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Sample GSM182839 Query DataSets for GSM182839
Status Public on Mar 17, 2008
Title X03399_Nsp_7
Sample type genomic
Source name breast-her2neg
Organism Homo sapiens
Characteristics Primary malignant neoplasm of female breast; INFILTRATING DUCTAL CARCINOMA OF BREAST., 75-90
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 ( 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
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
VALUE GLAD segmented copy number

Data table
SNP_A-1780520 2.12847995758057
SNP_A-1780618 1.99591255187988
SNP_A-1780632 2.03248834609985
SNP_A-1780654 1.99116623401642
SNP_A-4192495 1.75402855873108
SNP_A-4192498 2.08182740211487
SNP_A-1780732 2.12279343605042
SNP_A-1780848 1.97242224216461
SNP_A-1780985 2.00774097442627
SNP_A-1781022 1.98756718635559
SNP_A-1781076 2.03248834609985
SNP_A-1781249 1.75534832477570
SNP_A-1781276 1.99591255187988
SNP_A-1781302 2.00290656089783
SNP_A-1781510 1.75402855873108
SNP_A-4192564 1.99388146400452
SNP_A-1781614 2.00290656089783
SNP_A-1781633 1.98756718635559
SNP_A-1781764 2.00774097442627
SNP_A-1781829 2.61597728729248

Total number of rows: 262264

Table truncated, full table size 7937 Kbytes.

Supplementary file Size Download File type/resource
GSM182839.CEL.gz 26.7 Mb (ftp)(http) CEL
GSM182839.exp.gz 270 b (ftp)(http) EXP

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