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Sample GSM1588808 Query DataSets for GSM1588808
Status Public on Sep 15, 2015
Title Pt20-DD-DP1-1
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
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 0.880270114176552
cg00212031 0.0939205955334988
cg00213748 0.771036585365854
cg00214611 0.0807884170823701
cg00455876 0.778914240755311
cg01707559 0.105509885182417
cg02004872 0.0339824360442917
cg02011394 0.966424020186251
cg02050847 0.953928181337057
cg02233190 0.0823289331037561
cg02494853 0.0429849518390292
cg02839557 0.0834370139968896
cg02842889 0.0739156994502138
cg03052502 0.958878913947887
cg03155755 0.922819984365006
cg03244189 0.169525731584258
cg03443143 0.876134738802248
cg03683899 0.0588996763754045
cg03695421 0.765615865071187
cg03706273 0.108106171866605

Total number of rows: 485512

Table truncated, full table size 13807 Kbytes.

Supplementary file Size Download File type/resource
GSM1588808_9283265061_R04C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588808_9283265061_R04C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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