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Sample GSM1588785 Query DataSets for GSM1588785
Status Public on Sep 15, 2015
Title Pt15-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 15 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 0.553768844221106
cg00212031 0.486624203821656
cg00213748 0.454137267479153
cg00214611 0.367169638774577
cg00455876 0.200375117224133
cg01707559 0.290717859695701
cg02004872 0.393307468477207
cg02011394 0.453003533568905
cg02050847 0.271547729379055
cg02233190 0.217348447511089
cg02494853 0.020271657816763
cg02839557 0.387997930677703
cg02842889 0.389803705868198
cg03052502 0.593886462882096
cg03155755 0.493852459016393
cg03244189 0.301618634030794
cg03443143 0.58488120950324
cg03683899 0.316890881913303
cg03695421 0.234768480909829
cg03706273 0.0230307910153539

Total number of rows: 485512

Table truncated, full table size 13811 Kbytes.

Supplementary file Size Download File type/resource
GSM1588785_9341679003_R02C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588785_9341679003_R02C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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