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Sample GSM1588773 Query DataSets for GSM1588773
Status Public on Sep 15, 2015
Title Pt10-DP7-2
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, 7th 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 0.859674428188749
cg00212031 0.0740126120146034
cg00213748 0.649678800856531
cg00214611 0.0991439887568673
cg00455876 0.707690144715442
cg01707559 0.137626546681665
cg02004872 0.0373014813826238
cg02011394 0.963707234997196
cg02050847 0.964990244959896
cg02233190 0.0491247011644945
cg02494853 0.026423165514972
cg02839557 0.0726396018043242
cg02842889 0.0615991503565468
cg03052502 0.972002216355399
cg03155755 0.921609441063049
cg03244189 0.156094084105488
cg03443143 0.914714748715626
cg03683899 0.0453686200378072
cg03695421 0.720277616191603
cg03706273 0.0283848879334368

Total number of rows: 485512

Table truncated, full table size 13831 Kbytes.

Supplementary file Size Download File type/resource
GSM1588773_9341679010_R03C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588773_9341679010_R03C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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