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Sample GSM1588821 Query DataSets for GSM1588821
Status Public on Sep 15, 2015
Title Pt22-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 22 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 0.884271469926021
cg00212031 0.279580629056415
cg00213748 0.522157996146435
cg00214611 0.262901259650549
cg00455876 0.712384696809315
cg01707559 0.252723776970733
cg02004872 0.0907708681769804
cg02011394 0.982727614905274
cg02050847 0.952469651230008
cg02233190 0.0843200223401285
cg02494853 0.0417817545224664
cg02839557 0.143901324805847
cg02842889 0.202386212991604
cg03052502 0.951016630643951
cg03155755 0.866235355831439
cg03244189 0.379408960915157
cg03443143 0.902485819152486
cg03683899 0.107042253521127
cg03695421 0.38908475532365
cg03706273 0.0350315558401171

Total number of rows: 485512

Table truncated, full table size 13799 Kbytes.

Supplementary file Size Download File type/resource
GSM1588821_9283265037_R04C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588821_9283265037_R04C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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