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Sample GSM1588742 Query DataSets for GSM1588742
Status Public on Sep 15, 2015
Title Pt7-DP1-1
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 7 melanoma, post BRAFi resistance, 1st 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 0.59766022380468
cg00212031 0.45433658816772
cg00213748 0.497863247863248
cg00214611 0.585546633724521
cg00455876 0.272321428571429
cg01707559 0.386774399319583
cg02004872 0.236813186813187
cg02011394 0.331205673758865
cg02050847 0.309137489325363
cg02233190 0.244489795918367
cg02494853 0.0358261341126317
cg02839557 0.4278972207656
cg02842889 0.535765535313202
cg03052502 0.519877675840979
cg03155755 0.490594059405941
cg03244189 0.455048998721772
cg03443143 0.51119023397762
cg03683899 0.281144781144781
cg03695421 0.233199598796389
cg03706273 0.0995584901157472

Total number of rows: 485512

Table truncated, full table size 13817 Kbytes.

Supplementary file Size Download File type/resource
GSM1588742_8795207137_R04C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588742_8795207137_R04C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

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