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Sample GSM188226 Query DataSets for GSM188226
Status Public on Nov 02, 2007
Title Melanoma (AF500KNSPSKMEL28)
Sample type genomic
Source name SKMEL28 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
VALUE Log2(estimated test/reference intensity ratio)

Data table
SNP_A-1794317 -0.205
SNP_A-1786243 -0.729
SNP_A-1967971 0.154
SNP_A-1791488 -0.537
SNP_A-1798049 0.049
SNP_A-2138981 1.363
SNP_A-2308310 0.332
SNP_A-1976263 -0.247
SNP_A-1784239 0.199
SNP_A-1898104 -0.114
SNP_A-4212440 -0.374
SNP_A-2094651 -0.460
SNP_A-2107677 0.482
SNP_A-2071979 -0.038
SNP_A-2029699 0.188
SNP_A-2260858 -0.153
SNP_A-4203142 -0.355
SNP_A-2154361 0.136
SNP_A-2118532 0.094
SNP_A-1980258 -0.027

Total number of rows: 260353

Table truncated, full table size 5244 Kbytes.

Supplementary file Size Download File type/resource
GSM188226.CEL.gz 21.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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