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Sample GSM1588816 Query DataSets for GSM1588816
Status Public on Sep 15, 2015
Title Pt21-DP2-1
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 21 melanoma, post BRAFi resistance, 2nd biopsy (surrogate baseline for BRAFi+MEKi tumors)
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 0.836386172703484
cg00212031 0.077180280061342
cg00213748 0.697429544750697
cg00214611 0.107848673066064
cg00455876 0.743577657317935
cg01707559 0.0922783198981756
cg02004872 0.0392288348700754
cg02011394 0.97205352682914
cg02050847 0.960861227336123
cg02233190 0.0474284867348451
cg02494853 0.0339793235663543
cg02839557 0.0343496415347042
cg02842889 0.0975280898876404
cg03052502 0.963191627635972
cg03155755 0.916924297364431
cg03244189 0.191910282258065
cg03443143 0.862802126165881
cg03683899 0.0738909090909091
cg03695421 0.81156621607887
cg03706273 0.0371188784261561

Total number of rows: 485512

Table truncated, full table size 13810 Kbytes.

Supplementary file Size Download File type/resource
GSM1588816_9513149079_R04C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588816_9513149079_R04C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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