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Sample GSM158641 Query DataSets for GSM158641
Status Public on Mar 10, 2007
Title Tumorigenic (T1TG)
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 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 2069.333333 0.005733333
200001_at 2115.333333 0.020333333
200002_at 14897 0.002833333
200003_s_at 11957 0.0017
200004_at 12257.66667 0.0017
200005_at 2488 0.003533333
200006_at 12000.66667 0.0017
200007_at 13851.33333 0.0019
200008_s_at 422.6666667 0.039333333
200009_at 12582.33333 0.0017
200010_at 3431.333333 0.029566667
200011_s_at 4447 0.0023
200012_x_at 18922.33333 0.0017
200013_at 14071 0.0026
200014_s_at 7023.333333 0.0019
200015_s_at 4823.666667 0.0021
200016_x_at 24288.66667 0.0017
200017_at 22572.66667 0.0026
200018_at 44951.33333 0.0017
200019_s_at 45555 0.0017

Total number of rows: 22215

Table truncated, full table size 643 Kbytes.

Supplementary file Size Download File type/resource
GSM158641_1.CEL.gz 3.4 Mb (ftp)(http) CEL
GSM158641_2.CEL.gz 3.4 Mb (ftp)(http) CEL
GSM158641_3.CEL.gz 3.4 Mb (ftp)(http) CEL
Raw data provided as supplementary file

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