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Sample GSM158654 Query DataSets for GSM158654
Status Public on Mar 10, 2007
Title Tumorigenic (T2TG_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 8843.666667 0.0017
200080_s_at 27612 0.0017
200099_s_at 34963 0.0017
222523_at 602.6666667 0.0029
222575_at 367.3333333 0.017333333
222721_at 104 0.024
222802_at 682.3333333 0.020666667
222838_at 281.3333333 0.025
222918_at 27.6666667 0.206666667
223176_at 65.3333333 0.166
224122_at -143.6666667 0.576666667
224185_at 425.3333333 0.0235
224249_at 8.3333333 0.423333333
224284_x_at 752.6666667 0.007466667
224288_x_at 413.3333333 0.076
224321_at 123 0.024333333
224322_at 4.6666667 0.42
224340_at 482.3333333 0.002866667
224343_x_at -173.3333333 0.942666667
224351_at 80.3333333 0.128666667

Total number of rows: 22577

Table truncated, full table size 637 Kbytes.




Supplementary file Size Download File type/resource
GSM158654_1.CEL.gz 3.5 Mb (ftp)(http) CEL
GSM158654_2.CEL.gz 3.4 Mb (ftp)(http) CEL
GSM158654_3.CEL.gz 3.4 Mb (ftp)(http) CEL
Raw data provided as supplementary file

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