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Sample GSM1588793 Query DataSets for GSM1588793
Status Public on Sep 15, 2015
Title Pt17-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 17 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 0.467551622418879
cg00212031 0.326582278481013
cg00213748 0.405585106382979
cg00214611 0.282107574094402
cg00455876 0.46421568627451
cg01707559 0.232573877735168
cg02004872 0.262440758293839
cg02011394 0.454673225579761
cg02050847 0.237756010685663
cg02233190 0.166570936243538
cg02494853 0.045355281404302
cg02839557 0.355947136563877
cg02842889 0.687728761317665
cg03052502 0.536764705882353
cg03155755 0.388976377952756
cg03244189 0.435722411831627
cg03443143 0.367237163814181
cg03683899 0.300086730268864
cg03695421 0.425651867512333
cg03706273 0.0959012086179716

Total number of rows: 485512

Table truncated, full table size 13804 Kbytes.

Supplementary file Size Download File type/resource
GSM1588793_9513149040_R01C01_Grn.idat.gz 4.0 Mb (ftp)(http) IDAT
GSM1588793_9513149040_R01C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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