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Sample GSM1588807 Query DataSets for GSM1588807
Status Public on Sep 15, 2015
Title Pt20-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 20 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 0.885771931866682
cg00212031 0.0666990448437753
cg00213748 0.561009817671809
cg00214611 0.10475138121547
cg00455876 0.696229547071378
cg01707559 0.117726759503199
cg02004872 0.0377358490566038
cg02011394 0.966372425388819
cg02050847 0.939885496183206
cg02233190 0.052710843373494
cg02494853 0.0239400343415665
cg02839557 0.0433086227077643
cg02842889 0.091100076394194
cg03052502 0.956792318634424
cg03155755 0.94006852419194
cg03244189 0.168456755228943
cg03443143 0.867489730739742
cg03683899 0.0844155844155844
cg03695421 0.667016622922135
cg03706273 0.306212447510035

Total number of rows: 485512

Table truncated, full table size 13840 Kbytes.

Supplementary file Size Download File type/resource
GSM1588807_8795194168_R01C01_Grn.idat.gz 4.0 Mb (ftp)(http) IDAT
GSM1588807_8795194168_R01C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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