GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM1588777 Query DataSets for GSM1588777
Status Public on Sep 15, 2015
Title Pt10-DP9-2
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, 9th 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 0.875368325616035
cg00212031 0.181994400172302
cg00213748 0.602284527518172
cg00214611 0.185764246039909
cg00455876 0.728848276393131
cg01707559 0.16111723631018
cg02004872 0.0407018042335559
cg02011394 0.950671212806244
cg02050847 0.945177048763057
cg02233190 0.0652805520246958
cg02494853 0.0190251316289421
cg02839557 0.0456369626180947
cg02842889 0.0959517923362175
cg03052502 0.970477247502775
cg03155755 0.887470231450473
cg03244189 0.211699844559342
cg03443143 0.88529752778639
cg03683899 0.0751091703056769
cg03695421 0.597950377562028
cg03706273 0.0191392509828264

Total number of rows: 485512

Table truncated, full table size 13836 Kbytes.

Supplementary file Size Download File type/resource
GSM1588777_9341679010_R05C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588777_9341679010_R05C02_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