NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM208462 Query DataSets for GSM208462
Status Public on May 28, 2008
Title Fusion:Yes, Deletion:No (prostate_2469615)
Sample type RNA
 
Source name primary prostate cancer
Organism Homo sapiens
Characteristics FUSION:YES
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 0.234256456
DAP1_0010 0.765147693
DAP1_0021 -1.147041735
DAP1_0023 -1.227807895
DAP1_0027 0.066063758
DAP1_0028 -1.698779466
DAP1_0030 0.608493798
DAP1_0031 1.369122709
DAP1_0033 -0.765282074
DAP1_0036 -1.30105806
DAP1_0038 -0.514183243
DAP1_0040 1.055333088
DAP1_0041 -1.327892543
DAP1_0042 -0.284724653
DAP1_0050 0.737609479
DAP1_0051 -1.537491121
DAP1_0054 0.507171026
DAP1_0056 1.304744808
DAP1_0061 -0.476968983
DAP1_0062 -0.564449403

Total number of rows: 6144

Table truncated, full table size 134 Kbytes.




Supplementary file Size Download File type/resource
GSM208462_1514599012_R004_C004.txt.gz 1021.7 Kb (ftp)(http) TXT
GSM208462_1514599022_R004_C004.txt.gz 1.0 Mb (ftp)(http) TXT
GSM208462_1514599026_R004_C004.txt.gz 1.0 Mb (ftp)(http) TXT
GSM208462_1514610008_R004_C004.txt.gz 1008.1 Kb (ftp)(http) TXT
Processed data included within Sample table

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