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Sample GSM1588739 Query DataSets for GSM1588739
Status Public on Sep 15, 2015
Title Pt6-DP2-2
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 6 melanoma, post BRAFi resistance, 2nd 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 0.841915995397008
cg00212031 0.562498295284074
cg00213748 0.705463182897862
cg00214611 0.0886877828054299
cg00455876 0.719510269296151
cg01707559 0.0927778160998827
cg02004872 0.0250336686999921
cg02011394 0.952368566166908
cg02050847 0.911306586274064
cg02233190 0.561643124221022
cg02494853 0.0278736838089425
cg02839557 0.0347507593353582
cg02842889 0.105461608775137
cg03052502 0.973720454122464
cg03155755 0.938516946427423
cg03244189 0.442127215849844
cg03443143 0.849766948459126
cg03683899 0.058890330953926
cg03695421 0.80296044649357
cg03706273 0.0177178153446034

Total number of rows: 485512

Table truncated, full table size 13809 Kbytes.

Supplementary file Size Download File type/resource
GSM1588739_9513149040_R03C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588739_9513149040_R03C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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