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Sample GSM1588844 Query DataSets for GSM1588844
Status Public on Sep 15, 2015
Title SKMel28R1-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 SKMel28, 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 0.357690041249263
cg00212031 0.387798036465638
cg00213748 0.367365542388332
cg00214611 0.398472310630172
cg00455876 0.346625766871166
cg01707559 0.886276403860456
cg02004872 0.291838417147568
cg02011394 0.53322528363047
cg02050847 0.607276819204801
cg02233190 0.0397234832851837
cg02494853 0.0221193800828602
cg02839557 0.95012439284445
cg02842889 0.0343953257634219
cg03052502 0.344528710725894
cg03155755 0.720724346076459
cg03244189 0.233366935483871
cg03443143 0.345871559633028
cg03683899 0.0427173763263056
cg03695421 0.413496051687006
cg03706273 0.0261728067850517

Total number of rows: 485512

Table truncated, full table size 13836 Kbytes.

Supplementary file Size Download File type/resource
GSM1588844_9702496109_R04C02_Grn.idat.gz 4.0 Mb (ftp)(http) IDAT
GSM1588844_9702496109_R04C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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