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Sample GSM1588841 Query DataSets for GSM1588841
Status Public on Sep 15, 2015
Title M238R1-PLX-2
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, 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 0.576825557809331
cg00212031 0.451103780766303
cg00213748 0.168771173390822
cg00214611 0.0810989738497186
cg00455876 0.496600055509298
cg01707559 0.207588617074388
cg02004872 0.021101638551303
cg02011394 0.934729989149487
cg02050847 0.0252254524815539
cg02233190 0.0419260829248907
cg02494853 0.0145047923322684
cg02839557 0.182125489265805
cg02842889 0.0563034062975536
cg03052502 0.96237069330001
cg03155755 0.874891129272803
cg03244189 0.100596034545676
cg03443143 0.632000599225566
cg03683899 0.0289372631825738
cg03695421 0.367905502736963
cg03706273 0.0198576466816287

Total number of rows: 485512

Table truncated, full table size 13855 Kbytes.

Supplementary file Size Download File type/resource
GSM1588841_8795207119_R04C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588841_8795207119_R04C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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