correction) between classes (Normal, Dyplasia/LGPIN, HGPIN/Cancer, AI-HGPIN, AI-Cancer-Met). Functional annotation was performed using the Database for Annotation, Visualization and Integrated Discovery (DAVID) 2007 at the National Institute of Allergy and Infectious Diseases (NIAID), NIH, to identify over-represented GO Biological Processes as well as KEGG and BioCarta pathways (p<0.05).
|
| |
|
| Submission date |
Jun 19, 2008 |
| Last update date |
Jun 27, 2008 |
| Contact name |
Cory Abate-Shen |
| E-mail(s) |
cabateshen@columbia.edu
|
| Organization name |
Columbia University
|
| Department |
Urology
|
| Street address |
1130 St. Nicholas Ave
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
11032 |
| Country |
USA |
| |
|
| Platform ID |
GPL339 |
| Series (1) |
| GSE11836 |
Role for AP-1 transcription factors (c-Jun, c-Fos) in prostate cancer progression and clinical outcome of prostate tumor |
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