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Sample GSM1588796 Query DataSets for GSM1588796
Status Public on Sep 15, 2015
Title Pt17-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 17 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 0.469122426868906
cg00212031 0.450967311541027
cg00213748 0.47749343832021
cg00214611 0.475446428571429
cg00455876 0.235500878734622
cg01707559 0.342271293375394
cg02004872 0.340395480225989
cg02011394 0.520295202952029
cg02050847 0.320503330866025
cg02233190 0.269510926118626
cg02494853 0.0345297547535913
cg02839557 0.40084388185654
cg02842889 0.572916666666667
cg03052502 0.460694698354662
cg03155755 0.502320783909232
cg03244189 0.525967235970721
cg03443143 0.394373965802537
cg03683899 0.415277777777778
cg03695421 0.36824644549763
cg03706273 0.0488702178325248

Total number of rows: 485512

Table truncated, full table size 13797 Kbytes.

Supplementary file Size Download File type/resource
GSM1588796_9513149079_R03C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588796_9513149079_R03C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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