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Sample GSM1588791 Query DataSets for GSM1588791
Status Public on Sep 15, 2015
Title Pt16-DP1-2
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 16 melanoma, post BRAFi 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 0.887203137795785
cg00212031 0.254528707399447
cg00213748 0.520099608680185
cg00214611 0.152118797537124
cg00455876 0.531655463498515
cg01707559 0.198684345770377
cg02004872 0.0539790641947282
cg02011394 0.96817253008312
cg02050847 0.888865894039735
cg02233190 0.0654371584699453
cg02494853 0.0293795589118682
cg02839557 0.135296897149157
cg02842889 0.14805119255381
cg03052502 0.949245614970411
cg03155755 0.85706672351311
cg03244189 0.192222495692838
cg03443143 0.885242607909453
cg03683899 0.120481927710843
cg03695421 0.518830973184694
cg03706273 0.0317341131836864

Total number of rows: 485512

Table truncated, full table size 13823 Kbytes.

Supplementary file Size Download File type/resource
GSM1588791_9341679003_R05C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588791_9341679003_R05C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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