Expression data from LNCaP cell line
From ArrayWiki
| PubMed ID: | none |
|---|---|
| Contact: | Wei Li
|
| Species: | Homo sapiens |
| Platform: | Affymetrix GeneChip Human Genome U133 Plus 2.0 Array |
| Number of Samples: | 9 |
| Date Range: | 08/03/2005 - 08/03/2005 |
| Experiment Quality: | 98.57 0.72 % |
| Link to Repository: | GSE7868 |
| Original Intensity Data: | Download |
| Clean Intensity Data: | Download |
| Original PLIER Data: | Download |
| Clean PLIER Data: | Download |
| Clean CEL Files: | |
| Data Rank: | 
|
Androgen receptor (AR) is a ligand-dependent transcription factor that plays a key role in the onset and progression of prostate cancer. Surprisingly little is known of AR binding sites and collaborating transcription factors in the human genome. Here we have identified the DNA sequence motifs that are significantly enriched within the authentic 90 AR target regions found on chromosomes 21 and 22 in human prostate cancer cells by combining chromatin immunoprecipitation for AR with chromosome-scale tiled oligonucleotide microarrays. By integrating the DNA sequence motif data with the gene expression profiles from human prostate cancers we identified the transcription factors that recognize each of these motifs. These factors form complexes with AR, bind to specific AR target regions and govern androgen-dependent transcription. Together with AR these collaborating transcription factors form a regulatory network that directs prostate cancer growth and survival and identify potential new opportunities for therapeutic intervention.
Design: The RNA samples are extracted from DHT 0, 4h and 16h treated LNCaP cells by using a RNeasy kit (Qiagen). The final RNAs submitted to Dana-Farber Cancer Institute (DFCI) Microarray Core Facility are all at 1.5ug/ul, A260/A280=2.1.
Type: time course
Contents |
[edit] Contributors
- Qianben Wang
- Wei Li
[edit] Protocols
[edit] References
[edit] Links
GEO Accession for this experiment: GSE7868. (Public on Sep 01 2007)
RAW data: tar file.
[edit] Analysis
 Before Normalization |
 After Normalization & Cleaning |
[edit] Samples/Quality Control
| Sample | Date Scanned | Source Link | Probe Variance Data | Artifact Mask | Quality Score |
|---|---|---|---|---|---|
| expression at 0hr, bio rep1 | 08/03/05 15:09:20 | GSM190812 | 
| 
| 97.4383 2.01 % |
| expression at 4hr, bio rep1 | 08/03/05 16:09:12 | GSM190813 | 
| 
| 98.6419 1.4 % |
| expression at 16hr, bio rep1 | 08/03/05 16:20:33 | GSM190814 | 
| 
| 98.8647 0.04 % |
| expression at 0hr, bio rep2 | 08/03/05 16:31:43 | GSM190815 | 
| 
| 98.7687 0.83 % |
| expression at 4hr, bio rep2 | 08/03/05 16:42:46 | GSM190816 | 
| 
| 99.073 0.04 % |
| expression at 16hr, bio rep2 | 08/03/05 17:02:32 | GSM190817 | 
| 
| 98.4906 0.04 % |
| expression at 0hr, bio rep3 | 08/03/05 17:13:37 | GSM190818 | 
| 
| 98.8292 0.12 % |
| expression at 4hr, bio rep3 | 08/03/05 17:24:44 | GSM190819 | 
| 
| 98.5168 0.08 % |
| expression at 16hr, bio rep3 | 08/03/05 17:35:51 | GSM190820 | 
| 
| 98.5415 1.92 % |
