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Sample GSM1588771 Query DataSets for GSM1588771
Status Public on Sep 15, 2015
Title Pt10-DP6-2
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 10 melanoma, post BRAFi resistance, 6th 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 0.847559375410051
cg00212031 0.079850417949846
cg00213748 0.732569558101473
cg00214611 0.0833738217860266
cg00455876 0.750718541885734
cg01707559 0.0977514899765216
cg02004872 0.0365982567959503
cg02011394 0.971933446386001
cg02050847 0.964651767411629
cg02233190 0.0278479452898774
cg02494853 0.017490445034657
cg02839557 0.0522029115628808
cg02842889 0.0466419883659439
cg03052502 0.992878620034816
cg03155755 0.926151761517615
cg03244189 0.0981004070556309
cg03443143 0.883919659825811
cg03683899 0.0456822266412459
cg03695421 0.653455524587841
cg03706273 0.0168789203573465

Total number of rows: 485512

Table truncated, full table size 13832 Kbytes.

Supplementary file Size Download File type/resource
GSM1588771_9341679010_R02C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588771_9341679010_R02C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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