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Sample GSM1588823 Query DataSets for GSM1588823
Status Public on Sep 15, 2015
Title Pt22-DD-DP2-2
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, 2nd 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 0.913808397397989
cg00212031 0.365266635205286
cg00213748 0.728874830546769
cg00214611 0.372767857142857
cg00455876 0.576949152542373
cg01707559 0.200501736781166
cg02004872 0.0667197868552433
cg02011394 0.954572759523513
cg02050847 0.832420238478891
cg02233190 0.164643799472296
cg02494853 0.0250679202295173
cg02839557 0.220661672908864
cg02842889 0.327182044887781
cg03052502 0.902817837698262
cg03155755 0.87800963081862
cg03244189 0.35710685483871
cg03443143 0.929482956347754
cg03683899 0.195068493150685
cg03695421 0.56456098529996
cg03706273 0.042123514712632

Total number of rows: 485512

Table truncated, full table size 13809 Kbytes.

Supplementary file Size Download File type/resource
GSM1588823_9283265037_R05C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588823_9283265037_R05C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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