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Sample GSM612085 Query DataSets for GSM612085
Status Public on Nov 26, 2010
Title M229
Sample type genomic
 
Source name Human melanoma cell lines
Organism Homo sapiens
Characteristics cell type: Human melanoma cell lines
cell line: M229
Growth protocol Selected melanoma cell lines were grown in DMEM supplemented with 10% serum
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted using FlexiGene DNA Kit (Qiagen) according to the manufacturer's protocol
Label C-Bio and A-DNP
Label protocol Fragmented template DNA was first captured on the BeadChip and then incorporation of labeled nucleotides during oligos extension were used to determine the genotype call for the sample
 
Hybridization protocol Fragmented DNA was first precipitated and then hybridized to BeadChip (Infinium II Assay) according to manufacturer's protocol
Scan protocol Array scanning was carried out with the GeneChip Scanner 3000 7G (Affymetrix) according to the manufacturer's instructions
Data processing Scanned array data were imported into BeadStudio software (Illumina Inc.) for data processing
 
Submission date Oct 22, 2010
Last update date Nov 26, 2010
Contact name Mikyung Lee
Organization name UCLA
Street address UCLA Med-Derm BOX 951781, 13-942 Factor, 13-952 Factor Los Angeles, CA 90095-1781
City Los Angeles
State/province CA
ZIP/Postal code 90024
Country USA
 
Platform ID GPL6988
Series (1)
GSE24890 Genome-wide copy number variation in human metastatic melanoma cell lines

Data table header descriptions
ID_REF
Genotype
GC_Score
Theta
R
B_Allele_Freq
VALUE Log_R_Ratio

Data table
ID_REF Genotype GC_Score Theta R B_Allele_Freq VALUE
rs3823184-107_T_F_IFB1161211720:0 BB 0.7477 0.985 0.624 1.0000 -0.1518
rs723490-126_T_R_IFB1161253789:0 BB 0.8157 0.989 1.127 1.0000 0.1751
rs4955547-123_T_F_IFB1161227890:0 AB 0.8364 0.635 2.011 0.4800 0.2922
rs8011562-126_T_R_IFB1161267227:0 AA 0.9199 0.055 0.591 0.0262 -0.1732
rs9468805-123_B_R_IFB1161276674:0 BB 0.8595 0.988 1.138 1.0000 -0.2251
rs2400669-123_T_R_IFB1161184024:0 AA 0.8191 0.053 0.576 0.0248 -0.3884
rs1058465-106_T_F_IFB1161110088:0 BB 0.4259 0.985 0.931 1.0000 0.0074
rs5999-126_T_F_IFB1161234109:0 AA 0.8697 0.016 1.247 0.0044 0.2297
rs2013854-126_B_R_IFB1161162309:0 NC 0.0000 0.635 1.119 0.4098 0.2630
rs16987048-123_B_F_IFB1161149544:0 AA 0.8357 0.023 1.828 0.0101 0.0787
rs8019730-126_B_F_IFB1161267374:0 AA 0.9342 0.023 0.689 0.0129 0.2269
rs941986-126_T_F_IFB1161276218:0 AB 0.8457 0.740 0.696 0.5903 0.0909
rs2294041-126_T_R_IFB1161179340:0 AA 0.8265 0.015 1.594 0.0052 0.5553
rs2232032-98_T_R_IFB1161170583:0 BB 0.7606 0.983 0.691 1.0000 0.3098
rs10005231-126_T_R_IFB1161282566:0 BB 0.7888 0.983 1.017 1.0000 -0.1742
rs203674-126_T_F_IFB1161163074:0 AA 0.8577 0.043 0.347 0.0046 -0.2789
rs2271173-126_B_F_IFB1161174408:0 BB 0.8782 0.974 0.726 0.9839 -0.3007
rs748741-126_B_F_IFB1161257614:0 AA 0.9159 0.034 1.243 0.0159 0.7544
rs10475542-119_B_R_IFB1161289850:0 AA 0.8506 0.001 1.626 0.0004 -0.3073
rs11191439-126_B_F_IFB1161117943:0 AA 0.9526 0.017 0.895 0.0145 -0.4925

Total number of rows: 511354

Table truncated, full table size 35414 Kbytes.




Supplementary file Size Download File type/resource
GSM612085_M229InfinumSNPReportCalls.txt.gz 11.3 Mb (ftp)(http) TXT
GSM612085_M229InfinumSNPReportRaw.txt.gz 9.7 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file

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