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Sample GSM1588797 Query DataSets for GSM1588797
Status Public on Sep 15, 2015
Title Pt17-DP2-2
Sample type genomic
Source name tumor biopsy
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 Patient 17 melanoma, post BRAFi resistance, 2nd biopsy, replicate
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 0.376594564614531
cg00212031 0.395440251572327
cg00213748 0.451127819548872
cg00214611 0.382371198013656
cg00455876 0.228775692582663
cg01707559 0.33654602675059
cg02004872 0.273465703971119
cg02011394 0.381057268722467
cg02050847 0.237551020408163
cg02233190 0.259501965923984
cg02494853 0.0241503836976849
cg02839557 0.33026920551543
cg02842889 0.570640937284631
cg03052502 0.430222222222222
cg03155755 0.603341288782816
cg03244189 0.462915601023018
cg03443143 0.5
cg03683899 0.372906045156591
cg03695421 0.324181626187962
cg03706273 0.060586748425046

Total number of rows: 485512

Table truncated, full table size 13793 Kbytes.

Supplementary file Size Download File type/resource
GSM1588797_9513149040_R03C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588797_9513149040_R03C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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