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Sample GSM1588809 Query DataSets for GSM1588809
Status Public on Sep 15, 2015
Title Pt20-DD-DP1-2
Sample type genomic
Source name tumor biopsy
Organism Homo sapiens
Characteristics cell type: melanoma
mapki sensitivity: resistant
mapki treatment: BRAFi+MEKi
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+MEKi 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 0.881296484110886
cg00212031 0.124714332353901
cg00213748 0.777543648404576
cg00214611 0.0824833251302592
cg00455876 0.75275722829992
cg01707559 0.104781442322866
cg02004872 0.0262084645332636
cg02011394 0.974833014668614
cg02050847 0.971183278743011
cg02233190 0.0432885906040268
cg02494853 0.0288077403245943
cg02839557 0.049481380717565
cg02842889 0.0670491618854764
cg03052502 0.967231501742888
cg03155755 0.927143526471966
cg03244189 0.201576729645236
cg03443143 0.908860426064338
cg03683899 0.0464157900444637
cg03695421 0.771189151154609
cg03706273 0.21110946964101

Total number of rows: 485512

Table truncated, full table size 13794 Kbytes.

Supplementary file Size Download File type/resource
GSM1588809_9283265037_R04C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588809_9283265037_R04C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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