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Sample GSM158635 Query DataSets for GSM158635
Status Public on Mar 10, 2007
Title Tumorigenic (SUMTG)
Sample type RNA
 
Source name breast tumor (ESA+ CD44+ CD24-/low Lin-)
Organism Homo sapiens
Characteristics tumorigenic population (ESA+ CD44+ CD24-/low Lin-)
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 Tumorigenic population (ESA+ CD44+ CD24-/low Lin-) 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 2622 0.0026
200001_at 3354 0.0056
200002_at 8888 0.0017
200003_s_at 26223 0.0017
200004_at 21036 0.0017
200005_at 5022 0.0017
200006_at 24685 0.0017
200007_at 20254 0.0017
200008_s_at 243 0.032
200009_at 10164 0.0017
200010_at 4596 0.003
200011_s_at 3918 0.0023
200012_x_at 23577 0.0017
200013_at 14062 0.0026
200014_s_at 10690 0.0017
200015_s_at 13282 0.0017
200016_x_at 41853 0.0017
200017_at 20074 0.0026
200018_at 49942 0.0017
200019_s_at 21315 0.0017

Total number of rows: 22215

Table truncated, full table size 455 Kbytes.




Supplementary file Size Download File type/resource
GSM158635.CEL.gz 3.5 Mb (ftp)(http) CEL
Raw data provided as supplementary file

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