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Sample GSM1588768 Query DataSets for GSM1588768
Status Public on Sep 15, 2015
Title Pt10-DP5-1
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 10 melanoma, post BRAFi resistance, 5th 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 0.862617924528302
cg00212031 0.0897084475454772
cg00213748 0.525357607282185
cg00214611 0.0909329829172142
cg00455876 0.656496227996647
cg01707559 0.143822092902421
cg02004872 0.0312539864778671
cg02011394 0.962902301203833
cg02050847 0.9461820231051
cg02233190 0.0423204945316215
cg02494853 0.0192882368921489
cg02839557 0.0853675547496164
cg02842889 0.0698301428956592
cg03052502 0.941364923260319
cg03155755 0.867739938080495
cg03244189 0.119720134749935
cg03443143 0.914032219548485
cg03683899 0.0672880862219633
cg03695421 0.626749045974923
cg03706273 0.0215331749505994

Total number of rows: 485512

Table truncated, full table size 13823 Kbytes.

Supplementary file Size Download File type/resource
GSM1588768_9247377060_R01C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588768_9247377060_R01C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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