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Sample GSM1588787 Query DataSets for GSM1588787
Status Public on Sep 15, 2015
Title Pt15-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 15 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 0.527927927927928
cg00212031 0.275549188156638
cg00213748 0.347155255544841
cg00214611 0.394132029339853
cg00455876 0.210670027305188
cg01707559 0.326430584487195
cg02004872 0.340507726269316
cg02011394 0.511130136986301
cg02050847 0.350756533700138
cg02233190 0.221721721721722
cg02494853 0.0159971000330974
cg02839557 0.38005249343832
cg02842889 0.368381804623415
cg03052502 0.476856316297011
cg03155755 0.507251264755481
cg03244189 0.294751477233229
cg03443143 0.368686868686869
cg03683899 0.269805680119581
cg03695421 0.28892455858748
cg03706273 0.0229650814970917

Total number of rows: 485512

Table truncated, full table size 13811 Kbytes.

Supplementary file Size Download File type/resource
GSM1588787_9341679003_R03C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588787_9341679003_R03C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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