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Sample GSM1588719 Query DataSets for GSM1588719
Status Public on Sep 15, 2015
Title Pt3-DP2-2
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 3 melanoma, post BRAFi 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 0.77187332259796
cg00212031 0.268015170670038
cg00213748 0.362084456424079
cg00214611 0.42360248447205
cg00455876 0.257582827811479
cg01707559 0.416303511920021
cg02004872 0.306110458284371
cg02011394 0.833969465648855
cg02050847 0.321146245059289
cg02233190 0.246070947462955
cg02494853 0.0321584769745305
cg02839557 0.291759465478842
cg02842889 0.423541247484909
cg03052502 0.68515406162465
cg03155755 0.501550387596899
cg03244189 0.465010496850945
cg03443143 0.72572706935123
cg03683899 0.264199655765921
cg03695421 0.373366834170854
cg03706273 0.049590348767288

Total number of rows: 485512

Table truncated, full table size 13809 Kbytes.

Supplementary file Size Download File type/resource
GSM1588719_9283265037_R02C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588719_9283265037_R02C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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