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Status |
Public on Jun 27, 2008 |
Title |
Prostate_Dysplasia, Rep 4 |
Sample type |
RNA |
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Source name |
Dysplasia Mouse Prostate
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Organism |
Mus musculus |
Characteristics |
Strain: mixed 129XC57Bl/6, Gender: male, Tissue: prostate Age (Months): 11.5 Genotyping: Nkx3.1-/-;Pten+/+
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Treatment protocol |
To obtain androgen-independent lesions, mice were castrated at 7 to 14 months of age.
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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.
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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.
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Label |
biotin
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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).
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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.
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Scan protocol |
GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
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Description |
no additional information
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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).
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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 |
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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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