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Sample GSM1588732 Query DataSets for GSM1588732
Status Public on Sep 15, 2015
Title Pt5-DP3-1
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 5 melanoma, post BRAFi resistance, 3rd 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 0.575280442054296
cg00212031 0.0895868653520121
cg00213748 0.628783199505868
cg00214611 0.0729391454466983
cg00455876 0.486654697785757
cg01707559 0.0860422287892415
cg02004872 0.0336671090066285
cg02011394 0.706191452560114
cg02050847 0.642664240004697
cg02233190 0.0425791437627894
cg02494853 0.0186679021093367
cg02839557 0.0227194963388763
cg02842889 0.0586977186311787
cg03052502 0.917876312990251
cg03155755 0.693355023517346
cg03244189 0.0826342777475838
cg03443143 0.573141792477474
cg03683899 0.0472464640385194
cg03695421 0.506134322492835
cg03706273 0.0231551074211975

Total number of rows: 485512

Table truncated, full table size 13831 Kbytes.

Supplementary file Size Download File type/resource
GSM1588732_8795207135_R05C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588732_8795207135_R05C01_Red.idat.gz 4.2 Mb (ftp)(http) IDAT
Processed data included within Sample table

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