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Sample GSM208317 Query DataSets for GSM208317
Status Public on May 28, 2008
Title Fusion: No, Deletion: unknown (prostate_40287)
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
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 0.4434
DAP1_0010 1.0678
DAP1_0021 -1.2594
DAP1_0023 -1.4203
DAP1_0027 -0.3624
DAP1_0028 -1.6686
DAP1_0030 0.404
DAP1_0031 1.4466
DAP1_0033 -0.6726
DAP1_0036 -1.3558
DAP1_0038 -0.5566
DAP1_0040 1.3721
DAP1_0041 -1.3617
DAP1_0042 -0.7072
DAP1_0050 1.2329
DAP1_0051 0.571
DAP1_0054 0.4425
DAP1_0056 0.8074
DAP1_0061 0.1816
DAP1_0062 -0.8833

Total number of rows: 6144

Table truncated, full table size 104 Kbytes.




Supplementary file Size Download File type/resource
GSM208317_1491585_R008_C002.txt.gz 989.7 Kb (ftp)(http) TXT
GSM208317_1514601003_R008_C002.txt.gz 1000.8 Kb (ftp)(http) TXT
GSM208317_1514610021_R008_C002.txt.gz 1002.9 Kb (ftp)(http) TXT
GSM208317_1514610023_R008_C002.txt.gz 977.7 Kb (ftp)(http) TXT
Processed data included within Sample table

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