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Sample GSM1588772 Query DataSets for GSM1588772
Status Public on Sep 15, 2015
Title Pt10-DP7-1
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, 7th 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 0.859855374650637
cg00212031 0.0678855595056712
cg00213748 0.636065573770492
cg00214611 0.0753979739507959
cg00455876 0.680815048348533
cg01707559 0.168146175469744
cg02004872 0.065292910153166
cg02011394 0.970486615647906
cg02050847 0.9365439423021
cg02233190 0.0508388408744281
cg02494853 0.0316132223229742
cg02839557 0.0617003127665624
cg02842889 0.101336783096162
cg03052502 0.954302428732408
cg03155755 0.892986067603449
cg03244189 0.158314855875831
cg03443143 0.911041252111098
cg03683899 0.0837334933973589
cg03695421 0.722929725766418
cg03706273 0.0510929565025392

Total number of rows: 485512

Table truncated, full table size 13811 Kbytes.

Supplementary file Size Download File type/resource
GSM1588772_9247377060_R03C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588772_9247377060_R03C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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