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Sample GSM1588782 Query DataSets for GSM1588782
Status Public on Sep 15, 2015
Title Pt15-baseline-1
Sample type genomic
Source name tumor biopsy
Organism Homo sapiens
Characteristics cell type: melanoma
mapki sensitivity: sensitive
mapki treatment: none
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 15 melanoma, pre MAPKi treatment, 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 0.302149178255373
cg00212031 0.335648148148148
cg00213748 0.293798449612403
cg00214611 0.33515625
cg00455876 0.140447504302926
cg01707559 0.309050154104791
cg02004872 0.315496872828353
cg02011394 0.269202087994034
cg02050847 0.288888888888889
cg02233190 0.190414507772021
cg02494853 0.0299165192564317
cg02839557 0.346334902488231
cg02842889 0.378378378378378
cg03052502 0.373807458803122
cg03155755 0.442603071948262
cg03244189 0.310556079170594
cg03443143 0.42627345844504
cg03683899 0.207920792079208
cg03695421 0.248793565683646
cg03706273 0.0392511789644167

Total number of rows: 485512

Table truncated, full table size 13810 Kbytes.

Supplementary file Size Download File type/resource
GSM1588782_9257625042_R01C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588782_9257625042_R01C02_Red.idat.gz 4.2 Mb (ftp)(http) IDAT
Processed data included within Sample table

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