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Sample GSM1588713 Query DataSets for GSM1588713
Status Public on Sep 15, 2015
Title Pt2-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 2 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 0.905571293673277
cg00212031 0.268617021276596
cg00213748 0.673706896551724
cg00214611 0.157150075795856
cg00455876 0.657703404500866
cg01707559 0.215127238454288
cg02004872 0.0582619557458958
cg02011394 0.971837446743444
cg02050847 0.941542772631743
cg02233190 0.06377313273865
cg02494853 0.0141082606298446
cg02839557 0.106076718571971
cg02842889 0.0654362416107383
cg03052502 0.944921891537192
cg03155755 0.895248549474675
cg03244189 0.202052284387979
cg03443143 0.884292217910721
cg03683899 0.100780234070221
cg03695421 0.540755040755041
cg03706273 0.105624713768267

Total number of rows: 485512

Table truncated, full table size 13805 Kbytes.

Supplementary file Size Download File type/resource
GSM1588713_8795194168_R06C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588713_8795194168_R06C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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