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Sample GSM1588786 Query DataSets for GSM1588786
Status Public on Sep 15, 2015
Title Pt15-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 15 melanoma, post BRAFi 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 0.403573305307409
cg00212031 0.329331046312178
cg00213748 0.314990512333966
cg00214611 0.524507326932794
cg00455876 0.182174594877156
cg01707559 0.35359765051395
cg02004872 0.431468961278427
cg02011394 0.440940366972477
cg02050847 0.16210295728368
cg02233190 0.187749003984064
cg02494853 0.015883557474127
cg02839557 0.434938892882818
cg02842889 0.385431215753687
cg03052502 0.479840999432141
cg03155755 0.501146263182027
cg03244189 0.32071122818571
cg03443143 0.428644501278772
cg03683899 0.233744855967078
cg03695421 0.32357813362783
cg03706273 0.0331139364702997

Total number of rows: 485512

Table truncated, full table size 13816 Kbytes.

Supplementary file Size Download File type/resource
GSM1588786_9257625042_R03C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588786_9257625042_R03C02_Red.idat.gz 4.2 Mb (ftp)(http) IDAT
Processed data included within Sample table

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