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Sample GSM1588804 Query DataSets for GSM1588804
Status Public on Sep 15, 2015
Title Pt19-DD-DP1-1
Sample type genomic
Source name tumor biopsy
Organism Homo sapiens
Characteristics cell type: melanoma
mapki sensitivity: resistant
mapki treatment: BRAFi+MEKi
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 19 melanoma, post BRAFi+MEKi resistance, 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 0.870568837592745
cg00212031 0.355177993527508
cg00213748 0.331282051282051
cg00214611 0.319757365684575
cg00455876 0.59400269541779
cg01707559 0.216182828906733
cg02004872 0.148047722342733
cg02011394 0.933899654897797
cg02050847 0.66887417218543
cg02233190 0.227484989993329
cg02494853 0.0195519348268839
cg02839557 0.223094170403587
cg02842889 0.26568551510457
cg03052502 0.85323012801429
cg03155755 0.540103866128102
cg03244189 0.164835164835165
cg03443143 0.868588925746364
cg03683899 0.262037037037037
cg03695421 0.283359497645212
cg03706273 0.057172131147541

Total number of rows: 485512

Table truncated, full table size 13909 Kbytes.

Supplementary file Size Download File type/resource
GSM1588804_9702496109_R02C02_Grn.idat.gz 4.0 Mb (ftp)(http) IDAT
GSM1588804_9702496109_R02C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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