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Sample GSM158655 Query DataSets for GSM158655
Status Public on Mar 10, 2007
Title Tumorigenic (T3TG_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
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 9668.333333 0.0017
200080_s_at 31909 0.0017
200099_s_at 40006.66667 0.0017
222523_at 475 0.003866667
222575_at 373.6666667 0.023666667
222721_at 61 0.07
222802_at 859.6666667 0.0062
222838_at 261 0.039666667
222918_at 23.6666667 0.223333333
223176_at 75.3333333 0.109666667
224122_at -178.6666667 0.536666667
224185_at 302 0.022666667
224249_at -9.6666667 0.376666667
224284_x_at 610.3333333 0.0064
224288_x_at 183.6666667 0.117
224321_at 345.3333333 0.014533333
224322_at 3 0.413333333
224340_at 492.6666667 0.002333333
224343_x_at -191 0.962666667
224351_at 74 0.145333333

Total number of rows: 22577

Table truncated, full table size 636 Kbytes.

Supplementary file Size Download File type/resource
GSM158655_1.CEL.gz 3.4 Mb (ftp)(http) CEL
GSM158655_2.CEL.gz 3.4 Mb (ftp)(http) CEL
GSM158655_3.CEL.gz 3.4 Mb (ftp)(http) CEL
Raw data provided as supplementary file

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