NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM208342 Query DataSets for GSM208342
Status Public on May 28, 2008
Title Fusion: No, Deletion: No (prostate_42804)
Sample type RNA
 
Source name primary prostate cancer
Organism Homo sapiens
Characteristics FUSION: NO
DELETION: NO
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 0.3507
DAP1_0010 0.5685
DAP1_0021 -0.806
DAP1_0023 -1.2776
DAP1_0027 0.1384
DAP1_0028 -0.6912
DAP1_0030 0.2755
DAP1_0031 1.3483
DAP1_0033 -1.2148
DAP1_0036 -0.6378
DAP1_0038 0.3156
DAP1_0040 1.5534
DAP1_0041 -0.7422
DAP1_0042 -0.7902
DAP1_0050 1.2313
DAP1_0051 -1.4727
DAP1_0054 -0.136
DAP1_0056 0.9595
DAP1_0061 -0.8594
DAP1_0062 1.1181

Total number of rows: 6144

Table truncated, full table size 104 Kbytes.




Supplementary file Size Download File type/resource
GSM208342_1491585_R006_C003.txt.gz 993.1 Kb (ftp)(http) TXT
GSM208342_1514601003_R006_C003.txt.gz 1.0 Mb (ftp)(http) TXT
GSM208342_1514610021_R006_C003.txt.gz 1015.2 Kb (ftp)(http) TXT
GSM208342_1514610023_R006_C003.txt.gz 1001.0 Kb (ftp)(http) TXT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap