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Sample GSM1588733 Query DataSets for GSM1588733
Status Public on Sep 15, 2015
Title Pt5-DP3-2
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 5 melanoma, post BRAFi resistance, 3rd 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 0.571395309457286
cg00212031 0.0986119970103347
cg00213748 0.611703847397349
cg00214611 0.0744828865596883
cg00455876 0.454046327660671
cg01707559 0.0675610694364301
cg02004872 0.0363422176409954
cg02011394 0.672313073245149
cg02050847 0.615618764162749
cg02233190 0.0506752646307337
cg02494853 0.0130523330366437
cg02839557 0.0213552674446774
cg02842889 0.0577004666949512
cg03052502 0.921049378476753
cg03155755 0.688073013897532
cg03244189 0.0958426686582026
cg03443143 0.580627120539875
cg03683899 0.0278169014084507
cg03695421 0.473385089444997
cg03706273 0.0287786976188444

Total number of rows: 485512

Table truncated, full table size 13831 Kbytes.

Supplementary file Size Download File type/resource
GSM1588733_8795207119_R03C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588733_8795207119_R03C02_Red.idat.gz 4.2 Mb (ftp)(http) IDAT
Processed data included within Sample table

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