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Sample GSM188224 Query DataSets for GSM188224
Status Public on Nov 02, 2007
Title Melanoma (AF500KNSPMEWO)
Sample type genomic
 
Source name MEWO 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 0.159
SNP_A-1786243 0.031
SNP_A-1967971 -0.048
SNP_A-1791488 -0.243
SNP_A-1798049 -0.419
SNP_A-2138981 0.259
SNP_A-2308310 -0.299
SNP_A-1976263 -0.111
SNP_A-1784239 0.245
SNP_A-1898104 0.138
SNP_A-4212440 -0.106
SNP_A-2094651 -0.342
SNP_A-2107677 0.123
SNP_A-2071979 0.098
SNP_A-2029699 0.673
SNP_A-2260858 -0.186
SNP_A-4203142 -0.159
SNP_A-2154361 0.037
SNP_A-2118532 -0.279
SNP_A-1980258 -0.434

Total number of rows: 260353

Table truncated, full table size 5229 Kbytes.




Supplementary file Size Download File type/resource
GSM188224.CEL.gz 23.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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