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Sample GSM1588757 Query DataSets for GSM1588757
Status Public on Sep 15, 2015
Title Pt9-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 9 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 0.498256624825662
cg00212031 0.494498777506112
cg00213748 0.336879432624113
cg00214611 0.409392789373814
cg00455876 0.162330097087379
cg01707559 0.343535027376106
cg02004872 0.228936921041023
cg02011394 0.762927605409706
cg02050847 0.30207908683245
cg02233190 0.288374433819829
cg02494853 0.019120140990257
cg02839557 0.472581638940234
cg02842889 0.427930813581038
cg03052502 0.65587044534413
cg03155755 0.566054243219598
cg03244189 0.316730149428655
cg03443143 0.644687666844634
cg03683899 0.269131556319862
cg03695421 0.361702127659574
cg03706273 0.0263003355704698

Total number of rows: 485512

Table truncated, full table size 13824 Kbytes.

Supplementary file Size Download File type/resource
GSM1588757_9341679003_R06C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588757_9341679003_R06C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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