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Sample GSM158658 Query DataSets for GSM158658
Status Public on Mar 10, 2007
Title Normal breast (068_Breast_B)
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 GPL97
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
200067_x_at 7119 0.0017
200080_s_at 30579 0.0017
200099_s_at 42300 0.0017
222523_at 455 0.0035
222575_at 327 0.021
222721_at 135 0.026
222802_at 2150 0.0017
222838_at 0 0.14
222918_at 193 0.14
223176_at 141 0.011
224122_at -33 0.35
224185_at 664 0.012
224249_at -2 0.49
224284_x_at 933 0.0026
224288_x_at 552 0.024
224321_at 183 0.055
224322_at 26 0.15
224340_at 403 0.0051
224343_x_at -337 0.985
224351_at 38 0.17

Total number of rows: 22577

Table truncated, full table size 442 Kbytes.

Supplementary file Size Download File type/resource
GSM158658.CEL.gz 2.1 Mb (ftp)(http) CEL
Raw data provided as supplementary file

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