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Sample GSM1588762 Query DataSets for GSM1588762
Status Public on Sep 15, 2015
Title Pt10-DP2-1
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, 2nd 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 0.821522309711286
cg00212031 0.0933991917377638
cg00213748 0.653532126375577
cg00214611 0.140418614102825
cg00455876 0.60185799601858
cg01707559 0.200789008298191
cg02004872 0.0361622533558278
cg02011394 0.962746970991906
cg02050847 0.91703318672531
cg02233190 0.0481334091339776
cg02494853 0.032824587079239
cg02839557 0.0726593315341499
cg02842889 0.075270410431175
cg03052502 0.950578034682081
cg03155755 0.895754861040415
cg03244189 0.155865197666883
cg03443143 0.857909600343028
cg03683899 0.0554477853216941
cg03695421 0.634354019977076
cg03706273 0.0357487577306689

Total number of rows: 485512

Table truncated, full table size 13827 Kbytes.

Supplementary file Size Download File type/resource
GSM1588762_9247377060_R04C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588762_9247377060_R04C01_Red.idat.gz 4.2 Mb (ftp)(http) IDAT
Processed data included within Sample table

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