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Sample GSM182848 Query DataSets for GSM182848
Status Public on Mar 17, 2008
Title X04860_Nsp_16
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 2.12287926673889
SNP_A-1780618 1.86266994476318
SNP_A-1780632 1.71064114570618
SNP_A-1780654 1.72667467594147
SNP_A-4192495 1.74420440196991
SNP_A-4192498 2.10451936721802
SNP_A-1780732 2.12558031082153
SNP_A-1780848 1.73710966110229
SNP_A-1780985 2.18696093559265
SNP_A-1781022 2.23755383491516
SNP_A-1781076 1.73135066032410
SNP_A-1781249 2.20421028137207
SNP_A-1781276 1.86266994476318
SNP_A-1781302 2.10176157951355
SNP_A-1781510 1.71088790893555
SNP_A-4192564 2.00403976440430
SNP_A-1781614 2.10176157951355
SNP_A-1781633 2.08395266532898
SNP_A-1781764 2.15928697586060
SNP_A-1781829 1.71757829189301

Total number of rows: 262264

Table truncated, full table size 7915 Kbytes.




Supplementary file Size Download File type/resource
GSM182848.CEL.gz 24.2 Mb (ftp)(http) CEL
GSM182848.exp.gz 270 b (ftp)(http) EXP

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