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Sample GSM1588731 Query DataSets for GSM1588731
Status Public on Sep 15, 2015
Title Pt5-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 5 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 0.637464929641793
cg00212031 0.567398337520737
cg00213748 0.610718492343934
cg00214611 0.0560195559177022
cg00455876 0.572502123766582
cg01707559 0.09089686701627
cg02004872 0.0238227582590456
cg02011394 0.755969481915562
cg02050847 0.703002660585329
cg02233190 0.0311096211867248
cg02494853 0.0173891772313452
cg02839557 0.0187155042649272
cg02842889 0.045045045045045
cg03052502 0.969819370064446
cg03155755 0.712992809323085
cg03244189 0.100366837857667
cg03443143 0.632037022238044
cg03683899 0.035067309290344
cg03695421 0.552778964065646
cg03706273 0.0205017237585271

Total number of rows: 485512

Table truncated, full table size 13834 Kbytes.

Supplementary file Size Download File type/resource
GSM1588731_8795207119_R02C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588731_8795207119_R02C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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