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Sample GSM1588750 Query DataSets for GSM1588750
Status Public on Sep 15, 2015
Title Pt8-DP3-1
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 8 melanoma, post BRAFi resistance, 3rd 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 0.692813141683778
cg00212031 0.334302325581395
cg00213748 0.276889134031991
cg00214611 0.399098083427283
cg00455876 0.291604421870332
cg01707559 0.291702948127877
cg02004872 0.283098591549296
cg02011394 0.664902573971614
cg02050847 0.489344262295082
cg02233190 0.208147044212618
cg02494853 0.0214980631043558
cg02839557 0.508831908831909
cg02842889 0.424537487828627
cg03052502 0.612618724559023
cg03155755 0.405767250257467
cg03244189 0.285075233834892
cg03443143 0.539837398373984
cg03683899 0.271632670442448
cg03695421 0.104085220476676
cg03706273 0.0210095324941196

Total number of rows: 485512

Table truncated, full table size 13830 Kbytes.

Supplementary file Size Download File type/resource
GSM1588750_9257625042_R03C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588750_9257625042_R03C01_Red.idat.gz 4.2 Mb (ftp)(http) IDAT
Processed data included within Sample table

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