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Sample GSM1588763 Query DataSets for GSM1588763
Status Public on Sep 15, 2015
Title Pt10-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 10 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 0.843288659092455
cg00212031 0.107341772151899
cg00213748 0.60073664825046
cg00214611 0.163141402271837
cg00455876 0.598364978902954
cg01707559 0.156657608695652
cg02004872 0.0329496162829496
cg02011394 0.943301377910703
cg02050847 0.946605102705263
cg02233190 0.0424674228930346
cg02494853 0.0218946047678795
cg02839557 0.0756871035940803
cg02842889 0.0882296282026584
cg03052502 0.957133162418941
cg03155755 0.899527004330498
cg03244189 0.100037608123355
cg03443143 0.853629387167439
cg03683899 0.0612516644474035
cg03695421 0.548002145347278
cg03706273 0.0227411094796404

Total number of rows: 485512

Table truncated, full table size 13833 Kbytes.

Supplementary file Size Download File type/resource
GSM1588763_9341679010_R04C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588763_9341679010_R04C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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