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Sample GSM1588845 Query DataSets for GSM1588845
Status Public on Sep 15, 2015
Title SKMel28R1-PLX-2
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, 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 0.459651387992253
cg00212031 0.420035149384886
cg00213748 0.467054263565891
cg00214611 0.333910034602076
cg00455876 0.276539278131635
cg01707559 0.830215096566965
cg02004872 0.295755045233125
cg02011394 0.513536379018612
cg02050847 0.737935192162773
cg02233190 0.0416012558869702
cg02494853 0.0179098697904061
cg02839557 0.938230825130475
cg02842889 0.0598143236074271
cg03052502 0.235827962646324
cg03155755 0.636731937879811
cg03244189 0.22560553633218
cg03443143 0.404717853839038
cg03683899 0.0625
cg03695421 0.304711246200608
cg03706273 0.0212640655117758

Total number of rows: 485512

Table truncated, full table size 13832 Kbytes.

Supplementary file Size Download File type/resource
GSM1588845_9702496159_R04C02_Grn.idat.gz 4.0 Mb (ftp)(http) IDAT
GSM1588845_9702496159_R04C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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