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Sample GSM1588811 Query DataSets for GSM1588811
Status Public on Sep 15, 2015
Title Pt20-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 20 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 0.848938826466916
cg00212031 0.119250829777146
cg00213748 0.53173719376392
cg00214611 0.137445209768316
cg00455876 0.740371321350978
cg01707559 0.121187638860836
cg02004872 0.0362546968619884
cg02011394 0.96779008660038
cg02050847 0.935368724842409
cg02233190 0.0546204620462046
cg02494853 0.0182420595627999
cg02839557 0.0485983331529386
cg02842889 0.0645334286735788
cg03052502 0.962669542494504
cg03155755 0.90000675630025
cg03244189 0.193722665294572
cg03443143 0.864429570310166
cg03683899 0.0618128512093819
cg03695421 0.583620221054539
cg03706273 0.467203050277886

Total number of rows: 485512

Table truncated, full table size 13841 Kbytes.

Supplementary file Size Download File type/resource
GSM1588811_8795194168_R02C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588811_8795194168_R02C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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