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Sample GSM1588817 Query DataSets for GSM1588817
Status Public on Sep 15, 2015
Title Pt21-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 21 melanoma, post BRAFi resistance, 2nd biopsy, replicate (surrogate baseline for BRAFi+MEKi tumors)
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 0.843413536437597
cg00212031 0.0506602641056423
cg00213748 0.590110339190846
cg00214611 0.0793764558322881
cg00455876 0.727901962218669
cg01707559 0.0817499621832436
cg02004872 0.0393113731869324
cg02011394 0.981658935546875
cg02050847 0.957889817747547
cg02233190 0.0425346197462232
cg02494853 0.0309597523219814
cg02839557 0.0516851980542043
cg02842889 0.10719131614654
cg03052502 0.976130538958479
cg03155755 0.926360950907301
cg03244189 0.225875535399345
cg03443143 0.889821749379693
cg03683899 0.0681469068565843
cg03695421 0.804304461942257
cg03706273 0.0202648244099021

Total number of rows: 485512

Table truncated, full table size 13813 Kbytes.

Supplementary file Size Download File type/resource
GSM1588817_9513149040_R04C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588817_9513149040_R04C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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