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Sample GSM1588815 Query DataSets for GSM1588815
Status Public on Sep 15, 2015
Title Pt21-DD-DP2-2
Sample type genomic
Source name tumor biopsy
Organism Homo sapiens
Characteristics cell type: melanoma
mapki sensitivity: resistant
mapki treatment: BRAFi+MEKi
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 21 melanoma, post BRAFi+MEKi 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 0.858523545136747
cg00212031 0.043670016629311
cg00213748 0.720336943441637
cg00214611 0.0508735403276908
cg00455876 0.773760802065018
cg01707559 0.10012667290852
cg02004872 0.0273245476414601
cg02011394 0.975765679187732
cg02050847 0.956582900348889
cg02233190 0.052545646231212
cg02494853 0.0306169410510847
cg02839557 0.0521554018094731
cg02842889 0.0822661586357511
cg03052502 0.9691657131486
cg03155755 0.913380740963704
cg03244189 0.177973199329983
cg03443143 0.868420203324189
cg03683899 0.0410024495948747
cg03695421 0.861640650946529
cg03706273 0.0185898568651705

Total number of rows: 485512

Table truncated, full table size 13814 Kbytes.

Supplementary file Size Download File type/resource
GSM1588815_9513149040_R06C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588815_9513149040_R06C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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