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Sample GSM158647 Query DataSets for GSM158647
Status Public on Mar 10, 2007
Title Tumorigenic (SUMTG_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
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 16031 0.0017
200080_s_at 38397 0.0017
200099_s_at 25388 0.0017
222523_at 280 0.0064
222575_at 359 0.0051
222721_at 29 0.07
222802_at 484 0.047
222838_at 382 0.011
222918_at 184 0.056
223176_at 26 0.19
224122_at 2 0.23
224185_at 146 0.086
224249_at -60 0.49
224284_x_at 761 0.012
224288_x_at 275 0.086
224321_at 650 0.0051
224322_at -75 0.67
224340_at 530 0.0017
224343_x_at -193 0.969
224351_at 11 0.37

Total number of rows: 22577

Table truncated, full table size 439 Kbytes.




Supplementary file Size Download File type/resource
GSM158647.CEL.gz 3.4 Mb (ftp)(http) CEL
Raw data provided as supplementary file

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