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Sample GSM1588794 Query DataSets for GSM1588794
Status Public on Sep 15, 2015
Title Pt17-DP1-1
Sample type genomic
Source name tumor biopsy
Organism Homo sapiens
Characteristics cell type: melanoma
mapki sensitivity: resistant
mapki treatment: BRAFi
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 17 melanoma, post BRAFi 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 0.418063314711359
cg00212031 0.470588235294118
cg00213748 0.511154855643045
cg00214611 0.520461699895068
cg00455876 0.244378916328787
cg01707559 0.330069221678204
cg02004872 0.270440251572327
cg02011394 0.417682926829268
cg02050847 0.190243902439024
cg02233190 0.288962381149235
cg02494853 0.0379208855894046
cg02839557 0.372340425531915
cg02842889 0.590844062947067
cg03052502 0.351308485329104
cg03155755 0.485906862745098
cg03244189 0.496727523251808
cg03443143 0.35755258126195
cg03683899 0.333806818181818
cg03695421 0.341145833333333
cg03706273 0.0611740355315357

Total number of rows: 485512

Table truncated, full table size 13799 Kbytes.

Supplementary file Size Download File type/resource
GSM1588794_9513149079_R02C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588794_9513149079_R02C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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