NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM158636 Query DataSets for GSM158636
Status Public on Mar 10, 2007
Title Non-tumorigenic (SUMNTG)
Sample type RNA
 
Source name non-tumorigenic breast tumor
Organism Homo sapiens
Characteristics non-tumorigenic breast tumor
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol
 
Hybridization protocol Following fragmentation, 15 ug of cRNA were hybridized according to the manufacturer's instructions.
Scan protocol none
Description Non-tumorigenic population of a breast tumor isolated using fluorescence activated cell sorting
Data processing To obtain an expression measure for a given probeset, the mismatch hybridization values were subtracted from the perfect match values, and the average of the middle 50% of these differences was used as the expression measure for the probe set. A quantile normalization procedure was then applied to adjust for differences in the probe intensity distribution across different chips. Specifically, we applied a monotone linear spline to each chip that mapped quantiles 0.01 up to 0.99 (in increments of 0.01) exactly to the corresponding quantiles of a standard chip. The transform log2 [200 + max(X;0)] was then applied.
 
Submission date Jan 26, 2007
Last update date Mar 09, 2007
Contact name Xinhao Wang
E-mail(s) xinhao.wang@oncomed.com
Phone 650-995-8211
Organization name OncoMed Pharmaceuticals Inc
Street address 800 Chesapeake
City Redwood City
State/province CA
ZIP/Postal code 94063
Country USA
 
Platform ID GPL96
Series (1)
GSE6883 The prognostic role of a gene signature from tumorigenic breast-cancer cells.

Data table header descriptions
ID_REF
VALUE Signal intensity
DETECTION P-VALUE 'detection p-value', p-value that indicates the significance level of the detection call

Data table
ID_REF VALUE DETECTION P-VALUE
200000_s_at 2758 0.0026
200001_at 1503 0.026
200002_at 8014 0.0017
200003_s_at 19903 0.0017
200004_at 24873 0.0017
200005_at 2622 0.0017
200006_at 23591 0.0017
200007_at 22629 0.0017
200008_s_at 331 0.014
200009_at 8752 0.0017
200010_at 3278 0.021
200011_s_at 2084 0.0023
200012_x_at 24243 0.0017
200013_at 11451 0.0026
200014_s_at 10678 0.0017
200015_s_at 11510 0.0023
200016_x_at 40177 0.0017
200017_at 19897 0.0026
200018_at 51493 0.0017
200019_s_at 23544 0.0017

Total number of rows: 22215

Table truncated, full table size 452 Kbytes.




Supplementary file Size Download File type/resource
GSM158636.CEL.gz 3.4 Mb (ftp)(http) CEL
Raw data provided as supplementary file

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