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Sample GSM1588706 Query DataSets for GSM1588706
Status Public on Sep 15, 2015
Title Pt1-DP1-1
Sample type genomic
Source name tumor biopsy
Organism Homo sapiens
Characteristics cell type: melanoma
mapki sensitivity: resistant
mapki treatment: BRAFi
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, post BRAFi 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 0.884532797672647
cg00212031 0.20332979100248
cg00213748 0.473352033660589
cg00214611 0.210403272939801
cg00455876 0.696285576459238
cg01707559 0.203650680028633
cg02004872 0.0331177520071365
cg02011394 0.970584939489018
cg02050847 0.941571402649247
cg02233190 0.0931899641577061
cg02494853 0.0127434653537036
cg02839557 0.11392898946547
cg02842889 0.0897435897435897
cg03052502 0.955141750308153
cg03155755 0.931499623210249
cg03244189 0.188995215311005
cg03443143 0.907896305125149
cg03683899 0.0928753180661578
cg03695421 0.542765420775052
cg03706273 0.442811869778162

Total number of rows: 485512

Table truncated, full table size 13841 Kbytes.

Supplementary file Size Download File type/resource
GSM1588706_8795207135_R02C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588706_8795207135_R02C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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