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Sample GSM158651 Query DataSets for GSM158651
Status Public on Mar 10, 2007
Title Tumorigenic (PE15TG_B)
Sample type RNA
 
Source name breast tumor
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
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 14848.66667 0.0017
200080_s_at 30053.33333 0.0017
200099_s_at 39389.33333 0.0017
222523_at 304.3333333 0.0113
222575_at 190.6666667 0.019
222721_at 225 0.0122
222802_at 305.6666667 0.039666667
222838_at 1770.333333 0.004
222918_at 221 0.031
223176_at 340 0.002766667
224122_at -157 0.563333333
224185_at 113.6666667 0.089
224249_at -59 0.456666667
224284_x_at 609 0.003633333
224288_x_at 420.3333333 0.035666667
224321_at 767 0.002666667
224322_at 5 0.247333333
224340_at 373 0.0043
224343_x_at -261 0.970666667
224351_at 13 0.27

Total number of rows: 22577

Table truncated, full table size 635 Kbytes.




Supplementary file Size Download File type/resource
GSM158651_1.CEL.gz 2.1 Mb (ftp)(http) CEL
GSM158651_2.CEL.gz 2.1 Mb (ftp)(http) CEL
GSM158651_3.CEL.gz 2.1 Mb (ftp)(http) CEL
Raw data provided as supplementary file

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