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Sample GSM1129158 Query DataSets for GSM1129158
Status Public on Apr 25, 2013
Title Pten f/f ;ERG prostate Intact Rep1
Sample type RNA
Source name Mouse Prostate
Organism Mus musculus
Characteristics organ: Prostate
strain: C57B6
genotype: Pten f/f;ERG
androgen: Intact
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 9268a_7b
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
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

Data table header descriptions
VALUE Partek Genomic Suite was used to Log2 transform raw data followed by Quartile normalization.
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_1212607 6.73659 0.1491228
ILMN_1212612 6.70611 0.2305764
ILMN_1212619 7.45198 0
ILMN_1212628 6.58903 0.7957394
ILMN_1212632 6.50953 0.9824561
ILMN_1212636 9.65405 0
ILMN_1212637 8.85716 0
ILMN_1212645 6.87335 0.00877193
ILMN_1212648 7.86836 0
ILMN_1212653 6.96876 0.001253133
ILMN_1212672 7.97162 0
ILMN_1212682 6.70411 0.2418546
ILMN_1212683 6.61554 0.6842105
ILMN_1212685 6.64081 0.5388471
ILMN_1212692 9.36306 0
ILMN_1212693 8.17263 0
ILMN_1212695 6.691 0.2882206
ILMN_1212698 6.5498 0.9260651
ILMN_1212702 10.5442 0
ILMN_1212703 7.35316 0

Total number of rows: 25697

Table truncated, full table size 696 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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