GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM1588724 Query DataSets for GSM1588724
Status Public on Sep 15, 2015
Title Pt4-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 4 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 0.883568014882766
cg00212031 0.0745328118209474
cg00213748 0.64053009387079
cg00214611 0.0831381184407796
cg00455876 0.781968390804598
cg01707559 0.111986153180441
cg02004872 0.0324088115666189
cg02011394 0.971399930844989
cg02050847 0.760152576370392
cg02233190 0.0265382347159426
cg02494853 0.024038594837386
cg02839557 0.0607428561834214
cg02842889 0.059953204607739
cg03052502 0.963101622314412
cg03155755 0.890658238619097
cg03244189 0.118380773649396
cg03443143 0.886583518143749
cg03683899 0.0233535655165698
cg03695421 0.607278529098921
cg03706273 0.0580754755938471

Total number of rows: 485512

Table truncated, full table size 13822 Kbytes.

Supplementary file Size Download File type/resource
GSM1588724_8795207137_R06C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588724_8795207137_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