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Sample GSM1588708 Query DataSets for GSM1588708
Status Public on Sep 15, 2015
Title Pt2-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 2 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 0.880457914434578
cg00212031 0.856793585118569
cg00213748 0.713177196334316
cg00214611 0.0968479718183969
cg00455876 0.744280630401627
cg01707559 0.0917470013632247
cg02004872 0.0290562036055143
cg02011394 0.970295223289457
cg02050847 0.959821719752147
cg02233190 0.0350647207656485
cg02494853 0.0251371007602325
cg02839557 0.0309473139237913
cg02842889 0.0564576221255654
cg03052502 0.971572602739726
cg03155755 0.906272273699216
cg03244189 0.144417475728155
cg03443143 0.854327116465706
cg03683899 0.037077525735629
cg03695421 0.374294080736248
cg03706273 0.489205717653994

Total number of rows: 485512

Table truncated, full table size 13802 Kbytes.

Supplementary file Size Download File type/resource
GSM1588708_8795207137_R04C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588708_8795207137_R04C02_Red.idat.gz 4.2 Mb (ftp)(http) IDAT
Processed data included within Sample table

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