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Sample GSM188194 Query DataSets for GSM188194
Status Public on Nov 02, 2007
Title Melanoma (AF500KNSPWM983)
Sample type genomic
 
Source name WM983 Cell Line
Organism Homo sapiens
Characteristics Melanoma
Growth protocol Cells were grown in in RPMI 1640 supplemented with 10% heat-inactivated FBS
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was isolated from cultured cells with Mini DNeasy kit (Qiagen, Inc.)
Label biotin
Label protocol 250 ng Genomic DNA was biotinylated as described by manufacturer (Genechip Mapping 500k assay manual 701930 Rev.3 or 100k assay manual 701684 Rev.3, Affymetrix).
 
Hybridization protocol Hybridizations were performed according to the standard manufacturer's describe in Genechip Mapping 500k assay manual 701930 Rev.3 or 100k assay manual 701684 Rev.3, Affymetrix.
Scan protocol Scanning was done using an Affymetrix 3000 microarray scanner. Specifications can be found in Genechip Mapping 500k assay manual 701930 Rev.3 or 100k assay manual 701684 Rev.3, Affymetrix
Description Melanoma
Data processing Image files were analyzed using the dChip software. A panel of chips (n = 12) assayed with germline DNA served as a reference in order to calculate a test/reference ratio. The ratios were then subject global normalization that assumed that the median copy number is diploid (2n; log2 Ratio = 0).
 
Submission date May 09, 2007
Last update date Oct 31, 2007
Contact name Joel Greshock
Organization name GlaxoSmithKline
Department Translational Medicine, Oncology
Street address 2301 Renaissance Blvd.
City King of Prussia
State/province PA
ZIP/Postal code 19406
Country USA
 
Platform ID GPL3718
Series (1)
GSE7822 A comparison of DNA copy number profiling platforms using a panel of melanoma cell lines

Data table header descriptions
ID_REF
VALUE Log2(estimated test/reference intensity ratio)

Data table
ID_REF VALUE
SNP_A-1794317 -0.240
SNP_A-1786243 0.540
SNP_A-1967971 0.650
SNP_A-1791488 -0.008
SNP_A-1798049 0.310
SNP_A-2138981 1.610
SNP_A-2308310 0.140
SNP_A-1976263 -0.290
SNP_A-1784239 -0.470
SNP_A-1898104 -0.130
SNP_A-4212440 0.100
SNP_A-2107677 0.260
SNP_A-2094651 0.070
SNP_A-2071979 -0.520
SNP_A-2029699 -0.490
SNP_A-4203142 -0.390
SNP_A-2260858 -0.490
SNP_A-2154361 0.500
SNP_A-2118532 -0.520
SNP_A-1980258 -0.460

Total number of rows: 262264

Table truncated, full table size 5266 Kbytes.




Supplementary file Size Download File type/resource
GSM188194.CEL.gz 25.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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