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Sample GSM2635498 Query DataSets for GSM2635498
Status Public on Jul 01, 2017
Title Melanoma UACC cell line 558
Sample type genomic
 
Source name Melanoma UACC cell line
Organism Homo sapiens
Characteristics disease state: Melanoma
tissue: Skin
Treatment protocol NA
Growth protocol Melanoma cell line was cultured in RPMI 1640 in the presence of 10% fetal bovine serum.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was isolated from melanoma cells using Qiagen DNeasy Blood and Tissue kit
Label C-Bio and A-DNP
Label protocol 200ng of genomic DNA, quantitated using Quant-iTâ„¢ PicoGreen dsDNA Reagent (ThermoFisher Scientific, Waltham, MA, USA) is denatured and neutralized, then isothermally amplified by whole-genome amplification. The amplified product is enzymatically fragmented, then precipitated and re-suspended.
 
Hybridization protocol Resuspended samples are denatured, then hybridized to locus-specific 50-mer oligonucleotides which are attached to 1-micron beads on the BeadChip. These 50-mer probes stop one base before the location of interest. Enzymatic single-base extension of the oligos on the BeadChip, using the captured DNA as a template, incorporates tagged nucleotides on the BeadChip, which are subsequently fluorophore-labeled during staining. The fluorescent label determines the genotype call for the sample.
Scan protocol The Illumina iScan scans the BeadChips at two wavelengths to detect the fluorescent label, creating image files that are converted into genotype calls based on the detected fluorescence.
Description Genomic DNA extracted from melanoma cell line was genotyped using HumanOmniExpress-12v1_A Genotyping BeadChips (Illumina)
UACC558
Data processing Genomic DNA extracted from melanoma cell lines was genotyped using Illumina Infinium human OmniExpress array
 
Submission date May 23, 2017
Last update date Jan 23, 2018
Contact name Jiyeon Choi
Organization name NCI
Street address 9615 Medical Center Drive, Rm 3116
City Rockville
State/province Maryland
ZIP/Postal code 20850
Country USA
 
Platform ID GPL13135
Series (2)
GSE99193 Genotype data from early passage UACC melanoma cell lines
GSE99221 A common intronic variant of PARP1 confers melanoma risk and mediates melanocyte growth and senescence escape via regulation of MITF

Data table header descriptions
ID_REF
VALUE Genotypes: AA,AB,BB or NC (no call)
Score
Theta
R
B Allele Freq
Log R Ratio

Data table
ID_REF VALUE Score Theta R B Allele Freq Log R Ratio
rs1000000 BB 0.7970361 0.9914041 1.581683 0.9998286 0.0189311
rs1000002 AA 0.7949939 0.03190913 1.015295 0.00 0.05081849
rs10000023 AB 0.7404771 0.529581 2.19495 0.539616 0.02231633
rs1000003 AA 0.8759668 0.04045142 1.061413 0.0009140745 -0.1509504
rs10000030 AB 0.2139434 0.7818676 0.3940611 0.7662458 -0.2127144
rs10000037 AB 0.7494124 0.469375 1.052069 0.4287671 -0.02564502
rs10000041 AA 0.7795854 0.03700472 1.25589 0.01079213 -0.2020236
rs10000042 BB 0.7877672 0.9695888 0.7812628 1 -0.1195848
rs10000049 AA 0.8594182 0.03081455 1.099303 0.007268905 -0.2195443
rs1000007 AA 0.7938727 0.01030537 1.424039 0.00 0.0374134
rs10000073 AA 0.5119626 0.01997921 0.7586415 0.0001915446 -0.2604552
rs10000081 AA 0.8311692 0.04237429 0.7462645 0.004539335 -0.2173899
rs10000092 AB 0.7372996 0.4983728 0.6143081 0.4635777 -0.2969214
rs10000105 BB 0.5023558 0.9739662 1.056094 0.998035 -0.1129952
rs10000119 BB 0.7482945 0.9787049 1.193437 0.9990012 -0.1053755
rs10000124 BB 0.6439699 0.9902655 1.286668 1 -0.110433
rs10000147 AA 0.5196046 0.06611843 0.4657401 0.03372343 -0.1510437
rs10000154 AA 0.4878684 0.02783649 0.7032787 0.002246186 -0.2236097
rs1000016 AA 0.8008563 0.01941136 0.746073 0.00 0.05560615
rs10000160 BB 0.4809374 0.9523321 0.6282513 0.9917369 -0.101903

Total number of rows: 733202

Table truncated, full table size 43619 Kbytes.




Supplementary file Size Download File type/resource
GSM2635498_5697601066_R06C01_Grn.idat.gz 4.9 Mb (ftp)(http) IDAT
GSM2635498_5697601066_R06C01_Red.idat.gz 4.8 Mb (ftp)(http) IDAT
Processed data included within Sample table

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