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Sample GSM1588770 Query DataSets for GSM1588770
Status Public on Sep 15, 2015
Title Pt10-DP6-1
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, 6th 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 0.868485797360769
cg00212031 0.0584307178631052
cg00213748 0.629083245521602
cg00214611 0.105323411562679
cg00455876 0.718851570964247
cg01707559 0.116005360368234
cg02004872 0.0307608175541732
cg02011394 0.970189618611512
cg02050847 0.953671076194327
cg02233190 0.0584186374867631
cg02494853 0.0230118177534257
cg02839557 0.0246680748340374
cg02842889 0.0569767441860465
cg03052502 0.955813839438968
cg03155755 0.910847067842085
cg03244189 0.0903141361256544
cg03443143 0.896933671149224
cg03683899 0.0383909668313338
cg03695421 0.69708205706916
cg03706273 0.0280619701841567

Total number of rows: 485512

Table truncated, full table size 13817 Kbytes.

Supplementary file Size Download File type/resource
GSM1588770_9247377060_R02C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588770_9247377060_R02C02_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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