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Sample GSM1588822 Query DataSets for GSM1588822
Status Public on Sep 15, 2015
Title Pt22-DD-DP2-1
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 22 melanoma, post BRAFi+MEKi resistance, 2nd 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 0.877636476426799
cg00212031 0.288787023977433
cg00213748 0.567796610169492
cg00214611 0.327708006279435
cg00455876 0.553629100798912
cg01707559 0.249553411932833
cg02004872 0.109423485219664
cg02011394 0.948736827573513
cg02050847 0.819595228521646
cg02233190 0.150879730055435
cg02494853 0.0285510173200484
cg02839557 0.240029006526468
cg02842889 0.292842741935484
cg03052502 0.87136
cg03155755 0.7195885509839
cg03244189 0.339200477326969
cg03443143 0.899478739167049
cg03683899 0.155555555555556
cg03695421 0.501765824504211
cg03706273 0.0802522105734433

Total number of rows: 485512

Table truncated, full table size 13806 Kbytes.

Supplementary file Size Download File type/resource
GSM1588822_9283265061_R05C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588822_9283265061_R05C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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