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Sample GSM208041 Query DataSets for GSM208041
Status Public on May 28, 2008
Title Fusion: No, Deletion: unknown (prostate_1446)
Sample type RNA
 
Source name primary prostate cancer
Organism Homo sapiens
Characteristics FUSION: NO
DELETION:
Treatment protocol na
Growth protocol na
Extracted molecule total RNA
Extraction protocol Using 3 biopsy cores (0.6µm each) taken from formalin-fixed paraffin-embeded tissue blocks, total RNA was extracted using Trizol LS reagent (Invitrogen).
Label Cy3 and Cy5
Label protocol Refer to the Illumina DASL Assay System Manual
 
Hybridization protocol Refer to the Illumina DASL Assay System Manual. Hybridization was performed for 4 DASL assay oligo pool (DAP)s, DAP1~4, including 1536 probes each on 4 separate microarrays.
Scan protocol Refer to the Illumina DASL Assay System Manual
Description no additional information
Data processing For each probe, Red and Green intensities are computed as average of single bead values. The final signal is the sum of the Red and Green intensities. Data were median-centered by subtraction of median (log2 scale) within sample and within DAP, and median set to a target value computed as the overall within DAP median. Data were then normalized using the qspline algorithm (on the log2 intensity scale) with reference distribution computed as the marginal (always within DAP) mean of every gene.
 
Submission date Jul 06, 2007
Last update date Aug 14, 2011
Contact name Mark A. Rubin
E-mail(s) rubinma@med.cornell.edu
Phone 212-746-6313
Organization name Weill Cornell Medical Center
Department Pathology and Laboratory Medicine
Lab Rubin
Street address 1300 York Avenue Room C 410-A
City New York
State/province NY
ZIP/Postal code 10021
Country USA
 
Platform ID GPL5474
Series (1)
GSE8402 TMPRSS2-ERG fusion prostate cancer is a molecularly distinct estrogen-sensitive subclass of aggressive prostate cancer

Data table header descriptions
ID_REF
VALUE Normalized signal intensities by R statistical package

Data table
ID_REF VALUE
DAP1_0003 0.6095
DAP1_0010 0.9816
DAP1_0021 -0.5861
DAP1_0023 -0.7953
DAP1_0027 -1.0885
DAP1_0028 -1.5610
DAP1_0030 0.9434
DAP1_0031 1.2708
DAP1_0033 -0.9708
DAP1_0036 -1.6095
DAP1_0038 -0.5955
DAP1_0040 1.3953
DAP1_0041 -0.7588
DAP1_0042 -1.0242
DAP1_0050 1.0855
DAP1_0051 -0.6889
DAP1_0054 0.0013
DAP1_0056 -0.9761
DAP1_0061 -0.6875
DAP1_0062 -0.5335

Total number of rows: 6144

Table truncated, full table size 104 Kbytes.




Supplementary file Size Download File type/resource
GSM208041_1492001_R008_C002.txt.gz 991.2 Kb (ftp)(http) TXT
GSM208041_1514599002_R008_C002.txt.gz 979.6 Kb (ftp)(http) TXT
GSM208041_1514599005_R008_C002.txt.gz 990.1 Kb (ftp)(http) TXT
GSM208041_1514610019_R008_C002.txt.gz 961.6 Kb (ftp)(http) TXT
Processed data included within Sample table

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