|
| Status |
Public on Jul 13, 2010 |
| Title |
CONTROL_NORM_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
CONTROL_NORM
|
| Organism |
Mus musculus |
| Characteristics |
tissue: prostate tumor
strain: C57BL6
sex: male
cell type: TRAMP-C
|
| Treatment protocol |
TRAMP-C cells were transfected with pcDNA, or FoxA2, or HIF-1a, or HIF-1a + FoxA2 using Amax Nucleofector in duplicate. 48 hour post transfection, cells were treated with normoxia or 1% hypoxia for 12 h before isolation of total RNA. 500 ng of total RNA was used for synthesis of biotin-labeled cRNA using an RNA amplification kit (Ambion). The biotinylated cRNA is labeled by incubation with streptavidin-Cy3 to generate probe for hybridization with the Mouse-6 Expression BeadChip (Illumina) that represents 48K mouse gene transcripts.
|
| Growth protocol |
TRAMP-C cells were isotated from the prostate tumor of TRAMP mice, which is C57BL6. The TRAMP-C cells are wild-type.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
|
| Label |
streptavidin Cy3
|
| Label protocol |
As suggested by illumina
|
| |
|
| Hybridization protocol |
As recommended by illumina
|
| Scan protocol |
As suggested by illumina using the illumina scanner
|
| Description |
4323501007_A
|
| Data processing |
Raw data filtered on P value for <0.05 with the remaining data normalised using the affy tools R bioconductor normalize.quantiles routine
|
| |
|
| Submission date |
Oct 08, 2009 |
| Last update date |
Jul 02, 2010 |
| Contact name |
Roy M Williams |
| E-mail(s) |
rwillia@scripps.edu
|
| Organization name |
The Scripps Research Institute
|
| Department |
Regenerative Medicine
|
| Lab |
Loring
|
| Street address |
3030 Science Park Road
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL6887 |
| Series (1) |
| GSE18478 |
Siah2-dependent concerted activity of HIF and FoxA2 regulates formation of neuroendocrine prostate tumors |
|
