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Sample GSM1588754 Query DataSets for GSM1588754
Status Public on Sep 15, 2015
Title Pt9-DP1-1
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 9 melanoma, post BRAFi 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 0.32711966325917
cg00212031 0.557458957887223
cg00213748 0.361861861861862
cg00214611 0.415510204081633
cg00455876 0.211021069692058
cg01707559 0.384326424870466
cg02004872 0.183135023279876
cg02011394 0.404437720625315
cg02050847 0.354920100925147
cg02233190 0.202583675866119
cg02494853 0.0202368866328257
cg02839557 0.322208737864078
cg02842889 0.388986013986014
cg03052502 0.334889926617745
cg03155755 0.447342519685039
cg03244189 0.310331681280976
cg03443143 0.440948942753997
cg03683899 0.258485639686684
cg03695421 0.176950998185118
cg03706273 0.0265804924673433

Total number of rows: 485512

Table truncated, full table size 13825 Kbytes.

Supplementary file Size Download File type/resource
GSM1588754_9257625042_R05C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588754_9257625042_R05C01_Red.idat.gz 4.2 Mb (ftp)(http) IDAT
Processed data included within Sample table

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