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Sample GSM1588778 Query DataSets for GSM1588778
Status Public on Sep 15, 2015
Title Pt14-baseline-1
Sample type genomic
Source name tumor biopsy
Organism Homo sapiens
Characteristics cell type: melanoma
mapki sensitivity: sensitive
mapki treatment: none
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 14 melanoma, pre MAPKi treatment, 1st 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 0.389479008598887
cg00212031 0.3944817300522
cg00213748 0.574423480083857
cg00214611 0.493944636678201
cg00455876 0.306703397612489
cg01707559 0.342627013630731
cg02004872 0.323657474600871
cg02011394 0.457440293937538
cg02050847 0.439842209072978
cg02233190 0.330802603036876
cg02494853 0.0186359721243442
cg02839557 0.40929203539823
cg02842889 0.264623955431755
cg03052502 0.504474272930649
cg03155755 0.481389578163772
cg03244189 0.21451717433571
cg03443143 0.395959595959596
cg03683899 0.292425695110259
cg03695421 0.286225402504472
cg03706273 0.344076500796883

Total number of rows: 485512

Table truncated, full table size 13809 Kbytes.

Supplementary file Size Download File type/resource
GSM1588778_9702496109_R02C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588778_9702496109_R02C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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