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Sample GSM1588716 Query DataSets for GSM1588716
Status Public on Sep 15, 2015
Title Pt3-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 3 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 0.469801553062985
cg00212031 0.543017456359102
cg00213748 0.401952807160293
cg00214611 0.48378728923476
cg00455876 0.230795148247978
cg01707559 0.307325956016249
cg02004872 0.390182730204228
cg02011394 0.551151580074987
cg02050847 0.393925859758821
cg02233190 0.319378985306349
cg02494853 0.0741119406533834
cg02839557 0.356507857870256
cg02842889 0.584623323013416
cg03052502 0.385082872928177
cg03155755 0.619545618463758
cg03244189 0.551893858335117
cg03443143 0.439539944047249
cg03683899 0.426787252368648
cg03695421 0.454576856649396
cg03706273 0.0419802116178061

Total number of rows: 485512

Table truncated, full table size 13801 Kbytes.

Supplementary file Size Download File type/resource
GSM1588716_9513149079_R06C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588716_9513149079_R06C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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