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Sample GSM1588718 Query DataSets for GSM1588718
Status Public on Sep 15, 2015
Title Pt3-DP2-1
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 3 melanoma, post BRAFi resistance, 2nd 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 0.697867298578199
cg00212031 0.408148677626876
cg00213748 0.398722044728434
cg00214611 0.525700934579439
cg00455876 0.271688682613352
cg01707559 0.370588235294118
cg02004872 0.248375116063138
cg02011394 0.780821917808219
cg02050847 0.603988603988604
cg02233190 0.226741230299949
cg02494853 0.0263978382872584
cg02839557 0.199424736337488
cg02842889 0.464125560538117
cg03052502 0.624507874015748
cg03155755 0.544902093180284
cg03244189 0.346519589197413
cg03443143 0.554008280015055
cg03683899 0.212406015037594
cg03695421 0.372229760289462
cg03706273 0.0416610598272196

Total number of rows: 485512

Table truncated, full table size 13815 Kbytes.

Supplementary file Size Download File type/resource
GSM1588718_9283265061_R02C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588718_9283265061_R02C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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