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Sample GSM1588720 Query DataSets for GSM1588720
Status Public on Sep 15, 2015
Title Pt3-DP3-1
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 3 melanoma, post BRAFi resistance, 3rd biopsy
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 0.653005464480874
cg00212031 0.227472527472527
cg00213748 0.337972166998012
cg00214611 0.402898550724638
cg00455876 0.139138665404638
cg01707559 0.376552053486151
cg02004872 0.195013850415512
cg02011394 0.760047751691206
cg02050847 0.41502808988764
cg02233190 0.3813882532418
cg02494853 0.0289519617515368
cg02839557 0.507635467980296
cg02842889 0.477713178294574
cg03052502 0.581752484191509
cg03155755 0.387166546503244
cg03244189 0.434485530546624
cg03443143 0.647253201156547
cg03683899 0.37661351556568
cg03695421 0.42790426152948
cg03706273 0.0833046708399257

Total number of rows: 485512

Table truncated, full table size 13810 Kbytes.

Supplementary file Size Download File type/resource
GSM1588720_9283265061_R03C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588720_9283265061_R03C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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