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Sample GSM1588728 Query DataSets for GSM1588728
Status Public on Sep 15, 2015
Title Pt5-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 5 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 0.569964657703312
cg00212031 0.637404798717288
cg00213748 0.505823186871361
cg00214611 0.048653390078295
cg00455876 0.486198512585812
cg01707559 0.077871077788808
cg02004872 0.0339510748702743
cg02011394 0.702230145572639
cg02050847 0.644508670520231
cg02233190 0.0333474807494088
cg02494853 0.0161582603443069
cg02839557 0.0269359809780161
cg02842889 0.049536850583971
cg03052502 0.924537864440236
cg03155755 0.692215526658914
cg03244189 0.116339254205388
cg03443143 0.553984229454416
cg03683899 0.0421585160202361
cg03695421 0.545974089909406
cg03706273 0.0167062079873468

Total number of rows: 485512

Table truncated, full table size 13835 Kbytes.

Supplementary file Size Download File type/resource
GSM1588728_8795207135_R03C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588728_8795207135_R03C01_Red.idat.gz 4.2 Mb (ftp)(http) IDAT
Processed data included within Sample table

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