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Sample GSM1588830 Query DataSets for GSM1588830
Status Public on Sep 15, 2015
Title M229-DMSO2D-1
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
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 0.305206463195691
cg00212031 0.362754607177498
cg00213748 0.305630026809651
cg00214611 0.478040540540541
cg00455876 0.119647355163728
cg01707559 0.317796610169492
cg02004872 0.174480712166172
cg02011394 0.425847457627119
cg02050847 0.340782122905028
cg02233190 0.211009174311927
cg02494853 0.0204578665367755
cg02839557 0.232098765432099
cg02842889 0.389965792474344
cg03052502 0.463587921847247
cg03155755 0.408227848101266
cg03244189 0.257549611734254
cg03443143 0.363941018766756
cg03683899 0.315040650406504
cg03695421 0.270764119601329
cg03706273 0.0225502852621497

Total number of rows: 485512

Table truncated, full table size 13826 Kbytes.

Supplementary file Size Download File type/resource
GSM1588830_7973201138_R01C01_Grn.idat.gz 4.0 Mb (ftp)(http) IDAT
GSM1588830_7973201138_R01C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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