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Sample GSM158640 Query DataSets for GSM158640
Status Public on Mar 10, 2007
Title Non-tumorigenic (PE15NTG)
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. Sample consists of three replicates.
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 Jan 22, 2015
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 2457.333333 0.0026
200001_at 4398 0.0056
200002_at 8502.666667 0.0017
200003_s_at 47692 0.0017
200004_at 20550 0.0017
200005_at 5212.666667 0.0017
200006_at 40280 0.0017
200007_at 29652.33333 0.0017
200008_s_at 1030.666667 0.0031
200009_at 11745.66667 0.0017
200010_at 8654 0.0017
200011_s_at 9216.333333 0.0017
200012_x_at 16406.66667 0.0017
200013_at 13373 0.0026
200014_s_at 11606 0.0017
200015_s_at 9618.666667 0.0023
200016_x_at 42317 0.0017
200017_at 16384.66667 0.0026
200018_at 27276.66667 0.0017
200019_s_at 14448 0.0017

Total number of rows: 22215

Table truncated, full table size 633 Kbytes.




Supplementary file Size Download File type/resource
GSM158640_1.CEL.gz 2.3 Mb (ftp)(http) CEL
GSM158640_2.CEL.gz 2.4 Mb (ftp)(http) CEL
GSM158640_3.CEL.gz 2.3 Mb (ftp)(http) CEL
Raw data provided as supplementary file

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