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Sample GSM1588749 Query DataSets for GSM1588749
Status Public on Sep 15, 2015
Title Pt8-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 8 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 0.365566037735849
cg00212031 0.23898431665422
cg00213748 0.124128312412831
cg00214611 0.294771968854283
cg00455876 0.162504396763982
cg01707559 0.311605723370429
cg02004872 0.238429994141769
cg02011394 0.389014296463506
cg02050847 0.292508143322476
cg02233190 0.204186046511628
cg02494853 0.0259585234065104
cg02839557 0.51140544518028
cg02842889 0.321428571428571
cg03052502 0.409306742640076
cg03155755 0.591629676601141
cg03244189 0.337154150197628
cg03443143 0.0892380325838783
cg03683899 0.32791586998088
cg03695421 0.220537897310513
cg03706273 0.0256254431277221

Total number of rows: 485512

Table truncated, full table size 13835 Kbytes.

Supplementary file Size Download File type/resource
GSM1588749_9341679003_R02C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588749_9341679003_R02C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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