GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM1588745 Query DataSets for GSM1588745
Status Public on Sep 15, 2015
Title Pt8-baseline-2
Sample type genomic
Source name tumor biopsy
Organism Homo sapiens
Characteristics cell type: melanoma
mapki sensitivity: sensitive
mapki treatment: none
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 8 melanoma, pre MAPKi treatment, 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 0.635966190614981
cg00212031 0.486046511627907
cg00213748 0.405673758865248
cg00214611 0.481521156936261
cg00455876 0.138175046554935
cg01707559 0.341978458049887
cg02004872 0.217672413793103
cg02011394 0.558845577211394
cg02050847 0.317056396148556
cg02233190 0.331129476584022
cg02494853 0.0155427732223718
cg02839557 0.491859468723222
cg02842889 0.537390029325513
cg03052502 0.493292682926829
cg03155755 0.401321585903084
cg03244189 0.366807955656994
cg03443143 0.61033185083818
cg03683899 0.281274281274281
cg03695421 0.325977933801404
cg03706273 0.0226367903247509

Total number of rows: 485512

Table truncated, full table size 13834 Kbytes.

Supplementary file Size Download File type/resource
GSM1588745_9341679010_R06C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588745_9341679010_R06C02_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