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Sample GSM1588800 Query DataSets for GSM1588800
Status Public on Sep 15, 2015
Title Pt18-DD-DP1-1
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 18 melanoma, post BRAFi+MEKi resistance, 1st 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 0.402060048213894
cg00212031 0.0965039471564363
cg00213748 0.302134646962233
cg00214611 0.119239445697712
cg00455876 0.689247659024863
cg01707559 0.121526064791975
cg02004872 0.035226422373124
cg02011394 0.701989555570854
cg02050847 0.316554752725509
cg02233190 0.0340437167808863
cg02494853 0.0355328376703841
cg02839557 0.0544874634535306
cg02842889 0.106301531213192
cg03052502 0.872242015125945
cg03155755 0.533226723525231
cg03244189 0.149694330458086
cg03443143 0.450796561074818
cg03683899 0.046407046824293
cg03695421 0.398828125
cg03706273 0.0344639800840205

Total number of rows: 485512

Table truncated, full table size 13814 Kbytes.

Supplementary file Size Download File type/resource
GSM1588800_9283265061_R06C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588800_9283265061_R06C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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