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Sample GSM1588715 Query DataSets for GSM1588715
Status Public on Sep 15, 2015
Title Pt3-baseline-2
Sample type genomic
Source name tumor biopsy
Organism Homo sapiens
Characteristics cell type: melanoma
mapki sensitivity: sensitive
mapki treatment: none
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 3 melanoma, pre MAPKi treatment, 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 0.439322671683913
cg00212031 0.419124218051832
cg00213748 0.438524590163934
cg00214611 0.45843621399177
cg00455876 0.231240428790199
cg01707559 0.348125689084895
cg02004872 0.317278747742324
cg02011394 0.355130784708249
cg02050847 0.251287332646756
cg02233190 0.179763739085773
cg02494853 0.0222277207307518
cg02839557 0.447513812154696
cg02842889 0.558300395256917
cg03052502 0.548913043478261
cg03155755 0.666666666666667
cg03244189 0.462480252764613
cg03443143 0.278350515463918
cg03683899 0.299460431654676
cg03695421 0.256223436551305
cg03706273 0.0442712163553464

Total number of rows: 485512

Table truncated, full table size 13799 Kbytes.

Supplementary file Size Download File type/resource
GSM1588715_9283265037_R01C01_Grn.idat.gz 4.0 Mb (ftp)(http) IDAT
GSM1588715_9283265037_R01C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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