|
| Status |
Public on Apr 25, 2013 |
| Title |
Pten f/f ;ERG prostate Castrate Rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Mouse Prostate
|
| Organism |
Mus musculus |
| Characteristics |
organ: Prostate
strain: C57B6
genotype: Pten f/f;ERG
androgen: Castrate
|
| Treatment protocol |
Mice were either castrated or left intact and RNA was isolated 3 days after castration.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA is extracted using Rneasy per protocol. RNA quality was assessed using the Agilent 2100 Bioanalyzer and the RNA 6000 Nano kit (Agilent Technologies Inc., Palo Alto, CA).
|
| Label |
biotin
|
| Label protocol |
~500 ng of^ total RNA was used to prepare biotin-labeled RNA using Ambion Illumina TotalPrep RNA Amplification Kit (Cat# AMIL1791, Applied Biosystems, Foster City, CA). Briefly, 500 ng of total RNA was used to synthesize the first strand of cDNA using ArrayScript reverse transcriptase and an oligo(dT) primer bearing a T7 promoter. The single-stranded cDNA was then converted into a double-stranded DNA (dsDNA) by DNA polymerase^ I in the presence of /E. coli/ RNase H and DNA ligase. After column purification, the dsDNA was served as a template for in vitro transcription in a reaction containing biotin-labeled UTP, unlabeled NTPs and T7 RNA Polymerase.
|
| |
|
| Hybridization protocol |
The amplified, biotin-labeled antisense RNA (aRNA) was purified and quality was assessed using the Agilent 2100 Bioanalyzer and the RNA 6000 Nano kit. 750 ng of aRNA in 5 ul was mixed with 10 ul of hybridization reagents and heated at 65C for 10min. After cooled to room temperature, total 15 ul of the hyb solution was applied to Illumina MouseRef-8 v2 chip. The chip was incubated for about 18 hours at 58C.
|
| Scan protocol |
After washing and staining with streptavidin-Cy3, the chip was scanned using Illumina BeadArray Reader. The scanning was done using standard DirectHyb Gene Expression protocol with the following settings: Factor=1, PMT=587, Filter=100%.
|
| Description |
9417_8c
|
| Data processing |
The raw data was extracted using Illumina BeadStudio software without normalization. Raw data was imported into Partek genomic suite.
|
| |
|
| Submission date |
Apr 24, 2013 |
| Last update date |
Apr 25, 2013 |
| Contact name |
Yu Chen |
| E-mail(s) |
cheny1@mskcc.org
|
| Phone |
646-888-3356
|
| Organization name |
Memorial Sloan Kettering Cancer Center
|
| Department |
Human Oncology and Pathogenesis Program
|
| Lab |
Chen
|
| Street address |
1275 York Ave, Box 20
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL6885 |
| Series (2) |
| GSE46360 |
Response to catration in PTEN null and PTEN null ERG expressing mouse prostates |
| GSE47220 |
ETS factors reprogram the androgen receptor cistrome and prime prostate tumorigenesis in response to PTEN loss |
|
