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Sample GSM158650 Query DataSets for GSM158650
Status Public on Mar 10, 2007
Title Non-tumorigenic (PE13NTG_B)
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
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 GPL97
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
200067_x_at 11615 0.0017
200080_s_at 38203 0.0017
200099_s_at 29143 0.0017
222523_at 239 0.024
222575_at 511 0.021
222721_at 89 0.044
222802_at 421 0.039
222838_at 302 0.026
222918_at 34 0.23
223176_at 101 0.014
224122_at -179 0.44
224185_at 227 0.015
224249_at -105 0.49
224284_x_at 778 0.0085
224288_x_at 204 0.13
224321_at 1216 0.0017
224322_at -141 0.89
224340_at 554 0.0017
224343_x_at -151 0.929
224351_at 38 0.33

Total number of rows: 22577

Table truncated, full table size 438 Kbytes.




Supplementary file Size Download File type/resource
GSM158650.CEL.gz 3.3 Mb (ftp)(http) CEL
Raw data provided as supplementary file

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