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Sample GSM1588810 Query DataSets for GSM1588810
Status Public on Sep 15, 2015
Title Pt20-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 20 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 0.905100039231071
cg00212031 0.132630654369785
cg00213748 0.600646725949879
cg00214611 0.197078201088513
cg00455876 0.720193280143836
cg01707559 0.161011673151751
cg02004872 0.0455319530339697
cg02011394 0.978202999393796
cg02050847 0.9413510812009
cg02233190 0.117733878292461
cg02494853 0.0205065234075211
cg02839557 0.0687506600485796
cg02842889 0.0824378777703157
cg03052502 0.945742904841402
cg03155755 0.904501450389683
cg03244189 0.171485006284791
cg03443143 0.895986546788311
cg03683899 0.117891241178912
cg03695421 0.65187931475326
cg03706273 0.487887365666606

Total number of rows: 485512

Table truncated, full table size 13830 Kbytes.

Supplementary file Size Download File type/resource
GSM1588810_8795207137_R02C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588810_8795207137_R02C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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