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Sample GSM1588806 Query DataSets for GSM1588806
Status Public on Sep 15, 2015
Title Pt20-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 20 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 0.90404891435174
cg00212031 0.0697739585279283
cg00213748 0.707796193984039
cg00214611 0.138388303298198
cg00455876 0.727548627396882
cg01707559 0.138848129126926
cg02004872 0.0392209536601746
cg02011394 0.981778419501651
cg02050847 0.954547362236119
cg02233190 0.0792827504445762
cg02494853 0.0261765264292266
cg02839557 0.0749968541588021
cg02842889 0.0708788258457133
cg03052502 0.958962892114413
cg03155755 0.901614530776993
cg03244189 0.172882752936328
cg03443143 0.910732785413357
cg03683899 0.0675844806007509
cg03695421 0.739675965403825
cg03706273 0.332667755704584

Total number of rows: 485512

Table truncated, full table size 13833 Kbytes.

Supplementary file Size Download File type/resource
GSM1588806_8795207137_R01C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588806_8795207137_R01C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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