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Sample GSM1588717 Query DataSets for GSM1588717
Status Public on Sep 15, 2015
Title Pt3-DP1-2
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 3 melanoma, post BRAFi resistance, 1st 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 0.422153846153846
cg00212031 0.459777632439503
cg00213748 0.487569060773481
cg00214611 0.605342851989329
cg00455876 0.274200081004455
cg01707559 0.350017749378772
cg02004872 0.310187531677648
cg02011394 0.582590456213949
cg02050847 0.238367346938776
cg02233190 0.263828464885022
cg02494853 0.0278121757756284
cg02839557 0.445830597504924
cg02842889 0.519333729922665
cg03052502 0.449932341001353
cg03155755 0.578343949044586
cg03244189 0.527159855147439
cg03443143 0.458544839255499
cg03683899 0.278783958602846
cg03695421 0.507936507936508
cg03706273 0.0462511926881936

Total number of rows: 485512

Table truncated, full table size 13803 Kbytes.

Supplementary file Size Download File type/resource
GSM1588717_9513149040_R06C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588717_9513149040_R06C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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