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Sample GSM231335 Query DataSets for GSM231335
Status Public on Sep 18, 2008
Title Tumor (T-02_FFPE_01)
Sample type genomic
 
Source name Human tumor tissue
Organism Homo sapiens
Characteristics Female, primary breast tumor
Extracted molecule genomic DNA
Extraction protocol Protocol 1 and 2 are new DNA extraction protocols, protocol 3 is modified Qiagen extraction protocol and 4 is Qiagen DNA extraction protocol.
Label biotin
Label protocol Biotinylated DNA were prepared according to the standard Affymetrix protocol from 90 ug total DNA (250K StyI Mapping Asssay Technical Manual, 2006, Affymetrix).
 
Hybridization protocol Following fragmentation, 90 ug of DNA were hybridized for 16 hr at 49C on 250K StyI mapping Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol GeneChips were scanned using the Affymetrix Scanner 7000.
Description formalin fixed parafin embedded tissue
Data processing The data were analyzed with CNAG v2.0, AsCNAR and CNATv4.0.1.
 
Submission date Sep 25, 2007
Last update date Aug 14, 2011
Contact name Ralf Krahe
E-mail(s) rkrahe@mdanderson.org
Phone (713) 834-6345
Fax (713) 834-6319
Organization name University of Texas M.D. Anderson Cancer Center
Department Cancer Genetics
Lab Krahe Lab
Street address 1515 Holcombe Blvd., Unit #1010
City Houston
State/province TX
ZIP/Postal code 77030
Country USA
 
Platform ID GPL3720
Series (1)
GSE9154 Optimizations of DNA isolation and copy number analysis identifies regions of genomic gain/loss in early breast cancer

Data table header descriptions
ID_REF
VALUE log2 ratio AB call
N_AB
Call_test
LOH_likelihood

Data table
ID_REF VALUE N_AB Call_test LOH_likelihood
SNP_A-1909444 0.992889 2 3 0.355386
SNP_A-2237149 -0.952403 2 3 0.355386
SNP_A-4303947 -0.499282 2 1 0.355386
SNP_A-2236359 -0.027685 2 3 0.355386
SNP_A-2205441 -0.276412 2 1 0.355386
SNP_A-2116190 0.451750 2 2 0.000000
SNP_A-4291020 -0.320345 2 1 0.497541
SNP_A-2109914 -0.422968 2 1 0.497541
SNP_A-2291997 0.227593 2 1 0.497541
SNP_A-4277872 0.598843 2 1 0.497541
SNP_A-2118217 0.445086 2 1 0.497541
SNP_A-1866065 1.374569 2 0 0.497541
SNP_A-2288244 0.266079 2 3 0.497541
SNP_A-1783407 0.373812 2 2 0.000000
SNP_A-2169457 0.181891 2 2 0.000000
SNP_A-4271011 -0.430012 2 3 0.142154
SNP_A-2082515 0.533244 2 3 0.142154
SNP_A-1910751 0.378234 2 2 0.000000
SNP_A-2081399 0.238045 2 1 0.355386
SNP_A-2223642 0.380098 2 3 0.355386

Total number of rows: 238304

Table truncated, full table size 8480 Kbytes.




Supplementary file Size Download File type/resource
GSM231335.CEL.gz 25.5 Mb (ftp)(http) CEL
GSM231335.CHP.gz 710.8 Kb (ftp)(http) CHP
GSM231335.txt.gz 4.8 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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