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Sample GSM1588843 Query DataSets for GSM1588843
Status Public on Sep 15, 2015
Title SKMel28-DMSO-2
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 SKMel28, parental, MAPKi sensitive in DMSO, rep 2
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 0.422986708365911
cg00212031 0.330188679245283
cg00213748 0.38544474393531
cg00214611 0.376425855513308
cg00455876 0.200734956361966
cg01707559 0.830769230769231
cg02004872 0.300492610837438
cg02011394 0.285714285714286
cg02050847 0.763213160658033
cg02233190 0.0671821305841924
cg02494853 0.0277653381101657
cg02839557 0.932235054347826
cg02842889 0.072390278020633
cg03052502 0.501316944688323
cg03155755 0.655114116652578
cg03244189 0.199604743083004
cg03443143 0.247097844112769
cg03683899 0.079328165374677
cg03695421 0.326106594399277
cg03706273 0.0224719101123595

Total number of rows: 485512

Table truncated, full table size 13830 Kbytes.

Supplementary file Size Download File type/resource
GSM1588843_9702496159_R03C02_Grn.idat.gz 4.0 Mb (ftp)(http) IDAT
GSM1588843_9702496159_R03C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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