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Sample GSM1588801 Query DataSets for GSM1588801
Status Public on Sep 15, 2015
Title Pt18-DD-DP1-2
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 18 melanoma, post BRAFi+MEKi resistance, 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 0.451555266791196
cg00212031 0.122398146841244
cg00213748 0.247009880395216
cg00214611 0.147878346384994
cg00455876 0.652167746668297
cg01707559 0.134284160270744
cg02004872 0.0383162152094088
cg02011394 0.685661805264435
cg02050847 0.38305983154226
cg02233190 0.0550411189535712
cg02494853 0.0257942436012349
cg02839557 0.051142750093668
cg02842889 0.0820478426112229
cg03052502 0.868251637677886
cg03155755 0.53694199670766
cg03244189 0.195124894412936
cg03443143 0.446768497374875
cg03683899 0.0416749779158237
cg03695421 0.425692695214106
cg03706273 0.035391000294108

Total number of rows: 485512

Table truncated, full table size 13796 Kbytes.

Supplementary file Size Download File type/resource
GSM1588801_9283265037_R06C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588801_9283265037_R06C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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