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Sample GSM158639 Query DataSets for GSM158639
Status Public on Mar 10, 2007
Title Tumorigenic (PE15TG)
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. 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
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 2762.666667 0.0026
200001_at 5185.333333 0.0074
200002_at 8694.666667 0.0017
200003_s_at 19393.33333 0.0017
200004_at 21467.33333 0.0017
200005_at 9831 0.0017
200006_at 26984.66667 0.0017
200007_at 23076.66667 0.0017
200008_s_at 1045.666667 0.002766667
200009_at 14176.66667 0.0017
200010_at 9690.666667 0.0017
200011_s_at 7046 0.0017
200012_x_at 25552 0.0017
200013_at 15775.33333 0.0026
200014_s_at 8010 0.0017
200015_s_at 13679.33333 0.0021
200016_x_at 38527 0.0017
200017_at 20718 0.0026
200018_at 42210.66667 0.0017
200019_s_at 24868.33333 0.0017

Total number of rows: 22215

Table truncated, full table size 636 Kbytes.

Supplementary file Size Download File type/resource
GSM158639_1.CEL.gz 2.3 Mb (ftp)(http) CEL
GSM158639_2.CEL.gz 2.3 Mb (ftp)(http) CEL
GSM158639_3.CEL.gz 2.3 Mb (ftp)(http) CEL
Raw data provided as supplementary file

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