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Sample GSM1588710 Query DataSets for GSM1588710
Status Public on Sep 15, 2015
Title Pt2-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 2 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 0.883651469376545
cg00212031 0.642363775901765
cg00213748 0.521071428571429
cg00214611 0.30930064888248
cg00455876 0.644800455019433
cg01707559 0.240897362385321
cg02004872 0.0745901639344262
cg02011394 0.965954590691323
cg02050847 0.876633559853633
cg02233190 0.0752980054290098
cg02494853 0.0209486940755623
cg02839557 0.0921738498701393
cg02842889 0.142132969389745
cg03052502 0.959016056835448
cg03155755 0.899689853788214
cg03244189 0.273559190031153
cg03443143 0.866907844630617
cg03683899 0.117764030048608
cg03695421 0.349927501208313
cg03706273 0.0683230417186915

Total number of rows: 485512

Table truncated, full table size 13790 Kbytes.

Supplementary file Size Download File type/resource
GSM1588710_8795207137_R05C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588710_8795207137_R05C02_Red.idat.gz 4.2 Mb (ftp)(http) IDAT
Processed data included within Sample table

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