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Sample GSM1588832 Query DataSets for GSM1588832
Status Public on Sep 15, 2015
Title M229-DMSO2D-3
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 3
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 0.41243961352657
cg00212031 0.331645569620253
cg00213748 0.410315186246418
cg00214611 0.508689839572192
cg00455876 0.284310284310284
cg01707559 0.496059544658494
cg02004872 0.192277070063694
cg02011394 0.557069846678024
cg02050847 0.304678998911861
cg02233190 0.271563981042654
cg02494853 0.0214242169129387
cg02839557 0.528236316246742
cg02842889 0.322705314009662
cg03052502 0.423076923076923
cg03155755 0.468498168498168
cg03244189 0.382370283018868
cg03443143 0.44518103008669
cg03683899 0.278584392014519
cg03695421 0.263437292634373
cg03706273 0.0220038369680122

Total number of rows: 485512

Table truncated, full table size 13817 Kbytes.

Supplementary file Size Download File type/resource
GSM1588832_7878191071_R05C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588832_7878191071_R05C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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