GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM1588824 Query DataSets for GSM1588824
Status Public on Sep 15, 2015
Title Pt22-DD-DP3-1
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 22 melanoma, post BRAFi+MEKi resistance, 3rd 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 0.854329827701947
cg00212031 0.349284253578732
cg00213748 0.551289083927592
cg00214611 0.385660377358491
cg00455876 0.530716474536699
cg01707559 0.23
cg02004872 0.0830351818723912
cg02011394 0.950351911736732
cg02050847 0.881826502593308
cg02233190 0.157574528493206
cg02494853 0.0419048402352264
cg02839557 0.161773517076093
cg02842889 0.262405716554188
cg03052502 0.913130713236651
cg03155755 0.828365293335865
cg03244189 0.320095486111111
cg03443143 0.882200728289563
cg03683899 0.119617224880383
cg03695421 0.600212841433132
cg03706273 0.0620985010706638

Total number of rows: 485512

Table truncated, full table size 13792 Kbytes.

Supplementary file Size Download File type/resource
GSM1588824_9283265061_R06C02_Grn.idat.gz 4.1 Mb (ftp)(http) IDAT
GSM1588824_9283265061_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