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Sample GSM1588741 Query DataSets for GSM1588741
Status Public on Sep 15, 2015
Title Pt7-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 7 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 0.417017691659646
cg00212031 0.341118623232944
cg00213748 0.478363493312353
cg00214611 0.445566778900112
cg00455876 0.289109613338063
cg01707559 0.364961375892727
cg02004872 0.142159522517634
cg02011394 0.332432432432432
cg02050847 0.274757281553398
cg02233190 0.17688679245283
cg02494853 0.0153183318099053
cg02839557 0.503352704514975
cg02842889 0.411609071274298
cg03052502 0.445229681978799
cg03155755 0.424641833810888
cg03244189 0.352206865804726
cg03443143 0.350918511540273
cg03683899 0.356617647058824
cg03695421 0.181997371879106
cg03706273 0.0180175446086948

Total number of rows: 485512

Table truncated, full table size 13829 Kbytes.

Supplementary file Size Download File type/resource
GSM1588741_8795194168_R03C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588741_8795194168_R03C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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