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Sample GSM1588743 Query DataSets for GSM1588743
Status Public on Sep 15, 2015
Title Pt7-DP1-2
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 7 melanoma, post BRAFi resistance, 1st 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 0.552572706935123
cg00212031 0.445472249269718
cg00213748 0.395230847285642
cg00214611 0.397326852976914
cg00455876 0.271060455896928
cg01707559 0.280215665718137
cg02004872 0.248943165805543
cg02011394 0.426577042399173
cg02050847 0.203940203940204
cg02233190 0.270676691729323
cg02494853 0.0301661281560061
cg02839557 0.335112059765208
cg02842889 0.405687949640288
cg03052502 0.360914534567229
cg03155755 0.384892086330935
cg03244189 0.362701908957416
cg03443143 0.369241192411924
cg03683899 0.301403798513625
cg03695421 0.235507246376812
cg03706273 0.0692338709677419

Total number of rows: 485512

Table truncated, full table size 13822 Kbytes.

Supplementary file Size Download File type/resource
GSM1588743_8795194168_R04C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588743_8795194168_R04C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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