GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM1588769 Query DataSets for GSM1588769
Status Public on Sep 15, 2015
Title Pt10-DP5-2
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 10 melanoma, post BRAFi resistance, 5th 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 0.878861636397678
cg00212031 0.0770240700218818
cg00213748 0.659554140127389
cg00214611 0.128582034149963
cg00455876 0.746307237813885
cg01707559 0.130365265623851
cg02004872 0.0320515390121689
cg02011394 0.975723042855986
cg02050847 0.964413481453587
cg02233190 0.0422689457740661
cg02494853 0.0208536128790715
cg02839557 0.0522172658094988
cg02842889 0.0648803772550942
cg03052502 0.954844878878028
cg03155755 0.891713815082719
cg03244189 0.116062778531292
cg03443143 0.881076635986969
cg03683899 0.0398902104300091
cg03695421 0.655572483300129
cg03706273 0.0193110647181628

Total number of rows: 485512

Table truncated, full table size 13835 Kbytes.

Supplementary file Size Download File type/resource
GSM1588769_9341679010_R01C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588769_9341679010_R01C02_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