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Sample GSM1588792 Query DataSets for GSM1588792
Status Public on Sep 15, 2015
Title Pt17-baseline-1
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 17 melanoma, pre MAPKi treatment, 1st biopsy
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 0.396499238964992
cg00212031 0.421417565485362
cg00213748 0.337694194603434
cg00214611 0.522641509433962
cg00455876 0.360264900662252
cg01707559 0.333931374747701
cg02004872 0.287486515641855
cg02011394 0.45368492224476
cg02050847 0.305989285804961
cg02233190 0.257505773672055
cg02494853 0.0338043662210188
cg02839557 0.397163120567376
cg02842889 0.555385613644791
cg03052502 0.374501992031873
cg03155755 0.40819209039548
cg03244189 0.344277673545966
cg03443143 0.444384156266956
cg03683899 0.285
cg03695421 0.3469068128426
cg03706273 0.074967539123898

Total number of rows: 485512

Table truncated, full table size 13806 Kbytes.

Supplementary file Size Download File type/resource
GSM1588792_9513149079_R01C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588792_9513149079_R01C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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