GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM1588814 Query DataSets for GSM1588814
Status Public on Sep 15, 2015
Title Pt21-DD-DP2-1
Sample type genomic
Source name tumor biopsy
Organism Homo sapiens
Characteristics cell type: melanoma
mapki sensitivity: resistant
mapki treatment: BRAFi+MEKi
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 21 melanoma, post BRAFi+MEKi 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 0.852309930883958
cg00212031 0.0628575730201746
cg00213748 0.842696629213483
cg00214611 0.0825980573885964
cg00455876 0.801958983777166
cg01707559 0.103797004225961
cg02004872 0.0354146847703883
cg02011394 0.986223390506859
cg02050847 0.959735099337748
cg02233190 0.0495434315246245
cg02494853 0.0355173368922015
cg02839557 0.0345702291961299
cg02842889 0.0685281278313154
cg03052502 0.974079848543906
cg03155755 0.947356242045586
cg03244189 0.13532034346103
cg03443143 0.87807421580333
cg03683899 0.0515510265248014
cg03695421 0.853551154282831
cg03706273 0.0392117670574126

Total number of rows: 485512

Table truncated, full table size 13808 Kbytes.

Supplementary file Size Download File type/resource
GSM1588814_9513149079_R06C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588814_9513149079_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