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Sample GSM1138518 Query DataSets for GSM1138518
Status Public on May 10, 2013
Title ERG (Pb-Cre Pos;R26-ERG/ERG) Rep2
Sample type RNA
 
Source name Mouse Prostate
Organism Mus musculus
Characteristics organ: Prostate
strain: C57B6
genotype: ERG
androgen: Ventral Lobe
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 XG3660
Data processing The raw data was extracted using Illumina BeadStudio software without normalization. Raw data was imported into Partek genomic suite.
 
Submission date May 09, 2013
Last update date May 10, 2013
Contact name Yu Chen
E-mail(s) cheny1@mskcc.org
Phone 646-888-2163
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 GPL6887
Series (2)
GSE46799 Expression profile of Pten loss and ERG overexpression in mouse prostate
GSE47220 ETS factors reprogram the androgen receptor cistrome and prime prostate tumorigenesis in response to PTEN loss

Data table header descriptions
ID_REF
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_1212602 7.19548 0.002136752
ILMN_1212603 5.99395 0.7211539
ILMN_1212605 9.58526 0
ILMN_1212607 6.55763 0.07692308
ILMN_1212612 6.65697 0.0491453
ILMN_1212614 5.895 0.883547
ILMN_1212619 7.66618 0
ILMN_1212623 6.06494 0.5779914
ILMN_1212625 9.76391 0
ILMN_1212626 8.46276 0
ILMN_1212628 6.25763 0.2852564
ILMN_1212632 6.29921 0.2467949
ILMN_1212633 7.11528 0.003205128
ILMN_1212636 11.2603 0
ILMN_1212637 11.9509 0
ILMN_1212638 13.8722 0
ILMN_1212639 7.64276 0
ILMN_1212644 6.25132 0.292735
ILMN_1212645 6.37658 0.1720085
ILMN_1212646 9.46922 0

Total number of rows: 45281

Table truncated, full table size 1256 Kbytes.




Supplementary data files not provided
Raw data are available on Series record
Processed data included within Sample table

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