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Status
Public on Sep 18, 2008
Title
Normal (N-06_FF_03)
Sample type
genomic
Source name
Human tumor tissue
Organism
Homo sapiens
Characteristics
Female, breast normal
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
fresh frozen 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
log2ratio_A
log2ratio_B
N_AB
N_A
N_B
Call_test
Call_reference
Data table
ID_REF
VALUE
log2ratio_A
log2ratio_B
N_AB
N_A
N_B
Call_test
Call_reference
SNP_A-1909444
0.400984
0.489099
0.019550
2
1
1
3
3
SNP_A-2237149
-0.360666
-0.112525
-0.420310
2
0
0
3
3
SNP_A-4303947
0.444900
0.487014
0.267718
2
1
1
1
1
SNP_A-2236359
-0.067818
-0.023342
-0.084163
2
0
0
3
3
SNP_A-2205441
-0.132560
0.122425
-0.178746
2
0
0
1
1
SNP_A-2116190
0.360308
0.365513
0.355860
2
1
1
2
2
SNP_A-4291020
-0.242205
0.085341
-0.375776
2
2
1
1
1
SNP_A-2109914
0.130051
0.487570
0.066849
2
1
1
1
1
SNP_A-2291997
-0.638342
-0.333563
-0.715486
2
2
1
1
1
SNP_A-4277872
0.042659
0.043686
0.029408
2
1
0
1
1
SNP_A-2118217
-0.118960
-0.067626
-0.199190
2
1
1
2
2
SNP_A-1866065
0.960947
1.019844
0.740048
2
2
1
3
3
SNP_A-2288244
0.261145
0.378104
0.240744
2
1
1
3
3
SNP_A-1783407
0.073312
0.127561
-0.088677
2
1
1
1
1
SNP_A-2169457
-0.048174
0.385714
-0.188366
2
1
0
3
3
SNP_A-4271011
-0.041216
0.015450
-0.057666
2
0
0
3
3
SNP_A-2082515
0.016163
0.023308
0.014062
2
1
1
3
3
SNP_A-1910751
-0.152507
-0.112432
-0.164623
2
1
0
1
1
SNP_A-2081399
-0.039503
-0.023451
-0.097658
2
1
0
1
1
SNP_A-2223642
-0.032200
0.001032
-0.036096
2
1
1
3
3
Total number of rows: 238304 Table truncated, full table size 12217 Kbytes .Supplementary file
Size
Download
File type/resource
GSM231370.CEL.gz
28.9 Mb
(ftp) (http)
CEL
GSM231370.CHP.gz
429.7 Kb
(ftp) (http)
CHP
GSM231370.txt.gz
6.5 Mb
(ftp) (http)
TXT
Processed data included within Sample table
Processed data provided as supplementary file