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Sample GSM1588831 Query DataSets for GSM1588831
Status Public on Sep 15, 2015
Title M229-DMSO2D-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 M229, 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 0.385714285714286
cg00212031 0.345302508607969
cg00213748 0.332613390928726
cg00214611 0.489096573208723
cg00455876 0.244458128078818
cg01707559 0.357779448083324
cg02004872 0.253880266075388
cg02011394 0.57713963963964
cg02050847 0.338884866039102
cg02233190 0.318453427065026
cg02494853 0.0262169709257702
cg02839557 0.440371991247265
cg02842889 0.495589856670342
cg03052502 0.436305732484076
cg03155755 0.510262725779967
cg03244189 0.424173027989822
cg03443143 0.482371794871795
cg03683899 0.36034255599473
cg03695421 0.472932005197055
cg03706273 0.0293382295491835

Total number of rows: 485512

Table truncated, full table size 13809 Kbytes.

Supplementary file Size Download File type/resource
GSM1588831_7973201138_R03C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588831_7973201138_R03C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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