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Sample GSM1588759 Query DataSets for GSM1588759
Status Public on Sep 15, 2015
Title Pt10-baseline2-2
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 10 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 0.85100347065037
cg00212031 0.120824135393672
cg00213748 0.573580533024334
cg00214611 0.200518990327908
cg00455876 0.717863273755428
cg01707559 0.206645775439011
cg02004872 0.0998470086158306
cg02011394 0.968264238228491
cg02050847 0.946972439213305
cg02233190 0.0868668642866349
cg02494853 0.02594314417014
cg02839557 0.0713748495788207
cg02842889 0.163946231397024
cg03052502 0.979957647117124
cg03155755 0.913054510523822
cg03244189 0.185274059105835
cg03443143 0.888834259304784
cg03683899 0.250511546331482
cg03695421 0.502710442876138
cg03706273 0.0382891360136869

Total number of rows: 485512

Table truncated, full table size 13815 Kbytes.

Supplementary file Size Download File type/resource
GSM1588759_7973201138_R02C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588759_7973201138_R02C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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