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Sample GSM1588829 Query DataSets for GSM1588829
Status Public on Sep 15, 2015
Title Pt23-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 23 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 0.857653946227233
cg00212031 0.100550964187328
cg00213748 0.779433086087706
cg00214611 0.10573199070488
cg00455876 0.801745860331173
cg01707559 0.1190413310445
cg02004872 0.0302290904161583
cg02011394 0.954443356562806
cg02050847 0.950806719893546
cg02233190 0.217228003201773
cg02494853 0.0358049663012082
cg02839557 0.108201581027668
cg02842889 0.108888160052476
cg03052502 0.94996400287977
cg03155755 0.885094179756241
cg03244189 0.256998133830978
cg03443143 0.881098353955338
cg03683899 0.0623813398426905
cg03695421 0.741382311977716
cg03706273 0.148511985247809

Total number of rows: 485512

Table truncated, full table size 13810 Kbytes.

Supplementary file Size Download File type/resource
GSM1588829_9513149040_R05C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588829_9513149040_R05C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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