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Sample GSM1588798 Query DataSets for GSM1588798
Status Public on Sep 15, 2015
Title Pt18-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 18 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 0.569533394327539
cg00212031 0.092179945343704
cg00213748 0.484189223374652
cg00214611 0.0785801986828887
cg00455876 0.413966130043905
cg01707559 0.128515235131803
cg02004872 0.0600473041463532
cg02011394 0.72379705400982
cg02050847 0.548594751547691
cg02233190 0.0390786591112145
cg02494853 0.0332465194045208
cg02839557 0.0495036399735275
cg02842889 0.0559933528665763
cg03052502 0.879983293306881
cg03155755 0.568905472636816
cg03244189 0.103254319003616
cg03443143 0.581411983500632
cg03683899 0.023179775638782
cg03695421 0.445544554455446
cg03706273 0.244746102067193

Total number of rows: 485512

Table truncated, full table size 13812 Kbytes.

Supplementary file Size Download File type/resource
GSM1588798_9283265061_R05C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588798_9283265061_R05C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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