GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM158644 Query DataSets for GSM158644
Status Public on Mar 10, 2007
Title Normal (022_Breast)
Sample type RNA
Source name Normal breast epithelium tissue obtained from reduction mammoplasties.
Organism Homo sapiens
Characteristics Normal breast epithelium cells
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 Normal breast epithelium cells 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
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
VALUE Signal intensity
DETECTION P-VALUE 'detection p-value', p-value that indicates the significance level of the detection call

Data table
200000_s_at 3470 0.0035
200001_at 2200 0.034
200002_at 15391 0.0017
200003_s_at 24778 0.0017
200004_at 15389 0.0017
200005_at 8248 0.0017
200006_at 21698 0.0017
200007_at 22418 0.0017
200008_s_at 220 0.15
200009_at 13570 0.0017
200010_at 7221 0.0017
200011_s_at 3736 0.003
200012_x_at 30950 0.0017
200013_at 16740 0.0026
200014_s_at 8528 0.0017
200015_s_at 9473 0.0023
200016_x_at 42193 0.0017
200017_at 24679 0.0026
200018_at 50368 0.0017
200019_s_at 43576 0.0017

Total number of rows: 22215

Table truncated, full table size 451 Kbytes.

Supplementary file Size Download File type/resource
GSM158644.CEL.gz 3.5 Mb (ftp)(http) CEL
Raw data provided as supplementary file

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