GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM1588725 Query DataSets for GSM1588725
Status Public on Sep 15, 2015
Title Pt4-DP1-2
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 4 melanoma, post BRAFi resistance, 1st 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 0.863068058273538
cg00212031 0.0579954954954955
cg00213748 0.664537712895377
cg00214611 0.153051249825443
cg00455876 0.768371049497272
cg01707559 0.0889781097744014
cg02004872 0.0230214355144012
cg02011394 0.966063396194539
cg02050847 0.704588562896001
cg02233190 0.029559915164369
cg02494853 0.0165966756355772
cg02839557 0.0423724792408066
cg02842889 0.0402234636871508
cg03052502 0.964139344262295
cg03155755 0.883479839480222
cg03244189 0.102282872082643
cg03443143 0.867218148186402
cg03683899 0.0252223788307335
cg03695421 0.47724876307892
cg03706273 0.0272874532504347

Total number of rows: 485512

Table truncated, full table size 13830 Kbytes.

Supplementary file Size Download File type/resource
GSM1588725_8795194168_R06C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588725_8795194168_R06C01_Red.idat.gz 4.1 Mb (ftp)(http) IDAT
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap