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Sample GSM1588820 Query DataSets for GSM1588820
Status Public on Sep 15, 2015
Title Pt22-DD-DP1-1
Sample type genomic
Source name tumor biopsy
Organism Homo sapiens
Characteristics cell type: melanoma
mapki sensitivity: resistant
mapki treatment: BRAFi+MEKi
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 22 melanoma, post BRAFi+MEKi resistance, 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 0.873846953358451
cg00212031 0.235069885641677
cg00213748 0.560714285714286
cg00214611 0.36118703631394
cg00455876 0.596144089294774
cg01707559 0.264671013633669
cg02004872 0.0940771995624316
cg02011394 0.966975926758491
cg02050847 0.920458553791887
cg02233190 0.124292682926829
cg02494853 0.0325250798506456
cg02839557 0.182661837935718
cg02842889 0.247571189279732
cg03052502 0.923164441747573
cg03155755 0.809112646121148
cg03244189 0.279620853080569
cg03443143 0.88730455596656
cg03683899 0.237048080506895
cg03695421 0.683365624135068
cg03706273 0.0395145049801339

Total number of rows: 485512

Table truncated, full table size 13807 Kbytes.

Supplementary file Size Download File type/resource
GSM1588820_9283265061_R04C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588820_9283265061_R04C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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