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Sample GSM1588740 Query DataSets for GSM1588740
Status Public on Sep 15, 2015
Title Pt7-baseline-1
Sample type genomic
Source name tumor biopsy
Organism Homo sapiens
Characteristics cell type: melanoma
mapki sensitivity: sensitive
mapki treatment: none
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 7 melanoma, pre MAPKi treatment, 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 0.433005893909627
cg00212031 0.387242268041237
cg00213748 0.393900889453621
cg00214611 0.549382716049383
cg00455876 0.266059027777778
cg01707559 0.367285419641441
cg02004872 0.229278794402583
cg02011394 0.438172043010753
cg02050847 0.240322580645161
cg02233190 0.208686800135731
cg02494853 0.0230525084915641
cg02839557 0.360207100591716
cg02842889 0.495980707395498
cg03052502 0.657923201730665
cg03155755 0.530973451327434
cg03244189 0.431775700934579
cg03443143 0.388037567968364
cg03683899 0.312379110251451
cg03695421 0.325993298228818
cg03706273 0.0296641717935656

Total number of rows: 485512

Table truncated, full table size 13822 Kbytes.

Supplementary file Size Download File type/resource
GSM1588740_8795207137_R03C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588740_8795207137_R03C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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