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Sample GSM1588825 Query DataSets for GSM1588825
Status Public on Sep 15, 2015
Title Pt22-DD-DP3-2
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 22 melanoma, post BRAFi+MEKi resistance, 3rd 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 0.8485559566787
cg00212031 0.236451612903226
cg00213748 0.580166821130677
cg00214611 0.36340206185567
cg00455876 0.608648870215709
cg01707559 0.197592778335005
cg02004872 0.0838657061302161
cg02011394 0.963620942841422
cg02050847 0.915925041603357
cg02233190 0.127400881057269
cg02494853 0.0297071284756105
cg02839557 0.181528662420382
cg02842889 0.171641791044776
cg03052502 0.923967262337159
cg03155755 0.868653872328842
cg03244189 0.4140831530882
cg03443143 0.883578991073282
cg03683899 0.109697123950115
cg03695421 0.637010676156584
cg03706273 0.0409940759870825

Total number of rows: 485512

Table truncated, full table size 13802 Kbytes.

Supplementary file Size Download File type/resource
GSM1588825_9283265037_R06C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588825_9283265037_R06C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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