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Sample GSM2538786 Query DataSets for GSM2538786
Status Public on Mar 16, 2020
Title Melanoma cell line subclone 3 MCM1DLN
Sample type genomic
 
Source name Melanoma cell line MCM1DLN
Organism Homo sapiens
Characteristics cell type: melanoma
origin: Melanoma cell line MCM1DLN derived from MCM1D
cell malignancy: tumor forming and metastasizing to lymph nodes and lung after injection into SCID mice
gender: male
Growth protocol Melanoma cells were cultured in MIM medium supplemented with 2 % FCS containing: 80 % MCDB153, 20 % Leibovitz`s l15, 5 µg/ml Insuline, bovine, 0.5 ng/ml Epidermal Growth Factor (EGF), 1.68 mM CaCl2, 100 IU/ml Penicillin, 100 µg/ml Streptomycin and 2 µg/ml Ciprofloxacin at 37°C at 5% CO2
Extracted molecule genomic DNA
Extraction protocol DNA was isolated by using the All Prep DNA Kit (Qiagen, Hilden, Germany) according to the manufacturer`s protocol.
Label biotin
Label protocol According to the manufacturer`s protocol (Affymetrix)
 
Hybridization protocol DNA was restriction digested, PCR amplified, fragmented, labeled, and hybridized to each array as per manufacturer`s instructions (Affymetrix).
Scan protocol The arrays were scanned using the appropriate Gene Chip Scanner.
Data processing CEL files were processed via the genotyping console 4.2.0 using default parameters. CHP files were generated via the genotyping console 4.2.0 using default parameters. Normalization was performed using the birdseed v2 algorithm.
primary data description: Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal
 
Submission date Mar 16, 2017
Last update date Mar 16, 2020
Contact name David Schörghofer
E-mail(s) david.schoerghofer@meduniwien.ac.at
Organization name Medical University of Vienna
Department Department for Pathobiochemistry and Genetics
Street address Währingerstraße 10
City Wien
ZIP/Postal code 1200
Country Austria
 
Platform ID GPL6801
Series (1)
GSE96708 Affymetrix SNP6.0 array data for isogenic melanoma cell lines

Data table header descriptions
ID_REF PROBE SET NAME
VALUE CALL
CONFIDENCE
FORCED CALL
SIGNAL A
SIGNAL B

Data table
ID_REF VALUE CONFIDENCE FORCED CALL SIGNAL A SIGNAL B
SNP_A-2131660 AB 0.078722 AB 1430.965210 2742.909424
SNP_A-1967418 AB 0.001888 AB 541.012207 651.793396
SNP_A-1969580 BB 0.043793 BB 1166.396484 2667.543457
SNP_A-4263484 BB 0.007671 BB 910.333008 2242.479248
SNP_A-1978185 AA 0.007102 AA 2501.069824 441.434540
SNP_A-4264431 AA 0.005908 AA 1999.822876 541.125732
SNP_A-1980898 AA 0.008216 AA 1717.685791 338.317688
SNP_A-1983139 AA 0.001621 AA 1273.378418 508.652283
SNP_A-4265735 NC 0.100434 AA 1564.243164 722.428040
SNP_A-1995832 AB 0.002898 AB 1388.526855 1438.839600
SNP_A-1995893 NC 0.581452 BB 1314.232422 2521.221191
SNP_A-1997689 BB 0.006698 BB 1305.118774 3590.707031
SNP_A-1997709 AA 0.006421 AA 2027.826782 426.472931
SNP_A-1997896 AA 0.008974 AA 1849.264038 956.638489
SNP_A-1997922 AB 0.007975 AB 1134.575317 1072.749146
SNP_A-2000230 AA 0.079690 AA 2584.139404 1425.005371
SNP_A-2000332 AA 0.013419 AA 2433.733887 872.302856
SNP_A-2000337 AA 0.001610 AA 1424.994385 326.274963
SNP_A-2000342 AA 0.076296 AA 3536.368896 1642.550049
SNP_A-4268173 AA 0.001766 AA 1703.796997 393.868011

Total number of rows: 909622

Table truncated, full table size 46158 Kbytes.




Supplementary file Size Download File type/resource
GSM2538786_MCM1DLN_melanoma_cell_line.CEL.gz 31.2 Mb (ftp)(http) CEL
GSM2538786_MCM1DLN_melanoma_cell_line.chp.gz 13.6 Mb (ftp)(http) CHP
Processed data included within Sample table

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