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Sample GSM1588755 Query DataSets for GSM1588755
Status Public on Sep 15, 2015
Title Pt9-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 9 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 0.592911877394636
cg00212031 0.515007898894155
cg00213748 0.265005662514156
cg00214611 0.316374269005848
cg00455876 0.251472116383789
cg01707559 0.341296928327645
cg02004872 0.244928253339931
cg02011394 0.582417582417582
cg02050847 0.350094876660342
cg02233190 0.233778625954198
cg02494853 0.0209606390605264
cg02839557 0.389617486338798
cg02842889 0.302272727272727
cg03052502 0.374024782010096
cg03155755 0.392670157068063
cg03244189 0.394652406417112
cg03443143 0.361411764705882
cg03683899 0.340126493323963
cg03695421 0.296707818930041
cg03706273 0.0363033473401366

Total number of rows: 485512

Table truncated, full table size 13818 Kbytes.

Supplementary file Size Download File type/resource
GSM1588755_9341679003_R05C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588755_9341679003_R05C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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