GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM1588730 Query DataSets for GSM1588730
Status Public on Sep 15, 2015
Title Pt5-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 5 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 0.629397366131936
cg00212031 0.542918443814489
cg00213748 0.55867903930131
cg00214611 0.0548154815481548
cg00455876 0.520171053160138
cg01707559 0.101538962625193
cg02004872 0.0264373038599309
cg02011394 0.752327777321619
cg02050847 0.701126794693161
cg02233190 0.0313844289609209
cg02494853 0.0165578592438482
cg02839557 0.0092180421508765
cg02842889 0.0451006168470017
cg03052502 0.929045256544002
cg03155755 0.774531989302613
cg03244189 0.0751404494382023
cg03443143 0.637638527234432
cg03683899 0.0578258547008547
cg03695421 0.55426235590061
cg03706273 0.0193065648478877

Total number of rows: 485512

Table truncated, full table size 13834 Kbytes.

Supplementary file Size Download File type/resource
GSM1588730_8795207135_R04C01_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588730_8795207135_R04C01_Red.idat.gz 4.2 Mb (ftp)(http) IDAT
Processed data included within Sample table

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