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Sample GSM1588838 Query DataSets for GSM1588838
Status Public on Sep 15, 2015
Title M238-DMSO2D-1
Sample type genomic
Source name tumor cell line
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 Melanoma cell line M238, parental, MAPKi sensitive in DMSO
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 0.80733402012143
cg00212031 0.228089773535087
cg00213748 0.172635878102419
cg00214611 0.0709284627092846
cg00455876 0.735119772634998
cg01707559 0.124343109001526
cg02004872 0.0219921732115387
cg02011394 0.973613084894245
cg02050847 0.0466391725865308
cg02233190 0.019998827048267
cg02494853 0.016767979948444
cg02839557 0.040485290196427
cg02842889 0.0274904976575621
cg03052502 0.979702020454811
cg03155755 0.922786065643928
cg03244189 0.11918016194332
cg03443143 0.758434365473538
cg03683899 0.0328033809619642
cg03695421 0.160009923096006
cg03706273 0.0179598291638035

Total number of rows: 485512

Table truncated, full table size 13851 Kbytes.

Supplementary file Size Download File type/resource
GSM1588838_8795207135_R03C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588838_8795207135_R03C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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