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Sample GSM1588760 Query DataSets for GSM1588760
Status Public on Sep 15, 2015
Title Pt10-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 10 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 0.811444557477111
cg00212031 0.045003203074952
cg00213748 0.638975155279503
cg00214611 0.202753441802253
cg00455876 0.614256579586287
cg01707559 0.169468292331001
cg02004872 0.0753894080996885
cg02011394 0.957612046478539
cg02050847 0.88860103626943
cg02233190 0.0492815219591176
cg02494853 0.0221978414512796
cg02839557 0.058144695960941
cg02842889 0.103552532123961
cg03052502 0.96413085793296
cg03155755 0.910650902058701
cg03244189 0.190684544812985
cg03443143 0.846341739228769
cg03683899 0.0635925256178421
cg03695421 0.603901261238365
cg03706273 0.0258999682934793

Total number of rows: 485512

Table truncated, full table size 13819 Kbytes.

Supplementary file Size Download File type/resource
GSM1588760_7878191071_R04C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588760_7878191071_R04C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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