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Sample GSM1588784 Query DataSets for GSM1588784
Status Public on Sep 15, 2015
Title Pt15-DP1-1
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 15 melanoma, post BRAFi resistance, 1st 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 0.590163934426229
cg00212031 0.337702871410737
cg00213748 0.440802675585284
cg00214611 0.508944027697634
cg00455876 0.1995430312262
cg01707559 0.298238590872698
cg02004872 0.289163722025913
cg02011394 0.487433862433862
cg02050847 0.253303964757709
cg02233190 0.22690992018244
cg02494853 0.0124308110949627
cg02839557 0.466111771700357
cg02842889 0.433209647495362
cg03052502 0.434540389972145
cg03155755 0.455721795390214
cg03244189 0.337924249877029
cg03443143 0.356379988757729
cg03683899 0.229015544041451
cg03695421 0.32704811443433
cg03706273 0.0197626714896996

Total number of rows: 485512

Table truncated, full table size 13817 Kbytes.

Supplementary file Size Download File type/resource
GSM1588784_9257625042_R02C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588784_9257625042_R02C02_Red.idat.gz 4.2 Mb (ftp)(http) IDAT
Processed data included within Sample table

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