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Sample GSM1588833 Query DataSets for GSM1588833
Status Public on Sep 15, 2015
Title M229R5-PLX-1
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 M229, BRAFi resistant subline
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 0.49509483322433
cg00212031 0.276567656765677
cg00213748 0.377541998231653
cg00214611 0.317307692307692
cg00455876 0.278026905829596
cg01707559 0.339453340695748
cg02004872 0.218891402714932
cg02011394 0.529667149059334
cg02050847 0.290957923008057
cg02233190 0.259116022099448
cg02494853 0.0261698369007025
cg02839557 0.393034825870647
cg02842889 0.540790148794253
cg03052502 0.270881670533643
cg03155755 0.477538461538462
cg03244189 0.436955820702999
cg03443143 0.36302294197031
cg03683899 0.34801016088061
cg03695421 0.353314527503526
cg03706273 0.0344363667781631

Total number of rows: 485512

Table truncated, full table size 13821 Kbytes.

Supplementary file Size Download File type/resource
GSM1588833_7973201138_R06C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588833_7973201138_R06C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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