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Sample GSM1588723 Query DataSets for GSM1588723
Status Public on Sep 15, 2015
Title Pt4-baseline-2
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 4 melanoma, pre MAPKi treatment, 1st 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 0.818221026994114
cg00212031 0.158116829389376
cg00213748 0.72125082320209
cg00214611 0.0329284231132636
cg00455876 0.691360553327924
cg01707559 0.118786971045834
cg02004872 0.0202708457541947
cg02011394 0.947953309253077
cg02050847 0.922670568112444
cg02233190 0.0369383677442492
cg02494853 0.0237026452996792
cg02839557 0.053145102102491
cg02842889 0.044842284739983
cg03052502 0.959518599562363
cg03155755 0.843774582297599
cg03244189 0.1272298544187
cg03443143 0.856314315171921
cg03683899 0.0391144084708755
cg03695421 0.640844596866384
cg03706273 0.0733461746824776

Total number of rows: 485512

Table truncated, full table size 13817 Kbytes.

Supplementary file Size Download File type/resource
GSM1588723_9341679003_R06C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588723_9341679003_R06C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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