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Sample GSM1588705 Query DataSets for GSM1588705
Status Public on Sep 15, 2015
Title Pt1-baseline-2
Sample type genomic
Source name tumor biopsy
Organism Homo sapiens
Characteristics cell type: melanoma
mapki sensitivity: sensitive
mapki treatment: none
Extracted molecule genomic DNA
Extraction protocol genomic DNA
Label Cy5 and Cy3
Label protocol Not provided
Hybridization protocol Not provided
Scan protocol Not provided
Description Patient 1 melanoma, pre MAPKi treatment, 1st biopsy, replicate
Data processing To identify the differentially methylated CpG sites, we analyze the Illumina 450K Methylation array output data using R-package minfi (Aryee et al., 2014). Raw image IDAT files were loaded into the R statistical computing environment using minfi, and the data was normalized using the SWAN function. This output a matrix of methylation indices (beta values), which were continuous values between 0 and 1 representing the ratio/fraction of the intensity of the methylated-probe signal to the total signal intensity for each probed CpG site. For each site, the methylation change was measured by the percent methylation difference (Δbeta) from paired baseline to DP/DD-DP samples. Minfi function dmpFinder was then applied to calculate the p-value of the logit transformed differential methylation. The p-values were corrected for multiple hypothesis testing with false discovery rates (FDR) q-values. We then used a cutoff of q-value ≤ 0.05 to define differential methylation
Submission date Jan 22, 2015
Last update date Sep 22, 2015
Contact name Willy Hugo
Organization name UCLA
Department Medicine
Street address 10833 Le Conte Ave, 52-121 CHS, Division of Dermatology
City Los Angeles
State/province California
ZIP/Postal code 90095
Country USA
Platform ID GPL13534
Series (2)
GSE65183 Methylation changes in pre MAPKi treatment and post MAPKi resistance Melanomas
GSE65186 Non-genomic and Immune Evolution in Melanoma with Acquired MAPKi Resistance

Data table header descriptions
VALUE Average Beta

Data table
cg00050873 0.858673127809481
cg00212031 0.320366972477064
cg00213748 0.414850686037127
cg00214611 0.117825690859399
cg00455876 0.651550690643732
cg01707559 0.161356068434952
cg02004872 0.0283462565145545
cg02011394 0.969506800840429
cg02050847 0.913058536653858
cg02233190 0.0962477120195241
cg02494853 0.013530833612896
cg02839557 0.116651133892513
cg02842889 0.096551724137931
cg03052502 0.967782520781847
cg03155755 0.910761525166661
cg03244189 0.288055624534393
cg03443143 0.883963706136785
cg03683899 0.0838459048235675
cg03695421 0.607037256061502
cg03706273 0.541989885759672

Total number of rows: 485512

Table truncated, full table size 13833 Kbytes.

Supplementary file Size Download File type/resource
GSM1588705_8795207119_R05C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588705_8795207119_R05C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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