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Sample GSM1588840 Query DataSets for GSM1588840
Status Public on Sep 15, 2015
Title M238R1-PLX-1
Sample type genomic
Source name tumor cell line
Organism Homo sapiens
Characteristics cell type: melanoma
mapki sensitivity: resistant
mapki treatment: BRAFi
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, BRAFi resistant subline
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 0.592397571748733
cg00212031 0.471548689870943
cg00213748 0.0469750889679715
cg00214611 0.0751614082105007
cg00455876 0.533952852610856
cg01707559 0.176197572037718
cg02004872 0.0201005025125628
cg02011394 0.945289328859434
cg02050847 0.030515134770062
cg02233190 0.0388888888888889
cg02494853 0.0162004385704972
cg02839557 0.187033757312295
cg02842889 0.0419892094768942
cg03052502 0.971145379104351
cg03155755 0.858588724933787
cg03244189 0.127240388562047
cg03443143 0.625792255176694
cg03683899 0.0306486101211689
cg03695421 0.330379936927467
cg03706273 0.0129343288847081

Total number of rows: 485512

Table truncated, full table size 13855 Kbytes.

Supplementary file Size Download File type/resource
GSM1588840_8795207119_R03C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588840_8795207119_R03C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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