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Sample GSM1588846 Query DataSets for GSM1588846
Status Public on Sep 15, 2015
Title SKMel28DDR1-PLXAZD-1
Sample type genomic
Source name tumor cell line
Organism Homo sapiens
Characteristics cell type: melanoma
mapki sensitivity: resistant
mapki treatment: BRAFi+MEKi
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 SKMel28, BRAF+MEKi 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 0.427433628318584
cg00212031 0.579365079365079
cg00213748 0.391791044776119
cg00214611 0.419504643962848
cg00455876 0.358031674208145
cg01707559 0.829132509482442
cg02004872 0.299368088467615
cg02011394 0.432801822323462
cg02050847 0.860853367483556
cg02233190 0.0861388000752304
cg02494853 0.0210507772933457
cg02839557 0.932241100323625
cg02842889 0.0715478177915574
cg03052502 0.425695110258869
cg03155755 0.462008141112619
cg03244189 0.244387427838358
cg03443143 0.423645320197044
cg03683899 0.0945945945945946
cg03695421 0.343939393939394
cg03706273 0.0265085010704213

Total number of rows: 485512

Table truncated, full table size 13823 Kbytes.

Supplementary file Size Download File type/resource
GSM1588846_9702496109_R05C02_Grn.idat.gz 4.0 Mb (ftp)(http) IDAT
GSM1588846_9702496109_R05C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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