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Sample GSM1588756 Query DataSets for GSM1588756
Status Public on Sep 15, 2015
Title Pt9-DP2-1
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 9 melanoma, post BRAFi resistance, 2nd 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 0.676830857440709
cg00212031 0.445793581960104
cg00213748 0.331958762886598
cg00214611 0.327913279132791
cg00455876 0.228302544440572
cg01707559 0.376264697839759
cg02004872 0.231434384537131
cg02011394 0.701647564469914
cg02050847 0.340214698596201
cg02233190 0.187913125590179
cg02494853 0.0215344429595432
cg02839557 0.285818713450292
cg02842889 0.418323249783924
cg03052502 0.638700947225981
cg03155755 0.487261146496815
cg03244189 0.392877492877493
cg03443143 0.701980859114178
cg03683899 0.258455647734525
cg03695421 0.282037533512064
cg03706273 0.0166704727106645

Total number of rows: 485512

Table truncated, full table size 13828 Kbytes.

Supplementary file Size Download File type/resource
GSM1588756_9257625042_R06C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588756_9257625042_R06C01_Red.idat.gz 4.2 Mb (ftp)(http) IDAT
Processed data included within Sample table

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