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Sample GSM1588747 Query DataSets for GSM1588747
Status Public on Sep 15, 2015
Title Pt8-DP1-2
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 8 melanoma, post BRAFi resistance, 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 0.477292202227935
cg00212031 0.234042553191489
cg00213748 0.417314095449501
cg00214611 0.372460496613995
cg00455876 0.197170645446508
cg01707559 0.300111731843575
cg02004872 0.228121927236971
cg02011394 0.405581395348837
cg02050847 0.281624758220503
cg02233190 0.180731889469754
cg02494853 0.021835203456702
cg02839557 0.409854423292273
cg02842889 0.445304937076476
cg03052502 0.350970017636684
cg03155755 0.413098236775819
cg03244189 0.285904255319149
cg03443143 0.206896551724138
cg03683899 0.226551226551227
cg03695421 0.188847583643123
cg03706273 0.0233163117834088

Total number of rows: 485512

Table truncated, full table size 13830 Kbytes.

Supplementary file Size Download File type/resource
GSM1588747_9341679003_R01C01_Grn.idat.gz 4.0 Mb (ftp)(http) IDAT
GSM1588747_9341679003_R01C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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