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Sample GSM1588765 Query DataSets for GSM1588765
Status Public on Sep 15, 2015
Title Pt10-DP3-2
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, 3rd 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 0.858670533327292
cg00212031 0.273014959723821
cg00213748 0.483718487394958
cg00214611 0.177343223196224
cg00455876 0.592801985659129
cg01707559 0.213316534212057
cg02004872 0.0633835457705678
cg02011394 0.947618550416135
cg02050847 0.939943889181133
cg02233190 0.0914678764817796
cg02494853 0.0235251335701698
cg02839557 0.10978775385555
cg02842889 0.145964510589582
cg03052502 0.957305894520967
cg03155755 0.878144580566726
cg03244189 0.233376123234917
cg03443143 0.890954877880502
cg03683899 0.157971014492754
cg03695421 0.54365181560649
cg03706273 0.0199677084714563

Total number of rows: 485512

Table truncated, full table size 13831 Kbytes.

Supplementary file Size Download File type/resource
GSM1588765_9341679010_R05C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588765_9341679010_R05C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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