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Sample GSM182849 Query DataSets for GSM182849
Status Public on Mar 17, 2008
Title X04866_Nsp_17
Sample type genomic
 
Source name breast-her2neg
Organism Homo sapiens
Characteristics Primary malignant neoplasm of female breast; BREAST: INFILTRATING DUCTAL CARCINOMA., >90
Extracted molecule genomic DNA
Extraction protocol A small piece of frozen tissue was removed from a sample of frozen tissue and incubated in a proteinase K digestion solution followed by cleanup using the Qiagen M48 robotics protocol.
Label biotin
Label protocol Following restriction enzyme digestion, biotin labeled DNA was prepared according to the Affymetrix protocol from 500ng of starting DNA (GeneChip Mapping 500K Assay Manual, Affymetrix, 2005). The fluidics station model FS450 was used.
 
Hybridization protocol Mapping 500K arrays were hybridized according to the Affymetrix protocol (GeneChip Mapping 500K Assay Manual, Affymetrix, 2005) using an Affymetrix model 640 hybridization oven.
Scan protocol Mapping 500K arrays were scanned according to the Affymetrix protocol (GeneChip Mapping 500K Assay Manual, Affymetrix, 2005) using a GS3000 scanner.
Description NA
Data processing Affymetrix 500K Mapping Array intensity signal CEL files were processed by dChip 2005 (Build date Nov 30, 2005) using the PM/MM difference model and invariant set normalization. Forty-eight normal samples were downloaded from the Affymetrix website (http://www.affymetrix.com/support/technical/byproduct.affx?product=500k) and analyzed at the same time. One CEL file for each set (Sty and Nsp) with the median signal intensity across the set was selected as the reference array. The dChip-normalized signal intensities were converted to log2 ratios and segmented as follows. For each autosomal probe set, the log2 tumor/normal ratio of each tumor sample was calculated using the average intensity for each probe set in the normal set. For Chromosome X, the average of the 20 normal female samples was used. Each probe set was mapped to the genome, NCBI assembly version 35, using annotation provided by the Affymetrix web site. The log2 ratios were centered to a median of zero and segmented using the GLAD package for the R statistical environment.
 
Submission date Apr 18, 2007
Last update date Jun 27, 2008
Contact name Peter Haverty
E-mail(s) phaverty@gene.com
Organization name Genentech, Inc.
Department Bioinformatics
Street address 1 DNA Way
City South San Francisco
State/province CA
ZIP/Postal code 94080
Country USA
 
Platform ID GPL3718
Series (1)
GSE7545 Affymetrix 500K Mapping Array data from breast tumors

Data table header descriptions
ID_REF
VALUE GLAD segmented copy number

Data table
ID_REF VALUE
SNP_A-1780520 2.27008771896362
SNP_A-1780618 1.80297029018402
SNP_A-1780632 1.78844010829926
SNP_A-1780654 1.60427916049957
SNP_A-4192495 1.80726313591003
SNP_A-4192498 1.82145941257477
SNP_A-1780732 2.10185170173645
SNP_A-1780848 2.27456378936768
SNP_A-1780985 1.82178544998169
SNP_A-1781022 1.86417734622955
SNP_A-1781076 1.78844010829926
SNP_A-1781249 1.85306680202484
SNP_A-1781276 1.79945242404938
SNP_A-1781302 2.24780392646790
SNP_A-1781510 2.01668334007263
SNP_A-4192564 2.63728284835815
SNP_A-1781614 1.65202748775482
SNP_A-1781633 1.79632472991943
SNP_A-1781764 1.56404769420624
SNP_A-1781829 1.79026162624359

Total number of rows: 262264

Table truncated, full table size 7931 Kbytes.




Supplementary file Size Download File type/resource
GSM182849.CEL.gz 22.9 Mb (ftp)(http) CEL
GSM182849.exp.gz 270 b (ftp)(http) EXP

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