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Sample GSM1588736 Query DataSets for GSM1588736
Status Public on Sep 15, 2015
Title Pt6-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 6 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 0.862882027541292
cg00212031 0.319442067431114
cg00213748 0.709168184578021
cg00214611 0.0778838561481588
cg00455876 0.760731545532076
cg01707559 0.126816681347819
cg02004872 0.0427200301110344
cg02011394 0.96078310467088
cg02050847 0.964621208580642
cg02233190 0.376471369987849
cg02494853 0.0267405611361275
cg02839557 0.061872025383395
cg02842889 0.0532625183123668
cg03052502 0.969968498424921
cg03155755 0.89803135683131
cg03244189 0.256600083810588
cg03443143 0.894703150719763
cg03683899 0.0591809555518562
cg03695421 0.751436112404906
cg03706273 0.0537180569411404

Total number of rows: 485512

Table truncated, full table size 13810 Kbytes.

Supplementary file Size Download File type/resource
GSM1588736_9513149079_R02C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588736_9513149079_R02C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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