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Sample GSM878869 Query DataSets for GSM878869
Status Public on May 23, 2012
Title WA53
Sample type RNA
 
Channel 1
Source name pooled benign prostate tissue (Clontech)
Organism Homo sapiens
Characteristics sample type: reference
Extracted molecule total RNA
Extraction protocol Total RNA was isolated with Trizol (Invitrogen Cat. No. 15596-026, Carlsbad, CA), according to the manufacturer's instructions. Total RNA was further purified using the Qiagen RNAeasy Mini Kit (Cat. No. 74104) according to the manufacturer's instructions
Label Cy3
Label protocol One ug of total RNA was reverse transcripted to cDNA using T7 Promoter Primer and MMLV-RT. Then the cDNA was converted to aRNA using T7 RNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two-Color Microarray-Based Gene Expression Analysis Protocol, Agilent).
 
Channel 2
Source name metastatic prostate cancer (obtained at rapid [warm] autopsy)
Organism Homo sapiens
Characteristics tissue: metastatic castrate resistant prostate cancer (WA)
Extracted molecule total RNA
Extraction protocol Total RNA was isolated with Trizol (Invitrogen Cat. No. 15596-026, Carlsbad, CA), according to the manufacturer's instructions. Total RNA was further purified using the Qiagen RNAeasy Mini Kit (Cat. No. 74104) according to the manufacturer's instructions
Label Cy5
Label protocol One ug of total RNA was reverse transcripted to cDNA using T7 Promoter Primer and MMLV-RT. Then the cDNA was converted to aRNA using T7 RNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two-Color Microarray-Based Gene Expression Analysis Protocol, Agilent).
 
 
Hybridization protocol 825ng of Cy3 and Cy5 labelled aRNA were hybridized competitively for 17 hrs in a 65 C hybridization oven (G2545A, Agilent) set to 10 rpm in a final concentration of 1X GEx Hybridization Buffer HI-RPM, according to the manufacturer's recommnded protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent). Arrays were washed according to the manufacturer's recommended protocol including the Stabilization and Drying Solution step (Two-Color Microarray-Based Gene Expression Analysis, Agilent).
Scan protocol Arrays were scanned at 5um resolution on an Agilent DNA Microarray Scanner (G2505B, Agilent) using the default settings for 1x44k or 4x44k format two-color arrays.
Data processing Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software (Version 9.1.3.1). Spot values were normalized using the default linear-lowess normalization. LogRatio for all probes, which were used for subsequent analysis, were converted to log(2). Although the 1x44k and 4x44k arrays have the same probes, the 4x44k arrays have 10 replicates of some probes. Thus, to generate a final data set, the median value of replicated probes was used for 4x44k arrays. The final data set (including benign prostate, localized prostate cancer and CRPC) was uploaded into a custom instance of Oncomine for automated analysis. In Oncomine, the dataset was median centered (per array) prior to indicated analyses.
 
Submission date Feb 21, 2012
Last update date May 23, 2012
Contact name Scott Tomlins
E-mail(s) tomlinss@med.umich.edu
Phone 734-615-1417
Organization name University of Michigan
Department Pathology
Lab Chinnaiyan Lab
Street address 1400 E. Medical Center Dr., 5410 CCGC
City Ann Arbor
State/province MI
ZIP/Postal code 48109
Country USA
 
Platform ID GPL6480
Series (1)
GSE35988 The Mutational Landscape of Lethal Castrate Resistant Prostate Cancer

Data table header descriptions
ID_REF
VALUE log2 ratio of test/reference

Data table
ID_REF VALUE
A_23_P170713 2.258257889
A_23_P107801 1.855856191
A_24_P544661 0.593412898
A_23_P110005 0.453744188
A_32_P77555 1.24855474
A_24_P936963
A_24_P714618 1.696010796
A_24_P130066 -2.251337812
A_23_P210158 2.237440938
A_24_P136484 1.773185653
A_23_P200143 -3.054003663
A_24_P230819 -0.0662598
A_32_P108396 -3.007180336
A_24_P247699 2.029118736
A_23_P429950 -1.151887274
A_32_P16848 2.670301853
A_24_P315873 -0.522496602
A_24_P125881 0.541300493
A_23_P141434 1.48401238
A_24_P6125

Total number of rows: 41000

Table truncated, full table size 964 Kbytes.




Supplementary file Size Download File type/resource
GSM878869_GEaWA53.txt.gz 14.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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