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Sample GSM1588847 Query DataSets for GSM1588847
Status Public on Sep 15, 2015
Title SKMel28DDR1-PLXAZD-2
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, 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 0.42826780021254
cg00212031 0.524699599465955
cg00213748 0.393298059964727
cg00214611 0.460732984293194
cg00455876 0.368913857677903
cg01707559 0.847516321317059
cg02004872 0.287690179806362
cg02011394 0.419921875
cg02050847 0.832580115036976
cg02233190 0.0820271682340648
cg02494853 0.0227106227106227
cg02839557 0.921972134342929
cg02842889 0.0645095645095645
cg03052502 0.422083704363313
cg03155755 0.554383651944628
cg03244189 0.244390539721043
cg03443143 0.345467032967033
cg03683899 0.133296763576522
cg03695421 0.289219982471516
cg03706273 0.0267823930564166

Total number of rows: 485512

Table truncated, full table size 13825 Kbytes.

Supplementary file Size Download File type/resource
GSM1588847_9702496159_R05C02_Grn.idat.gz 4.0 Mb (ftp)(http) IDAT
GSM1588847_9702496159_R05C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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